diff options
| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2019-08-30 18:22:13 -0500 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-08-30 18:22:13 -0500 |
| commit | 661a894c85f451a4ef868abcc9871653914361bd (patch) | |
| tree | c2f1a7d9edfd4adf30be743ea1aa2967bb5916cd | |
| parent | 9c983230807efe12b17ab30501c1c5e10674edfc (diff) | |
| download | spack-661a894c85f451a4ef868abcc9871653914361bd.tar.gz spack-661a894c85f451a4ef868abcc9871653914361bd.tar.bz2 spack-661a894c85f451a4ef868abcc9871653914361bd.tar.xz spack-661a894c85f451a4ef868abcc9871653914361bd.zip | |
Update R CRAN packages (#12019)
* Update R CRAN packages
This PR update R CRAN packages. It also ensures that spack built
packages that correspond to R recommended packages are specified in the
dependency list. This is needed for #12015.
* Add more updates to packages
* Updated dependencies of CRAN R packages
Also, use cloud.r-project.org rather than cran.r-project.org to use
automatic redirection to mirrors. This minimizes the load on the cran
server.
* Update to latest versions of CRAN R packages
* Fix flake8 issues
Some blank lines at the end of a coupple of package files crept in.
* Adjust r-animation dependencies
The r-magick package depends on image-magick, so r-animation should as
well. Also, add in texlive for LaTeX support.
* New package: r-magick
* Adjust line spaces in r-magick
* Add swftools dependenct to r-animation
* New package: swftools
This is needed bt r-animation
* Add 'when' clause to some package dependencies
- r-animation
- r-coin
- r-dt
- r-openssl
* New package: r-ellipsis
* New package: r-vctrs
* New package: r-zeallot
* New package: r-generics
* New package: r-cardata
* Add r-progress dependency to r-readxl
* New package: r-askpass
* New package: r-openxlsx
* New package: r-rio
* New package: r-sys
* New package: r-zip
* Add more updated packages
These are updates that have happened while working on this PR as well as
catching the ones from the cran.rstudio.com URL that were missed before.
* New package: r-gower
* New package: r-recipes
* New package: r-squarem
* New package: r-libcoin
* New package: r-rcmdcheck
* New package: r-remotes
* New package: r-sessioninfo
* New package: r-xopen
* New package: r-rgexf
* New package: r-rook
* New package: r-later
* New package: r-promises
* New package: r-xfun
* New package: r-urca
* New package: r-ggsignif
* New package: r-polynom
* New package: r-ucminf
* New package: r-ordinal
* New package: r-inum
* New package: r-debugme
* New package: r-fs
* New package: r-shinyfiles
* New package: r-gsa
* New package: r-nmof
* New package: r-dosnow
* New package: r-rann
* New package: r-reticulate
* New package: r-future
* New package: r-globals
* New package: r-listenv
* New package: r-future-apply
* New package: r-rsvd
* New package: r-sctransform
* New package: r-mitools
* Remove a stray FIXME line
* Fix typo in dependency for r-rcmdcheck
* Remove the dependency on r-splines
The r-splines package never existed in spack, but it does not exist on
CRAN either. There is an archive version from 1999 but it does not have
the proper extension format for modern R packages. The latest version
does not depend on r-splines, and apparently previous versions at least
built without it. Also, bump the required R version.
* Fix typo in r-rcpp dependency
* Fix typos in dependencies
- r-diagrammer
- r-janitor
- r-seurat
Also, bump minimum R version for r-rngtools.
* New package: r-clisymbols
* New package: r-fitdistrplus
* New package: r-gbrd
* New package: r-gh
* New package: r-ini
* New package: r-metap
* New package: r-npsurv
* New package: r-rdpack
* New package: r-snakecase
* New package: r-tinytex
* New package: r-usethis
* Make recommended changes
Made the changes that were recommended in the initial review.
- change cran.rstudio.com to cloud.r-project.org
- change R-project to r-project
- for packages with no listed homepage use the canonical link to the
package page
- for packages with a dependency constraint on R itself, specify the
dependency type
- add `list_url` where missing from package
* New package: r-hdf5r
This is needed for some older versions of r-seurat.
* Set R versions in packages
If the R version is specified in the DESCRIPTION file then set it in the
respective spack package.py file.
* Update var/spack/repos/builtin/packages/r-aer/package.py
Change dependency version of r-car.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Set constraint of mlbench dependency of r-adabag
* Set constraint on r-rcpp dependency of r-ape
* Removed "suggested" r-testthat from r-bibtex
* Update var/spack/repos/builtin/packages/r-bindrcpp/package.py
Fix dependency spec of r-bindr in r-bindrcpp.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/r-blob/package.py
Add r-vctrs version constraint.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove r-base64enc dependency from r-callr
* Update var/spack/repos/builtin/packages/r-car/package.py
Set constraint on r-cardata dependency.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove unneeded dependencies from r-clipr
* Add gmake dependency to r-construct
* Set the proper homepage for r-crayon
* Add r-jsonlite as a dependency for r-crul
The jsonlite package moved from "suggests" to "imports" with 0.8.4.
* Remove accidental colon after package name
* Add version constraint to r-fpc dependency in r-dendextend
* Additional constraints for R version with r-digest
* Add r-jsonlite dependency for latest verion of r-dt
* Add r-htmltools dependency in r-dygraphs package
* Removed unneeded dependencies from r-fnn
* Remove unneeded dependencies from r-formatr
* Add version constraint for r-mvtnorm dependency in r-fpc
* Added gmake dependency to r-fs
* Add r-globals dependency in r-future-apply
* Add perl dependency to r-gdata
* Add openssl dependency for r-ggally
* Removed unneeded dependencies from r-globaloptions
* Update r-haven
- Add version constraint on r-forcats
- Add gmake build dependency
* Fixed gmake dependency
Gmake is a build only dependency.
* Apply suggestions from code review
Apply a batch of suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove unneeded dependencies from r-hoardr
* Fix r-htmlwidgets homepage
* Add gmake build dependency to r-httpuv
* Remove unneeded dependency from r-log4r
* Remove unneeded dependency from r-maldiquant
* Add gmake build dependency to r-minqa
* Remove unneeded dependency from r-mlbench
* Set constraint on R6 dependenvy of r-pbdzmq
* Set constraints on r-callr dependency of r-pkgbuild
* Remove unneeded dependency from r-nloptr
* Remove unneeded dependencies from r-pkgmaker
* Set R version constraint for r-raster
* Set version constraint on rcpp for r-rcppprorgess
* Added gmake build dependency
* Remove unneeded dependencies from r-rematch
* Remove unneeded dependency from r-plogr
* Add gmake build dependency for r-rcurl
* Apply suggestions from code review
Bring in more suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove cnpy dependency from r-rcppcnpy
The r-rcppcnpy package has its own modified copy of the cnpy source and
will build from that internal source. The cnpy dependency is therefore
unnecessary.
* Add comment to reconcile dependencies
The CRAN site lists Perl, Getopt::Long as a dependency. The Spack Perl
will have the Getopt::Long package installed so just depend on Perl.
* Add dependency on udunits2 with newer versions of r-units
* Set additional proj constraint for r-sf
Support for PROJ6 was added in r-sf-0.7-4.
* New package: pandoc
This package installs the pandoc and pandoc-citeproc binaries in order
to satisfy dependencies on pandoc until the Haskell framework is in
Spack.
* Add pandoc dependency to r-bookdown
* Add comment about MPI in r-ergm
* Add pandoc dependency for r-reprex
* Add proj constraints to r-rgdal dependencies
Support for PROJ6 was added in version 1.4-2.
* Modifications to r-rgl
- Rearranged the dependencies to be more consistent with other packages
- put the type last on the depends_on lines to be consistent with other
packages
- Added version constraints for some dependencies
- Added pandoc build dependency
* Be more accurate with rjsonio constraint for r-rgooglemaps
* Remove unneeded dependencies from r-rhmmer
* Tweak constraints for r-rjava
- Set java version constraint
- add gmake build dependency
* Add pandoc dependency to r-markdown
* Remove unneeded dependencies from r-rrcov
* Tweak r-rstan package
- remove duplicate specifications
- remove unneeded when conditions
- add version constraints
- arrange to follow order on CRAN page more closely
- add gmake build dependency
- add pandoc build dependency
* Add pandoc build dependency for r-rstantools
* Remove unneeded dependency from r-runit
* Remove unneeded dependencies from r-selectr
* Remove example R code from description
The example would module loading to break, at least in the case of Lmod
using TCL module files. It could be during the TCL to Lua conversion but
the module fails due to interpreting ipart of the example as a command.
* Update r-seurat
New version of r-seurat with new dependencies.
* New package: r-dqrng
* New package: r-leiden
* New package: r-rcppannoy
* New package: r-rcppparallel
* New package: r-rspectra
* New package: r-sitmo
* New package: r-uwot
* Remove unneeded dependency from r-snow
* Remove unneeded dependency from r-sourcetools
* Added pandoc build dependency for r-stanheaders
* Remove unneeded dependencies from r-taxizedb
* Remove unneeded dependencies from r-tclust
* Add dependency constraints for r-threejs
The following are needed for version 0.2.2:
- r-matrix
- r-jsonlite
* Remove unneeded dependencies from r-vfs
* Remove unneeded dependencies from r-vgam
* Remove unneeded dependency from r-xlconnectjars
* Remove unneeded dependency from r-xlsxjars
* Remove unneeded dependency from r-xnomial
* Remove ~mpi from fftw dependency of swftools
* Apply suggestions from code review
Add latest round of suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix rjsonio spec for r-rgooglemaps
The r-rjsonio spec is a when conditional.
* Rename 3 R.* packages
- r-utils --> r-r-utils (R.utils)
- r-oo --> r-r-oo (R.oo)
- r-methodss3 --> r-r-methodss3 (R.methodsS3)
Also, renamed dependencies in packages that depend on these three.
* Loosen version constraint on mariadb for r-rmysql
Make the mariadb constraint on mariadb-5.5 rather than the more
specific, and limiting, mariadb-5.5.56. This will allow an external
mariadb, such as mariadb-5.5.60 on CentOS-7.5 to be used. It also allows
for r-rmysql to be built against newer versions of the mariadb-5.5
series that might be added to spack.
579 files changed, 4618 insertions, 1835 deletions
diff --git a/var/spack/repos/builtin/packages/pandoc/package.py b/var/spack/repos/builtin/packages/pandoc/package.py new file mode 100644 index 0000000000..c0efc2cb8c --- /dev/null +++ b/var/spack/repos/builtin/packages/pandoc/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import platform + + +class Pandoc(Package): + """If you need to convert files from one markup format into another, pandoc + is your swiss-army knife.""" + + homepage = "https://pandoc.org" + + # The following installs the binaries for pandoc and pandoc-cireproc. The + # reason for installing binaries is that pandoc is a Haskell package and + # the Haskell framework is not yet in Spack. See #1408 for a discussion of + # the challenges with Haskell. Until the Haskell framework is in Spack this + # package will meet the needs of packages that have a dependency on pandoc. + + if platform.system() == "Linux": + url = "https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-linux.tar.gz" + version('2.7.3', sha256='eb775fd42ec50329004d00f0c9b13076e707cdd44745517c8ce2581fb8abdb75') + elif platform.system() == "Darwin": + url = "https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-macOS.zip" + version('2.7.3', sha256='fb93800c90f3fab05dbd418ee6180d086b619c9179b822ddfecb608874554ff0') + + depends_on('texlive') + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index 62f948a4e2..0174733ccf 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -12,8 +12,11 @@ class RAbind(RPackage): higher-dimensional arrays. Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays.""" - homepage = "https://cran.r-project.org/" - url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/abind" + homepage = "https://cloud.r-project.org/package=abind" + url = "https://cloud.r-project.org/src/contrib/abind_1.4-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/abind" + version('1.4-5', sha256='3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c') version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5') + + depends_on('r@1.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acepack/package.py b/var/spack/repos/builtin/packages/r-acepack/package.py index 01eb083a7f..f10d79caba 100644 --- a/var/spack/repos/builtin/packages/r-acepack/package.py +++ b/var/spack/repos/builtin/packages/r-acepack/package.py @@ -9,8 +9,8 @@ from spack import * class RAcepack(RPackage): """ACE and AVAS for Selecting Multiple Regression Transformations.""" - homepage = "https://CRAN.R-project.org/package=acepack" - url = "https://cran.rstudio.com/src/contrib/acepack_1.4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/acepack" + homepage = "https://cloud.r-project.org/package=acepack" + url = "https://cloud.r-project.org/src/contrib/acepack_1.4.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/acepack" version('1.4.1', 'a35354655e5260afa0e1860fcc68d871') diff --git a/var/spack/repos/builtin/packages/r-ada/package.py b/var/spack/repos/builtin/packages/r-ada/package.py index 83d4ec8d94..ef015df04e 100644 --- a/var/spack/repos/builtin/packages/r-ada/package.py +++ b/var/spack/repos/builtin/packages/r-ada/package.py @@ -10,10 +10,11 @@ class RAda(RPackage): """Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.""" - homepage = "https://cran.r-project.org/web/packages/ada/index.html" - url = "https://cran.r-project.org/src/contrib/ada_2.0-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ada" + homepage = "https://cloud.r-project.org/package=ada" + url = "https://cloud.r-project.org/src/contrib/ada_2.0-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ada" version('2.0-5', '25ac0dc2650fba9e19f3d15c7c6721c1') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rpart', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adabag/package.py b/var/spack/repos/builtin/packages/r-adabag/package.py index a0c3f8583b..ce7a675430 100644 --- a/var/spack/repos/builtin/packages/r-adabag/package.py +++ b/var/spack/repos/builtin/packages/r-adabag/package.py @@ -9,12 +9,15 @@ from spack import * class RAdabag(RPackage): """Applies Multiclass AdaBoost.M1, SAMME and Bagging.""" - homepage = "https://cran.r-project.org/package=adabag" - url = "https://cran.r-project.org/src/contrib/adabag_4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/adabag" + homepage = "https://cloud.r-project.org/package=adabag" + url = "https://cloud.r-project.org/src/contrib/adabag_4.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/adabag" + version('4.2', sha256='47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81') version('4.1', '2e019f053d49f62ebb3b1697bbb50afa') depends_on('r-rpart', type=('build', 'run')) - depends_on('r-mlbench', type=('build', 'run')) + depends_on('r-mlbench', when='@:4.1', type=('build', 'run')) depends_on('r-caret', type=('build', 'run')) + depends_on('r-foreach', type=('build', 'run')) + depends_on('r-doparallel', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ade4/package.py b/var/spack/repos/builtin/packages/r-ade4/package.py index 86ef54bbe1..ef6ff1a84c 100644 --- a/var/spack/repos/builtin/packages/r-ade4/package.py +++ b/var/spack/repos/builtin/packages/r-ade4/package.py @@ -11,9 +11,12 @@ class RAde4(RPackage): Environmental Sciences""" homepage = "http://pbil.univ-lyon1.fr/ADE-4" - url = "https://cran.r-project.org/src/contrib/ade4_1.7-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ade4" + url = "https://cloud.r-project.org/src/contrib/ade4_1.7-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ade4" + version('1.7-13', sha256='f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b') + version('1.7-11', sha256='4ccd799ae99bd625840b866a697c4a48adb751660470bf0d6cf9207b1927a572') version('1.7-6', '63401ca369677538c96c3d7b75b3f4a1') - depends_on('r@2.10:') + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adegenet/package.py b/var/spack/repos/builtin/packages/r-adegenet/package.py index a3f9d73df9..563ed378a6 100644 --- a/var/spack/repos/builtin/packages/r-adegenet/package.py +++ b/var/spack/repos/builtin/packages/r-adegenet/package.py @@ -18,13 +18,16 @@ class RAdegenet(RPackage): to illustrate various methods.""" homepage = "https://github.com/thibautjombart/adegenet/wiki" - url = "https://cran.r-project.org/src/contrib/adegenet_2.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/adegenet" + url = "https://cloud.r-project.org/src/contrib/adegenet_2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/adegenet" + version('2.1.1', sha256='3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a') + version('2.1.0', sha256='7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a') version('2.0.1', 'ecb1220ce7c9affaba2987bc7f38adda') - depends_on('r@2.14:') + depends_on('r@2.14:', type=('build', 'run')) depends_on('r-ade4', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) depends_on('r-ape', type=('build', 'run')) depends_on('r-shiny', type=('build', 'run')) @@ -34,3 +37,4 @@ class RAdegenet(RPackage): depends_on('r-reshape2', type=('build', 'run')) depends_on('r-dplyr@0.4.1:', type=('build', 'run')) depends_on('r-vegan', type=('build', 'run')) + depends_on('r-boot', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-aer/package.py b/var/spack/repos/builtin/packages/r-aer/package.py index 3a8749dfa9..c31dc05fcc 100644 --- a/var/spack/repos/builtin/packages/r-aer/package.py +++ b/var/spack/repos/builtin/packages/r-aer/package.py @@ -12,16 +12,18 @@ class RAer(RPackage): Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.""" - homepage = "https://cran.r-project.org/web/packages/AER/index.html" - url = "https://cran.r-project.org/src/contrib/AER_1.2-5.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/AER" + homepage = "https://cloud.r-project.org/package=AER" + url = "https://cloud.r-project.org/src/contrib/AER_1.2-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/AER" + version('1.2-7', sha256='3aee5c606313710c2dca6c1e9b2c20a145aa33f2a3ecc5cfcec66c8e91838a93') + version('1.2-6', sha256='653c3a2d253819e0ce8c2cf12cff2ab222bf3d19dbf382b7c4b4c3d762469474') version('1.2-5', '419df9dc8ee6e5edd79678fee06719ae') - depends_on('r@2.13.0:', type=('build', 'run')) - depends_on('r-car@2.10-19:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-car@2.0-19:', type=('build', 'run')) depends_on('r-lmtest', type=('build', 'run')) - depends_on('r-sandwich', type=('build', 'run')) + depends_on('r-sandwich@2.4-0:', type=('build', 'run')) depends_on('r-survival@2.37-5:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) - depends_on('r-formula', type=('build', 'run')) + depends_on('r-formula@0.2-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-als/package.py b/var/spack/repos/builtin/packages/r-als/package.py index 6314a09564..685fbf5f62 100644 --- a/var/spack/repos/builtin/packages/r-als/package.py +++ b/var/spack/repos/builtin/packages/r-als/package.py @@ -15,11 +15,12 @@ class RAls(RPackage): decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets.""" - homepage = "https://cran.r-project.org/package=ALS" - url = "https://cran.rstudio.com/src/contrib/ALS_0.0.6.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ALS" + homepage = "https://cloud.r-project.org/package=ALS" + url = "https://cloud.r-project.org/src/contrib/ALS_0.0.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ALS" version('0.0.6', 'b72d97911e8ab7e4f8aed1a710b3d62d') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-iso', type=('build', 'run')) - depends_on('r-nnls', type=('build', 'run')) + depends_on('r-nnls@1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-amap/package.py b/var/spack/repos/builtin/packages/r-amap/package.py index b22d6ff6fb..36cdc693f3 100644 --- a/var/spack/repos/builtin/packages/r-amap/package.py +++ b/var/spack/repos/builtin/packages/r-amap/package.py @@ -11,9 +11,11 @@ class RAmap(RPackage): (With robust methods, and parallelized functions).""" homepage = "http://mulcyber.toulouse.inra.fr/projects/amap/" - url = "https://cran.rstudio.com/src/contrib/amap_0.8-16.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/amap/" + url = "https://cloud.r-project.org/src/contrib/amap_0.8-16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/amap/" + version('0.8-17', sha256='6b8473d1d35a9cbc611661882c8f681162e8f913f911ccd51629200ae72289c6') version('0.8-16', sha256='d3775ad7f660581f7d2f070e426be95ae0d6743622943e6f5491988e5217d4e2') - depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r@2.10.0:', when='@:0.8-16', type=('build', 'run')) + depends_on('r@3.6.0:', when='@0.8-17:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-animation/package.py b/var/spack/repos/builtin/packages/r-animation/package.py index dc39191fff..69426a1cd7 100644 --- a/var/spack/repos/builtin/packages/r-animation/package.py +++ b/var/spack/repos/builtin/packages/r-animation/package.py @@ -13,11 +13,16 @@ class RAnimation(RPackage): computational statistics, data mining and machine learning. These functions maybe helpful in teaching statistics and data analysis.""" - homepage = "https://cran.r-project.org/package=animation" - url = "https://cran.r-project.org/src/contrib/animation_2.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/animation" + homepage = "https://cloud.r-project.org/package=animation" + url = "https://cloud.r-project.org/src/contrib/animation_2.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/animation" + version('2.6', sha256='90293638920ac436e7e4de76ebfd92e1643ccdb0259b62128f16dd0b13245b0a') version('2.5', sha256='b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f') - extends('r') - depends_on('r', type=('build', 'run')) + depends_on('r@2.14:', type=('build', 'run')) + depends_on('r-magick', when='@2.6:', type=('build', 'run')) + depends_on('image-magick') + depends_on('ffmpeg') + depends_on('swftools') + depends_on('texlive') diff --git a/var/spack/repos/builtin/packages/r-ape/package.py b/var/spack/repos/builtin/packages/r-ape/package.py index 1d5aaabddb..c028e56842 100644 --- a/var/spack/repos/builtin/packages/r-ape/package.py +++ b/var/spack/repos/builtin/packages/r-ape/package.py @@ -24,9 +24,10 @@ class RApe(RPackage): whose results are returned into R.""" homepage = "http://ape-package.ird.fr/" - url = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ape" + url = "https://cloud.r-project.org/src/contrib/ape_4.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ape" + version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23') version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415') version('5.1', sha256='b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e') version('5.0', sha256='c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960') @@ -35,4 +36,4 @@ class RApe(RPackage): depends_on('r@3.2:', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-argparse/package.py b/var/spack/repos/builtin/packages/r-argparse/package.py index 902a17aa4d..25c05ebcf8 100644 --- a/var/spack/repos/builtin/packages/r-argparse/package.py +++ b/var/spack/repos/builtin/packages/r-argparse/package.py @@ -12,12 +12,14 @@ class RArgparse(RPackage): arguments and automatically generate usage.""" homepage = "https://github.com/trevorld/argparse" - url = "https://cran.r-project.org/src/contrib/argparse_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/argparse" + url = "https://cloud.r-project.org/src/contrib/argparse_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/argparse" + version('2.0.1', sha256='949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab') version('1.1.1', sha256='441449f0816411a868fd1b15cf4b2bc45931bbd4b67d6592dbe48875905cf93b') - depends_on('r-proto@1:', type=('build', 'run')) + depends_on('r-proto@1:', when='@1.0.0:1.9.9', type=('build', 'run')) + depends_on('r-getopt', when='@1.0.0:1.9.9', type=('build', 'run')) + depends_on('r-r6', when='@2.0.0:', type=('build', 'run')) depends_on('r-findpython', type=('build', 'run')) - depends_on('r-getopt', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-askpass/package.py b/var/spack/repos/builtin/packages/r-askpass/package.py new file mode 100644 index 0000000000..ea3bcd0572 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-askpass/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RAskpass(RPackage): + """Cross-platform utilities for prompting the user for credentials or a + passphrase, for example to authenticate with a server or read a protected + key. Includes native programs for MacOS and Windows, hence no 'tcltk' is + required. Password entry can be invoked in two different ways: directly + from R via the askpass() function, or indirectly as password-entry back-end + for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS + environment variables. Thereby the user can be prompted for credentials or + a passphrase if needed when R calls out to git or ssh.""" + + homepage = "https://github.com/jeroen/askpass#readme" + url = "https://cloud.r-project.org/src/contrib/askpass_1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/askpass" + + version('1.1', sha256='db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f') + + depends_on('r-sys@2.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py index 1bef74953c..2e88e9525e 100644 --- a/var/spack/repos/builtin/packages/r-assertthat/package.py +++ b/var/spack/repos/builtin/packages/r-assertthat/package.py @@ -12,8 +12,10 @@ class RAssertthat(RPackage): producing friendly error messages so that your users know what they've done wrong.""" - homepage = "https://cran.r-project.org/package=assertthat" - url = "https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/assertthat" + homepage = "https://cloud.r-project.org/package=assertthat" + url = "https://cloud.r-project.org/src/contrib/assertthat_0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/assertthat" + + version('0.2.1', sha256='85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f') version('0.2.0', '8134f0072c6a84fd738d3bfc5e7f68ef') version('0.1', '59f9d7f7c00077ea54d763b78eeb5798') diff --git a/var/spack/repos/builtin/packages/r-backports/package.py b/var/spack/repos/builtin/packages/r-backports/package.py index 045ae66022..6aef403750 100644 --- a/var/spack/repos/builtin/packages/r-backports/package.py +++ b/var/spack/repos/builtin/packages/r-backports/package.py @@ -15,9 +15,13 @@ class RBackports(RPackage): can make use of the new functions without worrying about the minimum required R version.""" - homepage = "https://cran.r-project.org/package=backports" - url = "https://cran.r-project.org/src/contrib/backports_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/backports" + homepage = "https://cloud.r-project.org/package=backports" + url = "https://cloud.r-project.org/src/contrib/backports_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/backports" + version('1.1.4', sha256='ee4b5efef22fa7ef27d7983ffcd31db52f81e1fbb7189c6e89ee09b69349ff03') + version('1.1.3', sha256='e41bd146824ec921994f1b176d0e4cca0b36dd3db32ca7a954d872a5ba214cc1') version('1.1.1', '969543a0af32dc23bba9bb37ec82008c') version('1.1.0', 'b97a71b026fd7ede0e449be93d160c17') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-base64/package.py b/var/spack/repos/builtin/packages/r-base64/package.py index 69d69f8c14..9aa2ae0864 100644 --- a/var/spack/repos/builtin/packages/r-base64/package.py +++ b/var/spack/repos/builtin/packages/r-base64/package.py @@ -11,9 +11,9 @@ class RBase64(RPackage): Francois. New applications should use the 'openssl' or 'base64enc' package instead.""" - homepage = "https://cran.r-project.org/package=base64" - url = "https://cran.rstudio.com/src/contrib/base64_2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/base64" + homepage = "https://cloud.r-project.org/package=base64" + url = "https://cloud.r-project.org/src/contrib/base64_2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/base64" version('2.0', 'f5a653842f75ad717ef6a00969868ae5') diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py index 081dba4745..5c1fcc9979 100644 --- a/var/spack/repos/builtin/packages/r-base64enc/package.py +++ b/var/spack/repos/builtin/packages/r-base64enc/package.py @@ -11,7 +11,9 @@ class RBase64enc(RPackage): flexible than the orphaned base64 package.""" homepage = "http://www.rforge.net/base64enc" - url = "https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc" + url = "https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/base64enc" version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190') + + depends_on('r@2.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bayesm/package.py b/var/spack/repos/builtin/packages/r-bayesm/package.py index cc30692af2..10dc0cc7f1 100644 --- a/var/spack/repos/builtin/packages/r-bayesm/package.py +++ b/var/spack/repos/builtin/packages/r-bayesm/package.py @@ -9,10 +9,13 @@ from spack import * class RBayesm(RPackage): """Bayesian Inference for Marketing/Micro-Econometrics""" - homepage = "https://cran.r-project.org/web/packages/bayesm/index.html" - url = "https://cran.r-project.org/src/contrib/bayesm_3.1-0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bayesm" + homepage = "https://cloud.r-project.org/package=bayesm" + url = "https://cloud.r-project.org/src/contrib/bayesm_3.1-0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bayesm" + version('3.1-3', sha256='51e4827eca8cd4cf3626f3c2282543df7c392b3ffb843f4bfb386fe104642a10') + version('3.1-2', sha256='a332f16e998ab10b17a2b1b9838d61660c36e914fe4d2e388a59f031d52ad736') + version('3.1-1', sha256='4854517dec30ab7c994de862aae1998c2d0c5e71265fd9eb7ed36891d4676078') version('3.1-0.1', '34998382cafd3e7972d8a03245eac768') depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bbmisc/package.py b/var/spack/repos/builtin/packages/r-bbmisc/package.py index 8bc2144b94..400b7c8972 100644 --- a/var/spack/repos/builtin/packages/r-bbmisc/package.py +++ b/var/spack/repos/builtin/packages/r-bbmisc/package.py @@ -11,8 +11,8 @@ class RBbmisc(RPackage): guys, mainly for package development.""" homepage = "https://github.com/berndbischl/BBmisc" - url = "https://cran.r-project.org/src/contrib/BBmisc_1.11.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/BBmisc" + url = "https://cloud.r-project.org/src/contrib/BBmisc_1.11.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/BBmisc" version('1.11', '681642628037406beb6088d5f773473d') diff --git a/var/spack/repos/builtin/packages/r-beanplot/package.py b/var/spack/repos/builtin/packages/r-beanplot/package.py index e23094434f..db560b5772 100644 --- a/var/spack/repos/builtin/packages/r-beanplot/package.py +++ b/var/spack/repos/builtin/packages/r-beanplot/package.py @@ -10,8 +10,8 @@ class RBeanplot(RPackage): """Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.""" - homepage = "https://cran.r-project.org/web/packages/beanplot/index.html" - url = "https://cran.rstudio.com/src/contrib/beanplot_1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/beanplot" + homepage = "https://cloud.r-project.org/package=beanplot" + url = "https://cloud.r-project.org/src/contrib/beanplot_1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/beanplot" version('1.2', 'b24943208a4e61ee9ee0dc152634d5da') diff --git a/var/spack/repos/builtin/packages/r-bfast/package.py b/var/spack/repos/builtin/packages/r-bfast/package.py index 49a92cb972..54b07e9e61 100644 --- a/var/spack/repos/builtin/packages/r-bfast/package.py +++ b/var/spack/repos/builtin/packages/r-bfast/package.py @@ -9,9 +9,9 @@ from spack import * class RBfast(RPackage): """bfast: Breaks For Additive Season and Trend (BFAST)""" - homepage = "https://cran.r-project.org/package=bfast" - url = "https://cran.r-project.org/src/contrib/bfast_1.5.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bfast" + homepage = "https://cloud.r-project.org/package=bfast" + url = "https://cloud.r-project.org/src/contrib/bfast_1.5.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bfast" version('1.5.7', sha256='01585fe8944d05ebdb13795214077bc1365f0c0372e2a1f7edb914356dace558') diff --git a/var/spack/repos/builtin/packages/r-bglr/package.py b/var/spack/repos/builtin/packages/r-bglr/package.py index f25c167b71..68f87952ed 100644 --- a/var/spack/repos/builtin/packages/r-bglr/package.py +++ b/var/spack/repos/builtin/packages/r-bglr/package.py @@ -9,9 +9,9 @@ from spack import * class RBglr(RPackage): """BGLR: Bayesian Generalized Linear Regression""" - homepage = "https://cran.r-project.org/package=BGLR" - url = "https://cran.r-project.org/src/contrib/BGLR_1.0.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/BGLR" + homepage = "https://cloud.r-project.org/package=BGLR" + url = "https://cloud.r-project.org/src/contrib/BGLR_1.0.8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/BGLR" version('1.0.8', sha256='5e969590d80b2f272c02a43b487ab1ffa13af386e0342993e6ac484fc82c9b95') diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py index 1ee6eb483e..23d2909ddd 100644 --- a/var/spack/repos/builtin/packages/r-bh/package.py +++ b/var/spack/repos/builtin/packages/r-bh/package.py @@ -22,9 +22,9 @@ class RBh(RPackage): 'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit' 'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'.""" - homepage = "https://cran.r-project.org/web/packages/BH/index.html" - url = "https://cran.r-project.org/src/contrib/BH_1.65.0-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/BH" + homepage = "https://cloud.r-project.org/package=BH" + url = "https://cloud.r-project.org/src/contrib/BH_1.65.0-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/BH" version('1.69.0-1', sha256='a0fd4364b7e368f09c56dec030823f52c16da0787580af7e4615eddeb99baca2') version('1.65.0-1', '7d0402188e4af59f4103f36616d6ee55') diff --git a/var/spack/repos/builtin/packages/r-biasedurn/package.py b/var/spack/repos/builtin/packages/r-biasedurn/package.py index 35224e3679..429ed842a9 100644 --- a/var/spack/repos/builtin/packages/r-biasedurn/package.py +++ b/var/spack/repos/builtin/packages/r-biasedurn/package.py @@ -15,7 +15,7 @@ class RBiasedurn(RPackage): explanation of these distributions.""" homepage = "http://www.agner.org/random/" - url = "https://cran.rstudio.com/src/contrib/BiasedUrn_1.07.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/BiasedUrn/" + url = "https://cloud.r-project.org/src/contrib/BiasedUrn_1.07.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/BiasedUrn/" version('1.07', sha256='2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e') diff --git a/var/spack/repos/builtin/packages/r-bibtex/package.py b/var/spack/repos/builtin/packages/r-bibtex/package.py index 8f91f3b945..8fd9a0154e 100644 --- a/var/spack/repos/builtin/packages/r-bibtex/package.py +++ b/var/spack/repos/builtin/packages/r-bibtex/package.py @@ -11,12 +11,11 @@ class RBibtex(RPackage): Utility to parse a bibtex file.""" - homepage = "https://cran.r-project.org/package=bibtex" - url = "https://cran.r-project.org/src/contrib/bibtex_0.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bibtex/" + homepage = "https://cloud.r-project.org/package=bibtex" + url = "https://cloud.r-project.org/src/contrib/bibtex_0.4.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bibtex/" version('0.4.2', sha256='1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372') depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bindr/package.py b/var/spack/repos/builtin/packages/r-bindr/package.py index 68183e8ddd..a3556e3b88 100644 --- a/var/spack/repos/builtin/packages/r-bindr/package.py +++ b/var/spack/repos/builtin/packages/r-bindr/package.py @@ -11,8 +11,8 @@ class RBindr(RPackage): bound function accepts additional arguments.""" homepage = "https://github.com/krlmlr/bindr" - url = "https://cran.r-project.org/src/contrib/bindr_0.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bindr" + url = "https://cloud.r-project.org/src/contrib/bindr_0.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bindr" version('0.1.1', 'cfa02c563196a79bf8bb4db2e66585fd') version('0.1', 'f3897a70cbad2d2981272772fa30bb59') diff --git a/var/spack/repos/builtin/packages/r-bindrcpp/package.py b/var/spack/repos/builtin/packages/r-bindrcpp/package.py index fc2e541f18..f20e62f729 100644 --- a/var/spack/repos/builtin/packages/r-bindrcpp/package.py +++ b/var/spack/repos/builtin/packages/r-bindrcpp/package.py @@ -11,12 +11,12 @@ class RBindrcpp(RPackage): call a C++ function.""" homepage = "https://github.com/krlmlr/bindrcpp" - url = "https://cran.r-project.org/src/contrib/bindrcpp_0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bindrcpp" + url = "https://cloud.r-project.org/src/contrib/bindrcpp_0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bindrcpp" version('0.2.2', '48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467') version('0.2', '2ed7f19fd9a12587f882d90060e7a343') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-bindr', type=('build', 'run')) + depends_on('r-rcpp@0.12.16:', type=('build', 'run')) + depends_on('r-bindr@0.1.1:', type=('build', 'run')) depends_on('r-plogr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-biom-utils/package.py b/var/spack/repos/builtin/packages/r-biom-utils/package.py index e20580db69..7377db73a1 100644 --- a/var/spack/repos/builtin/packages/r-biom-utils/package.py +++ b/var/spack/repos/builtin/packages/r-biom-utils/package.py @@ -12,8 +12,8 @@ class RBiomUtils(RPackage): """ homepage = "https://github.com/braithwaite/BIOM.utils/" - url = "https://cran.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/biom/" + url = "https://cloud.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/biom/" version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375') diff --git a/var/spack/repos/builtin/packages/r-bit/package.py b/var/spack/repos/builtin/packages/r-bit/package.py index 8a618951ac..ceb1975d7d 100644 --- a/var/spack/repos/builtin/packages/r-bit/package.py +++ b/var/spack/repos/builtin/packages/r-bit/package.py @@ -9,7 +9,11 @@ from spack import * class RBit(RPackage): """ A class for vectors of 1-bit booleans.""" - homepage = "https://cran.rstudio.com/web/packages/bit/index.html" - url = "https://cran.rstudio.com/src/contrib/bit_1.1-12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bit" + homepage = "https://cloud.r-project.org/package=bit" + url = "https://cloud.r-project.org/src/contrib/bit_1.1-12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bit" + + version('1.1-14', sha256='5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254') version('1.1-12', 'c4473017beb93f151a8e672e4d5747af') + + depends_on('r@2.9.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bit64/package.py b/var/spack/repos/builtin/packages/r-bit64/package.py index 141f3be1c8..5155c6a196 100644 --- a/var/spack/repos/builtin/packages/r-bit64/package.py +++ b/var/spack/repos/builtin/packages/r-bit64/package.py @@ -20,9 +20,11 @@ class RBit64(RPackage): inter- active data exploration and manipulation and optionally leverage caching.""" - homepage = "https://cran.rstudio.com/web/packages/bit64/index.html" - url = "https://cran.rstudio.com/src/contrib/bit64_0.9-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bit64" + homepage = "https://cloud.r-project.org/package=bit64" + url = "https://cloud.r-project.org/src/contrib/bit64_0.9-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bit64" + version('0.9-7', 'ac4bc39827338c552d329d3d4d2339c2') - depends_on('r-bit', type=('build', 'run')) + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r-bit@1.1-12:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py index 25dce86116..1d1cde59fd 100644 --- a/var/spack/repos/builtin/packages/r-bitops/package.py +++ b/var/spack/repos/builtin/packages/r-bitops/package.py @@ -10,8 +10,8 @@ from spack import * class RBitops(RPackage): """Functions for bitwise operations on integer vectors.""" - homepage = "https://cran.r-project.org/package=bitops" - url = "https://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/bitops" + homepage = "https://cloud.r-project.org/package=bitops" + url = "https://cloud.r-project.org/src/contrib/bitops_1.0-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bitops" version('1.0-6', 'fba16485a51b1ccd354abde5816b6bdd') diff --git a/var/spack/repos/builtin/packages/r-blob/package.py b/var/spack/repos/builtin/packages/r-blob/package.py index 89b1ccc225..3a979ba384 100644 --- a/var/spack/repos/builtin/packages/r-blob/package.py +++ b/var/spack/repos/builtin/packages/r-blob/package.py @@ -12,9 +12,14 @@ class RBlob(RPackage): package provides the blob object, a list of raw vectors, suitable for use as a column in data frame.""" - homepage = "https://cran.rstudio.com/web/packages/blob/index.html" - url = "https://cran.rstudio.com/src/contrib/blob_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/blob" + homepage = "https://cloud.r-project.org/package=blob" + url = "https://cloud.r-project.org/src/contrib/blob_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/blob" + + version('1.2.0', sha256='1af1cfa28607bc0e2f1f01598a00a7d5d1385ef160a9e79e568f30f56538e023') version('1.1.0', '1c729aca36fd5193d81b1cd5ed9d8a00') - depends_on('r-tibble', type=('build', 'run')) + depends_on('r-tibble', when='@:1.1.0', type=('build', 'run')) + depends_on('r-prettyunits', when='@1.2.0:', type=('build', 'run')) + depends_on('r-rlang', when='@1.2.0:', type=('build', 'run')) + depends_on('r-vctrs@0.2.0:', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-blockmodeling/package.py b/var/spack/repos/builtin/packages/r-blockmodeling/package.py index fcc0eedc2a..f1333ba7c0 100644 --- a/var/spack/repos/builtin/packages/r-blockmodeling/package.py +++ b/var/spack/repos/builtin/packages/r-blockmodeling/package.py @@ -10,10 +10,11 @@ class RBlockmodeling(RPackage): """blockmodeling: Generalized and Classical Blockmodeling of Valued Networks""" - homepage = "https://cran.r-project.org/package=blockmodeling" - url = "https://cran.rstudio.com/src/contrib/blockmodeling_0.3.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/blockmodeling/" + homepage = "https://cloud.r-project.org/package=blockmodeling" + url = "https://cloud.r-project.org/src/contrib/blockmodeling_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/blockmodeling/" + version('0.3.4', sha256='a269c83669dd5294cff0adddab36bc023db6a276a06b74b1fa94b7e407486987') version('0.3.1', sha256='39e8360400cec6baa920d5589d4e779568bdf2954f7331be0e3cadf22a217d31') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-bookdown/package.py b/var/spack/repos/builtin/packages/r-bookdown/package.py index 6757a11bab..1cbe28a120 100644 --- a/var/spack/repos/builtin/packages/r-bookdown/package.py +++ b/var/spack/repos/builtin/packages/r-bookdown/package.py @@ -10,13 +10,17 @@ class RBookdown(RPackage): """Output formats and utilities for authoring books and technical documents with R Markdown.""" - homepage = "https://cran.r-project.org/package=bookdown" - url = "https://cran.rstudio.com/src/contrib/bookdown_0.5.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/bookdown" + homepage = "https://cloud.r-project.org/package=bookdown" + url = "https://cloud.r-project.org/src/contrib/bookdown_0.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/bookdown" + version('0.12', sha256='38eb4c5b877ccd85b16cfe74a48c3bc53de2f276da98e5515f37e7a06e065bb0') version('0.5', '7bad360948e2b22d28397870b9319f17') - depends_on('r-yaml@2.1.14:', type=('build', 'run')) - depends_on('r-rmarkdown@1.5:', type=('build', 'run')) - depends_on('r-knitr@1.16:', type=('build', 'run')) + depends_on('r-yaml@2.1.14:', when='@:0.10', type=('build', 'run')) + depends_on('r-rmarkdown@1.12:', type=('build', 'run')) + depends_on('r-knitr@1.22:', type=('build', 'run')) depends_on('r-htmltools@0.3.6:', type=('build', 'run')) + depends_on('r-xfun@0.6:', when='@0.12:', type=('build', 'run')) + depends_on('r-tinytex@0.12:', when='@0.12:', type=('build', 'run')) + depends_on('pandoc@1.17.2:') diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py index a2fc84c4c9..3f7632f13d 100644 --- a/var/spack/repos/builtin/packages/r-boot/package.py +++ b/var/spack/repos/builtin/packages/r-boot/package.py @@ -11,9 +11,13 @@ class RBoot(RPackage): Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.""" - homepage = "https://cran.r-project.org/package=boot" - url = "https://cran.r-project.org/src/contrib/boot_1.3-18.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/boot" + homepage = "https://cloud.r-project.org/package=boot" + url = "https://cloud.r-project.org/src/contrib/boot_1.3-18.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/boot" + version('1.3-23', sha256='30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f') + version('1.3-22', sha256='cf1f0cb1e0a7a36dcb6ae038f5d0211a0e7a009c149bc9d21acb9c58c38b4dfc') version('1.3-20', 'bb879fb4204a4f94ab82c98dd1ad5eca') version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py index e2d4271bd8..c6e882e825 100644 --- a/var/spack/repos/builtin/packages/r-brew/package.py +++ b/var/spack/repos/builtin/packages/r-brew/package.py @@ -11,8 +11,8 @@ class RBrew(RPackage): report generation. brew template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.""" - homepage = "https://cran.r-project.org/package=brew" - url = "https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/brew" + homepage = "https://cloud.r-project.org/package=brew" + url = "https://cloud.r-project.org/src/contrib/brew_1.0-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/brew" version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806') diff --git a/var/spack/repos/builtin/packages/r-broom/package.py b/var/spack/repos/builtin/packages/r-broom/package.py index 3ec5b42779..5130507109 100644 --- a/var/spack/repos/builtin/packages/r-broom/package.py +++ b/var/spack/repos/builtin/packages/r-broom/package.py @@ -17,14 +17,22 @@ class RBroom(RPackage): model-level statistics.""" homepage = "http://github.com/tidyverse/broom" - url = "https://cran.r-project.org/src/contrib/broom_0.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/broom" + url = "https://cloud.r-project.org/src/contrib/broom_0.4.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/broom" + + version('0.5.2', sha256='16af7b446b24bc14461efbda9bea1521cf738c778c5e48fcc7bad45660a4ac62') + version('0.5.1', sha256='da9e6bf7cb8f960b83309cf107743976cc32b54524675f6471982abe3d1aae2e') version('0.4.2', '6eabab1f2eaec10f93cf9aa56d6a61de') - depends_on('r-plyr', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-plyr', when='@:0.4.2', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-psych', type=('build', 'run')) + depends_on('r-psych', when='@:0.4.2', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) + depends_on('r-backports', when='@0.5.0:', type=('build', 'run')) + depends_on('r-generics@0.0.2:', when='@0.5.1:', type=('build', 'run')) + depends_on('r-purrr', when='@0.5.0:', type=('build', 'run')) + depends_on('r-tibble', when='@0.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py index c81646f77e..0ca78a69be 100644 --- a/var/spack/repos/builtin/packages/r-c50/package.py +++ b/var/spack/repos/builtin/packages/r-c50/package.py @@ -10,10 +10,14 @@ from spack import * class RC50(RPackage): """C5.0 decision trees and rule-based models for pattern recognition.""" - homepage = "https://cran.r-project.org/package=C50" - url = "https://cran.r-project.org/src/contrib/C50_0.1.0-24.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/C50" + homepage = "https://cloud.r-project.org/package=C50" + url = "https://cloud.r-project.org/src/contrib/C50_0.1.0-24.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/C50" + version('0.1.2', sha256='8f459856e0309274bee24462b7145db4eba1d71031c236db39000a5375bdfaba') + version('0.1.1', sha256='03bc1fc2f64bcd5c680568a24902deafab1965074a66f8802bc4cd0335bd01df') version('0.1.0-24', '42631e65c5c579532cc6edf5ea175949') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-partykit', type=('build', 'run')) + depends_on('r-cubist@0.2.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cairo/package.py b/var/spack/repos/builtin/packages/r-cairo/package.py index 0240b9d159..e0004484e4 100644 --- a/var/spack/repos/builtin/packages/r-cairo/package.py +++ b/var/spack/repos/builtin/packages/r-cairo/package.py @@ -11,10 +11,12 @@ class RCairo(RPackage): bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output""" - homepage = "https://cran.r-project.org/web/packages/Cairo/index.html" - url = "https://cran.r-project.org/src/contrib/Cairo_1.5-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Cairo" + homepage = "https://cloud.r-project.org/package=Cairo" + url = "https://cloud.r-project.org/src/contrib/Cairo_1.5-9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Cairo" + version('1.5-10', sha256='7837f0c384cd49bb3342cb39a916d7a80b02fffbf123913a58014e597f69b5d5') version('1.5-9', '2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4') + depends_on('r@2.4.0:', type=('build', 'run')) depends_on('cairo@1.2:') diff --git a/var/spack/repos/builtin/packages/r-callr/package.py b/var/spack/repos/builtin/packages/r-callr/package.py index 21ce4194d0..1cce105259 100644 --- a/var/spack/repos/builtin/packages/r-callr/package.py +++ b/var/spack/repos/builtin/packages/r-callr/package.py @@ -12,13 +12,13 @@ class RCallr(RPackage): does exactly that.""" homepage = "https://github.com/MangoTheCat/callr" - url = "https://cran.r-project.org/src/contrib/callr_1.0.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/callr/" + url = "https://cloud.r-project.org/src/contrib/callr_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/callr/" + version('3.3.1', sha256='bf60da47357d3336aa395b0c9643235a621763c80d28bc9bb2257767d0a37967') + version('3.2.0', sha256='4bb47b1018e8eb5c683a86c05d0d9b8b25848db1f1b30e92cfebedc0ce14b0e8') version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7') version('1.0.0', 'd9af99bb95696310fa1e5d1cb7166c91') - depends_on('r-base64enc', type=('build', 'run'), when='@3.0.0:') - depends_on('r-processx@3.2.0:', type=('build', 'run'), when='@3.0.0') - depends_on('r-r6', type=('build', 'run'), when='@2.0.0') - depends_on('r-utils', type=('build', 'run'), when='@2.0.0') + depends_on('r-processx@3.4.0:', type=('build', 'run'), when='@3.0.0:') + depends_on('r-r6', type=('build', 'run'), when='@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py index b44421ea2d..fbd5266bfe 100644 --- a/var/spack/repos/builtin/packages/r-car/package.py +++ b/var/spack/repos/builtin/packages/r-car/package.py @@ -11,14 +11,24 @@ class RCar(RPackage): Companion to Applied Regression, Second Edition, Sage, 2011.""" homepage = "https://r-forge.r-project.org/projects/car/" - url = "https://cran.r-project.org/src/contrib/car_2.1-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/car" + url = "https://cloud.r-project.org/src/contrib/car_2.1-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/car" + version('3.0-3', sha256='fa807cb12f6e7fb38ec534cac4eef54747945c2119a7d51155a2492ad778c36f') + version('3.0-2', sha256='df59a9ba8fed67eef5ddb8f92f2b41745df715d5695c71d562d7031513f37c50') version('2.1-4', 'a66c307e8ccf0c336ed197c0f1799565') version('2.1-2', '0f78ad74ef7130126d319acec23951a0') + depends_on('r@3.2.0:', when='@:3.0-2', type=('build', 'run')) + depends_on('r@3.5.0:', when='@3.0-3:', type=('build', 'run')) + depends_on('r-cardata@3.0-0:', when='@3.0:', type=('build', 'run')) + depends_on('r-abind', when='@3.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-mgcv', type=('build', 'run')) depends_on('r-nnet', type=('build', 'run')) - depends_on('r-pbkrtest', type=('build', 'run')) + depends_on('r-pbkrtest@0.4-4:', type=('build', 'run')) depends_on('r-quantreg', type=('build', 'run')) + depends_on('r-maptools', when='@3.0:', type=('build', 'run')) + depends_on('r-rio', when='@3.0:', type=('build', 'run')) + depends_on('r-lme4', when='@3.0:', type=('build', 'run')) + depends_on('r-nlme', when='@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cardata/package.py b/var/spack/repos/builtin/packages/r-cardata/package.py new file mode 100644 index 0000000000..6e9c430d7f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-cardata/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RCardata(RPackage): + """Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied + Regression, Third Edition, Sage (forthcoming).""" + + homepage = "https://r-forge.r-project.org/projects/car/" + url = "https://cloud.r-project.org/src/contrib/carData_3.0-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/carData" + + version('3.0-2', sha256='3b5c4eff1cc1e456a5331084774503eaa06cf61fb7acf6b9e8a6bfabd5735494') + + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py index f37b5099ae..fcbf54004b 100644 --- a/var/spack/repos/builtin/packages/r-caret/package.py +++ b/var/spack/repos/builtin/packages/r-caret/package.py @@ -11,19 +11,23 @@ class RCaret(RPackage): models.""" homepage = "https://github.com/topepo/caret/" - url = "https://cran.r-project.org/src/contrib/caret_6.0-73.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/caret" + url = "https://cloud.r-project.org/src/contrib/caret_6.0-73.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/caret" + version('6.0-84', sha256='a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d') + version('6.0-83', sha256='9bde5e4da1f0b690bfe06c2439c0136504e851a8d360bf56b644f171fe20dcef') version('6.0-73', 'ca869e3357b5358f028fb926eb62eb70') version('6.0-70', '202d7abb6a679af716ea69fb2573f108') - depends_on('r@2.10:') - + depends_on('r@2.10:', when='@:6.0-81', type=('build', 'run')) + depends_on('r@3.2.0:', when='@6.0-82:', type=('build', 'run')) depends_on('r-lattice@0.20:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-car', type=('build', 'run')) + depends_on('r-car', when='@:6.0-73', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) depends_on('r-modelmetrics@1.1.0:', type=('build', 'run')) depends_on('r-nlme', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-recipes@0.1.4:', when='@6.0-83:', type=('build', 'run')) + depends_on('r-withr@2.0.0:', when='@6.0-83:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-caroline/package.py b/var/spack/repos/builtin/packages/r-caroline/package.py index 152edc7cfc..a72a4977db 100644 --- a/var/spack/repos/builtin/packages/r-caroline/package.py +++ b/var/spack/repos/builtin/packages/r-caroline/package.py @@ -10,9 +10,9 @@ class RCaroline(RPackage): """caroline: A Collection of Database, Data Structure, Visualization, andUtility Functions for R""" - homepage = "https://cran.r-project.org/package=caroline" - url = "https://cran.r-project.org/src/contrib/caroline_0.7.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/caroline" + homepage = "https://cloud.r-project.org/package=caroline" + url = "https://cloud.r-project.org/src/contrib/caroline_0.7.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/caroline" version('0.7.6', sha256='e7ba948f7d87f091b498dd0eec2ca4fdad7af4e2bbb67e0945c2f0d3f2eadda9') diff --git a/var/spack/repos/builtin/packages/r-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py index 5cbdcea39b..9898ab68b3 100644 --- a/var/spack/repos/builtin/packages/r-catools/package.py +++ b/var/spack/repos/builtin/packages/r-catools/package.py @@ -13,10 +13,13 @@ class RCatools(RPackage): files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.""" - homepage = "https://cran.r-project.org/package=caTools" - url = "https://cran.r-project.org/src/contrib/caTools_1.17.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/caTools" + homepage = "https://cloud.r-project.org/package=caTools" + url = "https://cloud.r-project.org/src/contrib/caTools_1.17.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/caTools" + version('1.17.1.2', sha256='69cc542fab5677462b1a768709d0c4a0a0790f5db53e1fe9ae7123787c18726b') + version('1.17.1.1', sha256='d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06') version('1.17.1', '5c872bbc78b177b306f36709deb44498') + depends_on('r@2.2.0:', type=('build', 'run')) depends_on('r-bitops', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cdcfluview/package.py b/var/spack/repos/builtin/packages/r-cdcfluview/package.py index e1a2e4770c..fa99d27ca9 100644 --- a/var/spack/repos/builtin/packages/r-cdcfluview/package.py +++ b/var/spack/repos/builtin/packages/r-cdcfluview/package.py @@ -14,12 +14,14 @@ class RCdcfluview(RPackage): to select and retrieve influenza data. Tools are provided to access the data provided by the portal's underlying 'API'.""" - homepage = "https://cran.r-project.org/package=cdcfluview" - url = "https://cran.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cdcfluview" + homepage = "https://cloud.r-project.org/package=cdcfluview" + url = "https://cloud.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/cdcfluview" + version('0.9.0', sha256='1b2064886858cbb1790ef808d88fbab75d3a9cf55e720638221a3377ff8dd244') version('0.7.0', 'd592606fab3da3536f39a15c0fdbcd17') + depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) @@ -29,4 +31,3 @@ class RCdcfluview(RPackage): depends_on('r-readr', type=('build', 'run')) depends_on('r-mmwrweek', type=('build', 'run')) depends_on('r-units@0.4-6:', type=('build', 'run')) - depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cellranger/package.py b/var/spack/repos/builtin/packages/r-cellranger/package.py index 8a9e55430c..4f8205d51f 100644 --- a/var/spack/repos/builtin/packages/r-cellranger/package.py +++ b/var/spack/repos/builtin/packages/r-cellranger/package.py @@ -10,11 +10,12 @@ class RCellranger(RPackage): """Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.""" - homepage = "https://cran.r-project.org/package=cellranger" - url = "https://cran.r-project.org/src/contrib/cellranger_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cellranger" + homepage = "https://cloud.r-project.org/package=cellranger" + url = "https://cloud.r-project.org/src/contrib/cellranger_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/cellranger" version('1.1.0', '1abcfea6af5ab2e277cb99e86880456f') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-rematch', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-checkmate/package.py b/var/spack/repos/builtin/packages/r-checkmate/package.py index 10e69d62c6..df1abd2b6b 100644 --- a/var/spack/repos/builtin/packages/r-checkmate/package.py +++ b/var/spack/repos/builtin/packages/r-checkmate/package.py @@ -11,10 +11,12 @@ class RCheckmate(RPackage): A substantial part of the package was written in C to minimize any worries about execution time overhead.""" - homepage = "https://cran.r-project.org/package=checkmate" - url = "https://cran.rstudio.com/src/contrib/checkmate_1.8.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/checkmate" + homepage = "https://cloud.r-project.org/package=checkmate" + url = "https://cloud.r-project.org/src/contrib/checkmate_1.8.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/checkmate" + version('1.9.4', sha256='faa25754b757fe483b876f5d07b73f76f69a1baa971420892fadec4af4bbad21') version('1.8.4', '00bd2c464386614da208f82c4b21910b') - depends_on('r-backports', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-backports@1.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py index f841bc8c9c..258a7ee767 100644 --- a/var/spack/repos/builtin/packages/r-checkpoint/package.py +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -12,11 +12,13 @@ class RCheckpoint(RPackage): install packages as they existed on CRAN on a specific snapshot date as if you had a CRAN time machine.""" - homepage = "https://cran.r-project.org/package=checkpoint" - url = "https://cran.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/checkpoint" + homepage = "https://cloud.r-project.org/package=checkpoint" + url = "https://cloud.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/checkpoint" + version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2') + version('0.4.3', sha256='c3e862f89f8838183d6028f7ed13683aec562e6dab77ad4b6a5e24ec653cfb64') version('0.3.18', '021d7faeb72c36167951e103b2b065ea') version('0.3.15', 'a4aa8320338f1434a330d984e97981ea') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py index 93fd4f5253..d2854903d1 100644 --- a/var/spack/repos/builtin/packages/r-chemometrics/package.py +++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py @@ -10,9 +10,9 @@ class RChemometrics(RPackage): """R companion to the book "Introduction to Multivariate Statistical Analysis in Chemometrics" written by K. Varmuza and P. Filzmoser (2009).""" - homepage = "https://cran.r-project.org/web/packages/chemometrics/index.html" - url = "https://cran.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/chemometrics" + homepage = "https://cloud.r-project.org/package=chemometrics" + url = "https://cloud.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/chemometrics" version('1.4.2', '8137b0ca4004add9cc2ea81d2c54427f') version('1.4.1', '1e5a89442bb4a61db0da884eedd74fc2') @@ -29,3 +29,6 @@ class RChemometrics(RPackage): depends_on('r-pls', type=('build', 'run')) depends_on('r-som', type=('build', 'run')) depends_on('r-pcapp', type=('build', 'run')) + depends_on('r-class', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-nnet', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py index 71c1575577..3defd1653b 100644 --- a/var/spack/repos/builtin/packages/r-chron/package.py +++ b/var/spack/repos/builtin/packages/r-chron/package.py @@ -9,8 +9,12 @@ from spack import * class RChron(RPackage): """Chronological objects which can handle dates and times.""" - homepage = "https://cran.r-project.org/package=chron" - url = "https://cran.r-project.org/src/contrib/chron_2.3-47.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/chron" + homepage = "https://cloud.r-project.org/package=chron" + url = "https://cloud.r-project.org/src/contrib/chron_2.3-47.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/chron" + version('2.3-53', sha256='521814b46ba958eae28e29d8766aebd285da5e6fa16c5806603df3ae39f77309') + version('2.3-52', sha256='c47fcf4abb635babe6337604c876d4853d8a24639a98b71523746c56ce75b4a0') version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f') + + depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-circlize/package.py b/var/spack/repos/builtin/packages/r-circlize/package.py index 89148b74f7..31dd662d76 100644 --- a/var/spack/repos/builtin/packages/r-circlize/package.py +++ b/var/spack/repos/builtin/packages/r-circlize/package.py @@ -18,13 +18,15 @@ class RCirclize(RPackage): convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.""" - homepage = "https://cran.r-project.org/package=circlize" - url = "https://cran.r-project.org/src/contrib/circlize_0.4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/circlize" + homepage = "https://cloud.r-project.org/package=circlize" + url = "https://cloud.r-project.org/src/contrib/circlize_0.4.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/circlize" + version('0.4.6', sha256='cec88cfc5e512a111cc37177552c25698ccc0e9bbecb0d6e60657e7b115a56fa') version('0.4.1', '6818830654f485abbdc8c74ec9087377') version('0.4.0', '0dbf1b481930a759d6f413d17f8ae1c4') - depends_on('r-globaloptions', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-globaloptions@0.1.0:', type=('build', 'run')) depends_on('r-shape', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py index aa31dfe6ef..472c8dbd4a 100644 --- a/var/spack/repos/builtin/packages/r-class/package.py +++ b/var/spack/repos/builtin/packages/r-class/package.py @@ -11,9 +11,11 @@ class RClass(RPackage): Learning Vector Quantization and Self-Organizing Maps.""" homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" - url = "https://cran.r-project.org/src/contrib/class_7.3-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/class" + url = "https://cloud.r-project.org/src/contrib/class_7.3-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/class" + version('7.3-15', sha256='f6bf33d610c726d58622b6cea78a808c7d6a317d02409d27c17741dfd1c730f4') version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-classint/package.py b/var/spack/repos/builtin/packages/r-classint/package.py index 3a9f11c66d..fb859c3e7c 100644 --- a/var/spack/repos/builtin/packages/r-classint/package.py +++ b/var/spack/repos/builtin/packages/r-classint/package.py @@ -10,11 +10,16 @@ class RClassint(RPackage): """Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.""" - homepage = "https://cran.r-project.org/package=classInt" - url = "https://cran.r-project.org/src/contrib/classInt_0.1-24.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/classInt" + homepage = "https://cloud.r-project.org/package=classInt" + url = "https://cloud.r-project.org/src/contrib/classInt_0.1-24.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/classInt" + version('0.4-1', sha256='39c63f8e37b379033d73d57929b5b8ea41b0023626cc1cec648d66bade5d0103') + version('0.3-3', sha256='a93e685ef9c40d5977bb91d7116505a25303b229897a20544722a94ea1365f30') + version('0.3-1', sha256='e2e6f857b544dfecb482b99346aa3ecfdc27b4d401c3537ee8fbaf91caca92b9') version('0.1-24', '45f1bde3ec7601ce17c99189be5c0fd5') + depends_on('r@2.2:', type=('build', 'run')) depends_on('r-e1071', type=('build', 'run')) depends_on('r-class', type=('build', 'run')) + depends_on('r-kernsmooth', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py index 883a34e8eb..e841226979 100644 --- a/var/spack/repos/builtin/packages/r-cli/package.py +++ b/var/spack/repos/builtin/packages/r-cli/package.py @@ -12,11 +12,13 @@ class RCli(RPackage): 'Unicode' symbols with 'ASCII' alternatives.""" homepage = "https://github.com/r-lib/cli#readme" - url = "https://cran.r-project.org/src/contrib/cli_1.0.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cli" + url = "https://cloud.r-project.org/src/contrib/cli_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/cli" + version('1.1.0', sha256='4fc00fcdf4fdbdf9b5792faee8c7cf1ed5c4f45b1221d961332cda82dbe60d0a') version('1.0.1', 'ef80fbcde15760fd55abbf9413b306e3971b2a7034ab8c415fb52dc0088c5ee4') version('1.0.0', 'e6c4169541d394d6d435c4b430b1dd77') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) + depends_on('r-crayon@1.3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-clipr/package.py b/var/spack/repos/builtin/packages/r-clipr/package.py index fe2f21736a..bd6a07923c 100644 --- a/var/spack/repos/builtin/packages/r-clipr/package.py +++ b/var/spack/repos/builtin/packages/r-clipr/package.py @@ -11,11 +11,11 @@ class RClipr(RPackage): and X11 clipboards.""" homepage = "https://github.com/mdlincoln/clipr" - url = "https://cran.r-project.org/src/contrib/clipr_0.4.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/clipr" + url = "https://cloud.r-project.org/src/contrib/clipr_0.4.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/clipr" + version('0.7.0', sha256='03a4e4b72ec63bd08b53fe62673ffc19a004cc846957a335be2b30d046b8c2e2') + version('0.5.0', sha256='fd303f8b7f29badcdf490bb2d579acdfc4f4e1aa9c90ac77ab9d05ce3d053dbf') version('0.4.0', '4012a31eb3b7a36bd3bac00f916e56a7') - depends_on('r-rstudioapi', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) depends_on('xclip') diff --git a/var/spack/repos/builtin/packages/r-clisymbols/package.py b/var/spack/repos/builtin/packages/r-clisymbols/package.py new file mode 100644 index 0000000000..057fa67b9b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-clisymbols/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RClisymbols(RPackage): + """A small subset of Unicode symbols, that are useful when building command + line applications. They fall back to alternatives on terminals that do not + support Unicode. Many symbols were taken from the 'figures' 'npm' package + (see <https://github.com/sindresorhus/figures>).""" + + homepage = "https://github.com/gaborcsardi/clisymbols" + url = "https://cloud.r-project.org/src/contrib/clisymbols_1.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/clisymbols" + + version('1.2.0', sha256='0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0') diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py index be9fdccdde..44a36e5b00 100644 --- a/var/spack/repos/builtin/packages/r-cluster/package.py +++ b/var/spack/repos/builtin/packages/r-cluster/package.py @@ -11,10 +11,15 @@ class RCluster(RPackage): Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".""" - homepage = "https://cran.r-project.org/web/packages/cluster/index.html" - url = "https://cran.rstudio.com/src/contrib/cluster_2.0.7-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cluster" + homepage = "https://cloud.r-project.org/package=cluster" + url = "https://cloud.r-project.org/src/contrib/cluster_2.0.7-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/cluster" + version('2.1.0', sha256='eaf955bef8f616ea563351ec7f597c445aec43e65991ca975e382ef1fd70aa14') version('2.0.7-1', 'a37add21b91d3e4f3883d005331e0d45') version('2.0.5', '7330f209ebce960bdee1a6d6679cb85a') version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59') + + depends_on('r@3.0.1:', when='@:2.0.6', type=('build', 'run')) + depends_on('r@3.2.0:', when='@2.0.7:2.0.7-1', type=('build', 'run')) + depends_on('r@3.3.0:', when='@2.0.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-clustergeneration/package.py b/var/spack/repos/builtin/packages/r-clustergeneration/package.py index 4dbcc13bb6..ccae368dde 100644 --- a/var/spack/repos/builtin/packages/r-clustergeneration/package.py +++ b/var/spack/repos/builtin/packages/r-clustergeneration/package.py @@ -9,10 +9,11 @@ from spack import * class RClustergeneration(RPackage): """Random Cluster Generation (with Specified Degree of Separation)""" - homepage = "https://cran.r-project.org/package=clusterGeneration" - url = "https://cran.r-project.org/src/contrib/clusterGeneration_1.3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/clusterGeneration/" + homepage = "https://cloud.r-project.org/package=clusterGeneration" + url = "https://cloud.r-project.org/src/contrib/clusterGeneration_1.3.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/clusterGeneration/" version('1.3.4', sha256='7c591ad95a8a9d7fb0e4d5d80dfd78f7d6a63cf7d11eb53dd3c98fdfb5b868aa') + depends_on('r@2.9.1:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py index 8c83b9d5da..bc06676d85 100644 --- a/var/spack/repos/builtin/packages/r-cner/package.py +++ b/var/spack/repos/builtin/packages/r-cner/package.py @@ -33,5 +33,5 @@ class RCner(RPackage): depends_on('r-annotate@1.50.0:', type=('build', 'run')) depends_on('r-go-db@3.3.0:', type=('build', 'run')) depends_on('r-keggrest@1.14.0:', type=('build', 'run')) - depends_on('r-utils@2.3.0:', type=('build', 'run')) + depends_on('r-r-utils@2.3.0:', type=('build', 'run')) depends_on('r@3.4.3:3.4.9', when='@1.14.0') diff --git a/var/spack/repos/builtin/packages/r-coda/package.py b/var/spack/repos/builtin/packages/r-coda/package.py index e7c7c8c11b..b69c0f5a80 100644 --- a/var/spack/repos/builtin/packages/r-coda/package.py +++ b/var/spack/repos/builtin/packages/r-coda/package.py @@ -12,10 +12,13 @@ class RCoda(RPackage): diagnostic tests of convergence to the equilibrium distribution of the Markov chain.""" - homepage = "https://cran.r-project.org/web/packages/coda/index.html" - url = "https://cran.r-project.org/src/contrib/coda_0.19-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/coda" + homepage = "https://cloud.r-project.org/package=coda" + url = "https://cloud.r-project.org/src/contrib/coda_0.19-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/coda" + version('0.19-3', sha256='d3df1fc848bcf1af8fae13d61eeab60e99a3d4b4db384bec4326f909f502c5d6') + version('0.19-2', sha256='678a7e6a87a2723089daeb780ea37ac3d4319b37eabe26928ea3fa9c9b1eda0d') version('0.19-1', '0d2aca6a5a3bdae9542708817c1ec001') + depends_on('r@2.14:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py index 4e451ba839..5ccaa4914c 100644 --- a/var/spack/repos/builtin/packages/r-codetools/package.py +++ b/var/spack/repos/builtin/packages/r-codetools/package.py @@ -9,9 +9,12 @@ from spack import * class RCodetools(RPackage): """Code analysis tools for R.""" - homepage = "https://cran.r-project.org/web/packages/codetools/index.html" - url = "https://cran.r-project.org/src/contrib/codetools_0.2-15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/codetools" + homepage = "https://cloud.r-project.org/package=codetools" + url = "https://cloud.r-project.org/src/contrib/codetools_0.2-15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/codetools" + version('0.2-16', sha256='f67a66175cb5d8882457d1e9b91ea2f16813d554fa74f80c1fd6e17cf1877501') version('0.2-15', '37419cbc3de81984cf6d9b207d4f62d4') version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d') + + depends_on('r@2.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-coin/package.py b/var/spack/repos/builtin/packages/r-coin/package.py index 81a8bf45d4..b52fff5e77 100644 --- a/var/spack/repos/builtin/packages/r-coin/package.py +++ b/var/spack/repos/builtin/packages/r-coin/package.py @@ -11,15 +11,19 @@ class RCoin(RPackage): including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.""" - homepage = "https://cran.r-project.org/package=coin" - url = "https://cran.r-project.org/src/contrib/coin_1.1-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/coin" + homepage = "https://cloud.r-project.org/package=coin" + url = "https://cloud.r-project.org/src/contrib/coin_1.1-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/coin" + version('1.3-0', sha256='adcebb37e0a7dfddbf8ec1e09c12a809bd76d90b5b8ff2b1048a75252ba11ef8') + version('1.2-2', sha256='d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb') version('1.1-3', '97d3d21f1e4a5762e36dd718dd2d0661') - depends_on('r@2.14.0:') - + depends_on('r@2.14.0:', when='@:1.2-2', type=('build', 'run')) + depends_on('r@3.4.0:', when='@1.3-0:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-modeltools@0.2-9:', type=('build', 'run')) depends_on('r-mvtnorm@1.0-5:', type=('build', 'run')) depends_on('r-multcomp', type=('build', 'run')) + depends_on('r-libcoin@1.0-0:', when='@1.3-0:', type=('build', 'run')) + depends_on('r-matrixstats@0.54.0:', when='@1.3-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py index ebe83745cc..9aaec8933e 100644 --- a/var/spack/repos/builtin/packages/r-colorspace/package.py +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -12,9 +12,13 @@ class RColorspace(RPackage): Qualitative, sequential, and diverging color palettes based on HCL colors are provided.""" - homepage = "https://cran.r-project.org/web/packages/colorspace/index.html" - url = "https://cran.r-project.org/src/contrib/colorspace_1.3-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/colorspace" + homepage = "https://cloud.r-project.org/package=colorspace" + url = "https://cloud.r-project.org/src/contrib/colorspace_1.3-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/colorspace" + version('1.4-1', sha256='693d713a050f8bfecdb7322739f04b40d99b55aed168803686e43401d5f0d673') + version('1.4-0', sha256='ce003c5958dd704697959e9dc8a108c8cb568f8d78ece113235732afc5dff556') version('1.3-2', '63000bab81d995ff167df76fb97b2984') version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-combinat/package.py b/var/spack/repos/builtin/packages/r-combinat/package.py index 98d89fffbd..7adf666972 100644 --- a/var/spack/repos/builtin/packages/r-combinat/package.py +++ b/var/spack/repos/builtin/packages/r-combinat/package.py @@ -9,8 +9,8 @@ from spack import * class RCombinat(RPackage): """routines for combinatorics""" - homepage = "https://cran.r-project.org/package=combinat" - url = "https://cran.r-project.org/src/contrib/combinat_0.0-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/combinat/" + homepage = "https://cloud.r-project.org/package=combinat" + url = "https://cloud.r-project.org/src/contrib/combinat_0.0-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/combinat/" version('0.0-8', sha256='1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1') diff --git a/var/spack/repos/builtin/packages/r-commonmark/package.py b/var/spack/repos/builtin/packages/r-commonmark/package.py index 6cbafa742f..27afc8cfea 100644 --- a/var/spack/repos/builtin/packages/r-commonmark/package.py +++ b/var/spack/repos/builtin/packages/r-commonmark/package.py @@ -9,8 +9,8 @@ from spack import * class RCommonmark(RPackage): """commonmark: CommonMark and Github Markdown Rendering in R""" - homepage = "https://cran.r-project.org/package=commonmark" - url = "https://cran.r-project.org/src/contrib/commonmark_1.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/commonmark/" + homepage = "https://cloud.r-project.org/package=commonmark" + url = "https://cloud.r-project.org/src/contrib/commonmark_1.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/commonmark/" version('1.7', sha256='d14a767a3ea9778d6165f44f980dd257423ca6043926e3cd8f664f7171f89108') diff --git a/var/spack/repos/builtin/packages/r-compositions/package.py b/var/spack/repos/builtin/packages/r-compositions/package.py index 1b5e22f4bd..112af5a1e5 100644 --- a/var/spack/repos/builtin/packages/r-compositions/package.py +++ b/var/spack/repos/builtin/packages/r-compositions/package.py @@ -9,9 +9,9 @@ from spack import * class RCompositions(RPackage): """Compositional Data Analysis""" - homepage = "https://cran.r-project.org/web/packages/compositions/index.html" - url = "https://cran.r-project.org/src/contrib/compositions_1.40-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/compositions" + homepage = "https://cloud.r-project.org/package=compositions" + url = "https://cloud.r-project.org/src/contrib/compositions_1.40-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/compositions" version('1.40-2', 'ad87efe2fb303d95472e73c8ca8d9a01') diff --git a/var/spack/repos/builtin/packages/r-construct/package.py b/var/spack/repos/builtin/packages/r-construct/package.py index 03f026dc2d..1ec973752f 100644 --- a/var/spack/repos/builtin/packages/r-construct/package.py +++ b/var/spack/repos/builtin/packages/r-construct/package.py @@ -10,9 +10,9 @@ class RConstruct(RPackage): """conStruct: Models Spatially Continuous and Discrete Population GeneticStructure""" - homepage = "https://cran.r-project.org/package=conStruct" - url = "https://cran.r-project.org/src/contrib/conStruct_1.0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/conStruct" + homepage = "https://cloud.r-project.org/package=conStruct" + url = "https://cloud.r-project.org/src/contrib/conStruct_1.0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/conStruct" version('1.0.3', sha256='b449c133a944ad05a28f84f312ed4ccbc1574c4659aa09c678618d2ae9008310') @@ -27,3 +27,4 @@ class RConstruct(RPackage): depends_on('r-rstan@2.18.1:', type=('build', 'run')) depends_on('r-rstantools@1.5.0:', type=('build', 'run')) depends_on('r-stanheaders@2.18.0:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-convevol/package.py b/var/spack/repos/builtin/packages/r-convevol/package.py index ea8d4595ec..398e905016 100644 --- a/var/spack/repos/builtin/packages/r-convevol/package.py +++ b/var/spack/repos/builtin/packages/r-convevol/package.py @@ -9,12 +9,13 @@ from spack import * class RConvevol(RPackage): """Quantifies and assesses the significance of convergent evolution""" - homepage = "https://cran.r-project.org/package=convevol" - url = "https://cran.r-project.org/src/contrib/convevol_1.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/convevol/" + homepage = "https://cloud.r-project.org/package=convevol" + url = "https://cloud.r-project.org/src/contrib/convevol_1.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/convevol/" version('1.3', sha256='d6b24b9796a559f5280e277746189d141151ade4b14cc6b4c2d9d496d7f314ac') + depends_on('r@3.5.0:', type=('build', 'run')) depends_on('r-ape', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) depends_on('r-geiger', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-corhmm/package.py b/var/spack/repos/builtin/packages/r-corhmm/package.py index 7d1632d5ac..41043b8a1c 100644 --- a/var/spack/repos/builtin/packages/r-corhmm/package.py +++ b/var/spack/repos/builtin/packages/r-corhmm/package.py @@ -14,9 +14,9 @@ class RCorhmm(RPackage): states in a Markov process and various other functions for evaluating models of binary character evolution.""" - homepage = "https://cran.r-project.org/package=corHMM" - url = "https://cran.r-project.org/src/contrib/corHMM_1.22.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/corHMM/" + homepage = "https://cloud.r-project.org/package=corHMM" + url = "https://cloud.r-project.org/src/contrib/corHMM_1.22.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/corHMM/" version('1.22', sha256='d262fa1183eab32087afb70f1789fabae6fb49bec01d627974c54a088a48b10d') diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py index bbebf81c22..3690284809 100644 --- a/var/spack/repos/builtin/packages/r-corpcor/package.py +++ b/var/spack/repos/builtin/packages/r-corpcor/package.py @@ -9,8 +9,10 @@ from spack import * class RCorpcor(RPackage): """Efficient Estimation of Covariance and (Partial) Correlation""" - homepage = "https://cran.r-project.org/package=corpcor" - url = "https://cran.r-project.org/src/contrib/corpcor_1.6.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/corpcor" + homepage = "https://cloud.r-project.org/package=corpcor" + url = "https://cloud.r-project.org/src/contrib/corpcor_1.6.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/corpcor" version('1.6.9', '7f447d9f389e5d7dedb5fe5baedca925') + + depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-corrplot/package.py b/var/spack/repos/builtin/packages/r-corrplot/package.py index 702fe40fab..71ded1da62 100644 --- a/var/spack/repos/builtin/packages/r-corrplot/package.py +++ b/var/spack/repos/builtin/packages/r-corrplot/package.py @@ -10,8 +10,9 @@ class RCorrplot(RPackage): """A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering.""" - homepage = "https://cran.r-project.org/package=corrplot" - url = "https://cran.r-project.org/src/contrib/corrplot_0.77.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/corrplot" + homepage = "https://cloud.r-project.org/package=corrplot" + url = "https://cloud.r-project.org/src/contrib/corrplot_0.77.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/corrplot" + version('0.84', sha256='0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc') version('0.77', '2a5d54fd5c65618b9afba1a32f6b4542') diff --git a/var/spack/repos/builtin/packages/r-covr/package.py b/var/spack/repos/builtin/packages/r-covr/package.py index 404543baa1..1f62a54c17 100644 --- a/var/spack/repos/builtin/packages/r-covr/package.py +++ b/var/spack/repos/builtin/packages/r-covr/package.py @@ -16,14 +16,20 @@ class RCovr(RPackage): or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.""" - homepage = "https://cran.r-project.org/package=covr" - url = "https://cran.r-project.org/src/contrib/covr_3.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/covr" + homepage = "https://cloud.r-project.org/package=covr" + url = "https://cloud.r-project.org/src/contrib/covr_3.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/covr" + version('3.3.0', sha256='c0aa0bd7b2dc05effdc2367c59d45294f46858930d1b14efb393b205021fc65a') + version('3.2.1', sha256='ea90daa48011e4ac4431ae47ee02fad98f54b529fc3900281cbeef7a2edef0a0') + version('3.2.0', sha256='b26135306b1d6b14dd4deb481359dd919a7ca1e802ca5479fed394dcf35f0ef9') version('3.0.1', 'f88383f751fe5aa830a2b2e5c14aa66a') + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-digest', when='@3.2.0:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-rex', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) - depends_on('r-withr', type=('build', 'run')) + depends_on('r-withr@1.0.2:', type=('build', 'run')) + depends_on('r-yaml', when='@3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cowplot/package.py b/var/spack/repos/builtin/packages/r-cowplot/package.py index 150844ec43..3d3bd5549b 100644 --- a/var/spack/repos/builtin/packages/r-cowplot/package.py +++ b/var/spack/repos/builtin/packages/r-cowplot/package.py @@ -15,18 +15,21 @@ class RCowplot(RPackage): theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke's plot package.""" - homepage = "https://cran.r-project.org/package=cowplot" - url = "https://cran.rstudio.com/src/contrib/cowplot_0.8.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/cowplot" + homepage = "https://cloud.r-project.org/package=cowplot" + url = "https://cloud.r-project.org/src/contrib/cowplot_0.8.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/cowplot" + version('1.0.0', sha256='70f9a7c46d10f409d1599f1afc9fd3c947051cf2b430f01d903c64ef1e6c98a5') version('0.9.3', sha256='3e10475fd7506ea9297ed72eb1a3acf858c6fa99d26e46fc39654eba000c3dcb') version('0.9.2', sha256='8b92ce7f92937fde06b0cfb86c7634a39b3b2101e362cc55c4bec6b3fde1d28f') version('0.9.1', sha256='953fd9d6ff370472b9f5a9ee867a423bea3e26e406d08a2192ec1872a2e60047') version('0.9.0', sha256='d5632f78294c3678c08d3eb090abe1eec5cc9cd15cb5d96f9c43794ead098cb5') version('0.8.0', sha256='a617fde25030fe764f20967fb753a953d73b47745a2146c97c2565eb4d06700d') - depends_on('r@3.3.0:', type=('build', 'run')) - depends_on('r-ggplot2@2.1.0:', type=('build', 'run')) - depends_on('r-gtable@0.1.2:', type=('build', 'run')) - depends_on('r-plyr@1.8.2:', type=('build', 'run')) + depends_on('r@3.3.0:', when='@:0.9.4', type=('build', 'run')) + depends_on('r@3.5.0:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-ggplot2@2.1.1:', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) + depends_on('r-plyr@1.8.2:', when='@:0.9.9', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) + depends_on('r-rlang', when='@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py index 843851a592..4a5cd95145 100644 --- a/var/spack/repos/builtin/packages/r-crayon/package.py +++ b/var/spack/repos/builtin/packages/r-crayon/package.py @@ -13,9 +13,9 @@ class RCrayon(RPackage): New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.""" - homepage = "https://cran.r-project.org/package=sourcetools" - url = "https://cran.rstudio.com/src/contrib/crayon_1.3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/crayon" + homepage = "https://github.com/r-lib/crayon#readme" + url = "https://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/crayon" version('1.3.4', '77c7c2906c59a3141306d86c89ffc7d3') version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9') diff --git a/var/spack/repos/builtin/packages/r-crosstalk/package.py b/var/spack/repos/builtin/packages/r-crosstalk/package.py index 39119c3e26..ad17c33aa6 100644 --- a/var/spack/repos/builtin/packages/r-crosstalk/package.py +++ b/var/spack/repos/builtin/packages/r-crosstalk/package.py @@ -10,13 +10,15 @@ class RCrosstalk(RPackage): """Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files).""" - homepage = "https://cran.r-project.org/web/packages/crosstalk/index.html" - url = "https://cran.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz" + homepage = "https://cloud.r-project.org/package=crosstalk" + url = "https://cloud.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/crosstalk" version('1.0.0', 'c13c21b81af2154be3f08870fd3a7077') - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-htmltools@0.3.5:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-lazyeval', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-shiny', type=('build', 'run')) + depends_on('r-shiny@0.11:', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-crul/package.py b/var/spack/repos/builtin/packages/r-crul/package.py index 6ce56a5584..e2d4410ebc 100644 --- a/var/spack/repos/builtin/packages/r-crul/package.py +++ b/var/spack/repos/builtin/packages/r-crul/package.py @@ -9,10 +9,11 @@ from spack import * class RCrul(RPackage): """crul: HTTP Client""" - homepage = "https://cran.r-project.org/package=crul" - url = "https://cran.r-project.org/src/contrib/crul_0.7.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/crul" + homepage = "https://cloud.r-project.org/package=crul" + url = "https://cloud.r-project.org/src/contrib/crul_0.7.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/crul" + version('0.8.4', sha256='dbd950ad3b68402e5a5955615b1abcb5c9bdc846c93aa25f96a7a58913d04c8b') version('0.7.4', sha256='c963dd666ae3fc89b661ce19fce2fa19a16fc3825e1502105cae98ceb92c6014') depends_on('r-curl@3.3:', type=('build', 'run')) @@ -20,3 +21,4 @@ class RCrul(RPackage): depends_on('r-mime', type=('build', 'run')) depends_on('r-r6@2.2.0:', type=('build', 'run')) depends_on('r-urltools@1.6.0:', type=('build', 'run')) + depends_on('r-jsonlite', when='@0.8.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py index 0b5a475b81..7ed968d5bc 100644 --- a/var/spack/repos/builtin/packages/r-cubature/package.py +++ b/var/spack/repos/builtin/packages/r-cubature/package.py @@ -9,8 +9,12 @@ from spack import * class RCubature(RPackage): """Adaptive multivariate integration over hypercubes""" - homepage = "https://cran.r-project.org/package=cubature" - url = "https://cran.r-project.org/src/contrib/cubature_1.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cubature" + homepage = "https://cloud.r-project.org/package=cubature" + url = "https://cloud.r-project.org/src/contrib/cubature_1.1-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/cubature" + version('2.0.3', sha256='79bf03ebdb64b0de1ef19d24051b9d922df9310254bee459bb47764522407a73') + version('2.0.2', sha256='641165c665ff490c523bccc05c42bb6851e42676b6b366b55fc442a51a8fbe8c') version('1.1-2', '5617e1d82baa803a3814d92461da45c9') + + depends_on('r-rcpp', when='@2.0.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-cubist/package.py b/var/spack/repos/builtin/packages/r-cubist/package.py index 1a89f3c21f..a41928e663 100644 --- a/var/spack/repos/builtin/packages/r-cubist/package.py +++ b/var/spack/repos/builtin/packages/r-cubist/package.py @@ -9,10 +9,12 @@ from spack import * class RCubist(RPackage): """Regression modeling using rules with added instance-based corrections""" - homepage = "https://cran.r-project.org/package=Cubist" - url = "https://cran.r-project.org/src/contrib/Cubist_0.0.19.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Cubist" + homepage = "https://cloud.r-project.org/package=Cubist" + url = "https://cloud.r-project.org/src/contrib/Cubist_0.0.19.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Cubist" + version('0.2.2', sha256='cd3e152cc72ab33f720a8fb6b8b6787171e1c037cfda48f1735ab692ed6d85d4') + version('0.2.1', sha256='b310c3f166f15fa3e16f8d110d39931b0bb1b0aa8d0c9ac2af5a9a45081588a3') version('0.0.19', 'bf9364f655536ec03717fd2ad6223a47') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py index 785b4487c5..2a720b2a99 100644 --- a/var/spack/repos/builtin/packages/r-curl/package.py +++ b/var/spack/repos/builtin/packages/r-curl/package.py @@ -18,14 +18,15 @@ class RCurl(RPackage): package with http specific tools and logic.""" homepage = "https://github.com/jeroenooms/curl" - url = "https://cran.r-project.org/src/contrib/curl_2.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/curl" + url = "https://cloud.r-project.org/src/contrib/curl_2.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/curl" + version('4.0', sha256='09a99c9c86666449188fbb211cb1e9fbdb5108ab56f0d09322cd0ae50e926171') version('3.3', sha256='0cb0b9a9280edc42ebed94708541ec86b4f48779e722171e45227eab8a88a5bd') version('3.0', '741202626eacd1f9c022b0a4d7be6d6a') version('2.3', '7250ee8caed98ba76906ab4d32da60f8') version('1.0', '93d34926d6071e1fba7e728b482f0dd9') version('0.9.7', 'a101f7de948cb828fef571c730f39217') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('curl') diff --git a/var/spack/repos/builtin/packages/r-data-table/package.py b/var/spack/repos/builtin/packages/r-data-table/package.py index 4b669b8a76..e9e2bc0440 100644 --- a/var/spack/repos/builtin/packages/r-data-table/package.py +++ b/var/spack/repos/builtin/packages/r-data-table/package.py @@ -13,9 +13,11 @@ class RDataTable(RPackage): syntax, for faster development.""" homepage = "https://github.com/Rdatatable/data.table/wiki" - url = "https://cran.r-project.org/src/contrib/data.table_1.10.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/data.table" + url = "https://cloud.r-project.org/src/contrib/data.table_1.10.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/data.table" + version('1.12.2', sha256='db55c18f0d703a8bc1c806dd1f7551bb405cb867717f52ef9dd64405394d22f5') + version('1.12.0', sha256='611b112123dbd4ebd5200770fcdfaaeaab622adeb2b290d36018d3092742e3f7') version('1.11.8', sha256='dc427465599cadd848b28a78e2fce3362867847b44148252054385999fe566d9') version('1.11.6', sha256='ac6783c18e94d1bc05702ddec9fd87c542c744f640132f5ffc373348be84d9e9') version('1.11.4', sha256='fdccf1dec3f38bb344163163decf3ffa0c0f8e2c70daa1bec8aac422716e81d5') diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py index 866b19dd4c..bd8e4289e3 100644 --- a/var/spack/repos/builtin/packages/r-dbi/package.py +++ b/var/spack/repos/builtin/packages/r-dbi/package.py @@ -12,7 +12,11 @@ class RDbi(RPackage): virtual and need to be extended by the various R/DBMS implementations.""" homepage = "http://rstats-db.github.io/DBI" - url = "https://cran.rstudio.com/src/contrib/DBI_0.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DBI" + url = "https://cloud.r-project.org/src/contrib/DBI_0.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/DBI" + + version('1.0.0', sha256='ff16f118eb3f759183441835e932b87358dd80ab9800ce576a8f3df1b6f01cf5') version('0.4-1', 'c7ee8f1c5037c2284e99c62698d0f087') version('0.7', '66065dd687d758b72d638adb6a8cab2e') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dbplyr/package.py b/var/spack/repos/builtin/packages/r-dbplyr/package.py index 5950fb4a02..2f88bb3fc8 100644 --- a/var/spack/repos/builtin/packages/r-dbplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dbplyr/package.py @@ -14,21 +14,23 @@ class RDbplyr(RPackage): author.""" homepage = "https://github.com/tidyverse/dbplyr" - url = "https://cran.r-project.org/src/contrib/dbplyr_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dbplyr" + url = "https://cloud.r-project.org/src/contrib/dbplyr_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dbplyr" + version('1.4.2', sha256='b783f0da2c09a1e63f41168b02c0715b08820f02a351f7ab0aaa688432754de0') + version('1.4.1', sha256='cfe829f56acdc785c5af21bf3927cf08327504d78c4ae1477c405c81b131da95') version('1.2.2', sha256='9d410bb0055fffe10f1f8da55a5b24d98322c7b571d74df61427d5888332bc48') version('1.2.1', sha256='b348e7a02623f037632c85fb11be16c40c01755ae6ca02c8c189cdc192a699db') version('1.2.0', sha256='02a5fa8dcf8a81c061fdaefa74f17896bee913720418b44dbd226a0d6b30799d') version('1.1.0', sha256='7b1e456a2d1056fa6284582cd82d2df66d06b3eea92e9995f5a91a45f246f69d') - depends_on('r@3.2:', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-assertthat@0.2.0:', type=('build', 'run')) - depends_on('r-dbi@0.7:', type=('build', 'run')) - depends_on('r-dplyr@0.7.4:', type=('build', 'run')) + depends_on('r-dbi@1.0.0:', type=('build', 'run')) + depends_on('r-dplyr@0.8.0:', type=('build', 'run')) depends_on('r-glue@1.2.0:', type=('build', 'run')) - depends_on('r-purrr@0.2.4:', type=('build', 'run')) + depends_on('r-purrr@0.2.5:', type=('build', 'run')) depends_on('r-r6@2.2.2:', type=('build', 'run')) - depends_on('r-rlang@0.1.6:', type=('build', 'run')) - depends_on('r-tibble@1.4.1:', type=('build', 'run')) - depends_on('r-tidyselect@0.2.2:', type=('build', 'run')) + depends_on('r-rlang@0.2.0:', type=('build', 'run')) + depends_on('r-tibble@1.4.2:', type=('build', 'run')) + depends_on('r-tidyselect@0.2.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-debugme/package.py b/var/spack/repos/builtin/packages/r-debugme/package.py new file mode 100644 index 0000000000..590fe5f23a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-debugme/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDebugme(RPackage): + """Specify debug messages as special string constants, and control + debugging of packages via environment variables.""" + + homepage = "https://github.com/r-lib/debugme#readme" + url = "https://cloud.r-project.org/src/contrib/debugme_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/debugme" + + version('1.1.0', sha256='4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1') + + depends_on('r-crayon', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deldir/package.py b/var/spack/repos/builtin/packages/r-deldir/package.py index 299ef640ac..f206bc6a6b 100644 --- a/var/spack/repos/builtin/packages/r-deldir/package.py +++ b/var/spack/repos/builtin/packages/r-deldir/package.py @@ -13,10 +13,12 @@ class RDeldir(RPackage): tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.""" - homepage = "https://CRAN.R-project.org/package=deldir" - url = "https://cran.r-project.org/src/contrib/deldir_0.1-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/deldir" + homepage = "https://cloud.r-project.org/package=deldir" + url = "https://cloud.r-project.org/src/contrib/deldir_0.1-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/deldir" + version('0.1-23', sha256='e0112bce9fc94daf73596a0fff9b3958b80872e3bbb487be73e157b13a6f201d') + version('0.1-21', sha256='b9dabcc1813c7a0f8edaf720a94bdd611a83baf3d3e52e861d352369e815690c') version('0.1-14', '6a22b13d962615cd9d51b6eae403409f') - depends_on('r@0.99:') + depends_on('r@0.99:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dendextend/package.py b/var/spack/repos/builtin/packages/r-dendextend/package.py index 3fe9677f90..b1e578164c 100644 --- a/var/spack/repos/builtin/packages/r-dendextend/package.py +++ b/var/spack/repos/builtin/packages/r-dendextend/package.py @@ -9,15 +9,17 @@ from spack import * class RDendextend(RPackage): """dendextend: Extending 'Dendrogram' Functionality in R""" - homepage = "https://CRAN.R-project.org/package=dendextend" - url = "https://cran.r-project.org/src/contrib/dendextend_1.5.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dendextend" + homepage = "https://cloud.r-project.org/package=dendextend" + url = "https://cloud.r-project.org/src/contrib/dendextend_1.5.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dendextend" + version('1.12.0', sha256='b487fed8c1878a23b9e28394ee11f16a1831b76c90793eb486e6963c7162fa55') + version('1.10.0', sha256='88f0fb3362d69144daf4f35d0ea09f32c2df1adf614e040327a42552a8fd3224') version('1.5.2', '1134869d94005727c63cf3037e2f1bbf') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-magrittr@1.0.1:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-fpc', type=('build', 'run')) - depends_on('r-whisker', type=('build', 'run')) + depends_on('r-fpc', when='@:1.10.0', type=('build', 'run')) + depends_on('r-whisker', when='@:1.5.2', type=('build', 'run')) depends_on('r-viridis', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py index 4a993a7185..a17bd18179 100644 --- a/var/spack/repos/builtin/packages/r-deoptim/package.py +++ b/var/spack/repos/builtin/packages/r-deoptim/package.py @@ -11,8 +11,9 @@ class RDeoptim(RPackage): """Implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector.""" - homepage = "https://cran.r-project.org/package=DEoptim" - url = "https://cran.r-project.org/src/contrib/DEoptim_2.2-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DEoptim" + homepage = "https://cloud.r-project.org/package=DEoptim" + url = "https://cloud.r-project.org/src/contrib/DEoptim_2.2-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/DEoptim" + version('2.2-4', sha256='0a547784090d1e9b93efc53768110621f35bed3692864f6ce5c0dda2ebd6d482') version('2.2-3', 'ed406e6790f8f1568aa9bec159f80326') diff --git a/var/spack/repos/builtin/packages/r-deoptimr/package.py b/var/spack/repos/builtin/packages/r-deoptimr/package.py index 5c24834833..a48e98af48 100644 --- a/var/spack/repos/builtin/packages/r-deoptimr/package.py +++ b/var/spack/repos/builtin/packages/r-deoptimr/package.py @@ -11,8 +11,8 @@ class RDeoptimr(RPackage): Evolution stochastic algorithm for global optimization of nonlinear programming problems.""" - homepage = "https://cran.r-project.org/web/packages/DEoptimR/index.html" - url = "https://cran.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DEoptimR" + homepage = "https://cloud.r-project.org/package=DEoptimR" + url = "https://cloud.r-project.org/src/contrib/DEoptimR_1.0-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/DEoptimR" version('1.0-8', 'c85836a504fbe4166e3c8eba0efe705d') diff --git a/var/spack/repos/builtin/packages/r-desc/package.py b/var/spack/repos/builtin/packages/r-desc/package.py index 3aa442852f..9504ed5052 100644 --- a/var/spack/repos/builtin/packages/r-desc/package.py +++ b/var/spack/repos/builtin/packages/r-desc/package.py @@ -9,9 +9,9 @@ from spack import * class RDesc(RPackage): """desc: Manipulate DESCRIPTION Files""" - homepage = "https://cran.r-project.org/package=desc" - url = "https://cran.r-project.org/src/contrib/desc_1.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/desc/" + homepage = "https://cloud.r-project.org/package=desc" + url = "https://cloud.r-project.org/src/contrib/desc_1.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/desc/" version('1.2.0', sha256='e66fb5d4fc7974bc558abcdc107a1f258c9177a29dcfcf9164bc6b33dd08dae8') diff --git a/var/spack/repos/builtin/packages/r-desolve/package.py b/var/spack/repos/builtin/packages/r-desolve/package.py index f26872629c..466c8107ed 100644 --- a/var/spack/repos/builtin/packages/r-desolve/package.py +++ b/var/spack/repos/builtin/packages/r-desolve/package.py @@ -12,8 +12,12 @@ class RDesolve(RPackage): equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations.""" - homepage = "https://cran.r-project.org/package=deSolve" - url = "https://cran.r-project.org/src/contrib/deSolve_1.20.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/deSolve" + homepage = "https://cloud.r-project.org/package=deSolve" + url = "https://cloud.r-project.org/src/contrib/deSolve_1.20.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/deSolve" + version('1.24', sha256='3aa52c822abb0348a904d5bbe738fcea2b2ba858caab9f2831125d07f0d57b42') + version('1.21', sha256='45c372d458fe4c7c11943d4c409517849b1be6782dc05bd9a74b066e67250c63') version('1.20', '85c6a2d8568944ae8eef27ac7c35fb25') + + depends_on('r@2.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py index 8a4ed3db3c..b5a1151702 100644 --- a/var/spack/repos/builtin/packages/r-devtools/package.py +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -10,19 +10,30 @@ class RDevtools(RPackage): """Collection of package development tools.""" homepage = "https://github.com/hadley/devtools" - url = "https://cran.r-project.org/src/contrib/devtools_1.12.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/devtools" + url = "https://cloud.r-project.org/src/contrib/devtools_1.12.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/devtools" + version('2.1.0', sha256='c1f75346a90adf0669b5508fe68cc78bd3b114c1303fa7d22bf90991edd9230d') + version('2.0.2', sha256='99a2fa957068254b8ecdb3fc2d50e2950230910ea31c314fc0e7d934e4bd1709') version('1.12.0', '73b46c446273566e5b21c9f5f72aeca3') version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2') - depends_on('r@3.0.2:') - + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-httr@0.4:', type=('build', 'run')) depends_on('r-memoise@1.0.0:', type=('build', 'run')) - depends_on('r-whisker', type=('build', 'run')) + depends_on('r-whisker', when='@:1.9.9', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-rstudioapi@0.2.0:', type=('build', 'run')) + depends_on('r-rstudioapi@0.7.0:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-git2r@0.11.0:', type=('build', 'run')) + depends_on('r-git2r@0.23.0:', type=('build', 'run')) depends_on('r-withr', type=('build', 'run')) + depends_on('r-usethis@1.5.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-callr', when='@2.0.0:', type=('build', 'run')) + depends_on('r-cli', when='@2.0.0:', type=('build', 'run')) + depends_on('r-pkgbuild@1.0.3:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-pkgload@1.0.2:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-rcmdcheck@1.3.3:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-remotes@2.1.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-roxygen2@6.1.1:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-sessioninfo@1.1.1:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-testthat@2.1.1:', when='@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py index 713740f1b0..23ad11daf8 100644 --- a/var/spack/repos/builtin/packages/r-diagrammer/package.py +++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py @@ -10,15 +10,31 @@ class RDiagrammer(RPackage): """Create graph diagrams and flowcharts using R.""" homepage = "https://github.com/rich-iannone/DiagrammeR" - url = "https://cran.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DiagrammeR" + url = "https://cloud.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/DiagrammeR" + version('1.0.1', sha256='ccee8acf608fc909e73c6de4374cef5a570cb62e5f454ac55dda736f22f3f013') + version('1.0.0', sha256='2b186dae1b19018681b979e9444bf16559c42740d8382676fbaf3b0f8a44337e') version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a') - depends_on('r-htmlwidgets', type=('build', 'run')) - depends_on('r-igraph', type=('build', 'run')) - depends_on('r-influencer', type=('build', 'run')) - depends_on('r-rstudioapi@0.6:', type=('build', 'run')) - depends_on('r-stringr', type=('build', 'run')) - depends_on('r-visnetwork', type=('build', 'run')) - depends_on('r-scales', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.9.2:', type=('build', 'run')) + depends_on('r-htmlwidgets@1.0:', type=('build', 'run')) + depends_on('r-igraph@1.1.2:', type=('build', 'run')) + depends_on('r-influencer@0.1.0:', type=('build', 'run')) + depends_on('r-rstudioapi@0.7:', type=('build', 'run')) + depends_on('r-stringr@1.3.0:', type=('build', 'run')) + depends_on('r-visnetwork@2.0.3:', type=('build', 'run')) + depends_on('r-scales@0.5.0:', type=('build', 'run')) + depends_on('r-dplyr@0.7.4:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-downloader@0.4:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-glue@1.2.0:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-htmltools@0.3.6:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-magrittr@1.5:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-purrr@0.2.4:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-rcolorbrewer@1.1-2:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-readr@1.1.1:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-rlang@0.2.0:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-rgexf@0.15.3:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-tibble@1.4.2:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-tidyr@0.8.0:', when='@1.0.0:', type=('build', 'run')) + depends_on('r-viridis@0.5.0:', when='@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dicekriging/package.py b/var/spack/repos/builtin/packages/r-dicekriging/package.py index 4372047e89..0f00d6ea5a 100644 --- a/var/spack/repos/builtin/packages/r-dicekriging/package.py +++ b/var/spack/repos/builtin/packages/r-dicekriging/package.py @@ -11,7 +11,8 @@ class RDicekriging(RPackage): functions : km, print.km, plot.km, predict.km.""" homepage = "http://dice.emse.fr/" - url = "https://cran.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DiceKriging" + url = "https://cloud.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/DiceKriging" + version('1.5.6', sha256='25466d2db9f17083d1c7b9545e5ec88f630be934f9373c2f7b36c38de4e64e92') version('1.5.5', 'ee3e2d7a91d4a712467ef4f0b69c2844') diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py index aced519038..cda6906901 100644 --- a/var/spack/repos/builtin/packages/r-dichromat/package.py +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -10,8 +10,10 @@ class RDichromat(RPackage): """Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.""" - homepage = "https://cran.r-project.org/web/packages/dichromat/index.html" - url = "https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dichromat" + homepage = "https://cloud.r-project.org/package=dichromat" + url = "https://cloud.r-project.org/src/contrib/dichromat_2.0-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dichromat" version('2.0-0', '84e194ac95a69763d740947a7ee346a6') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diffusionmap/package.py b/var/spack/repos/builtin/packages/r-diffusionmap/package.py index eac9587155..84fb7c2084 100644 --- a/var/spack/repos/builtin/packages/r-diffusionmap/package.py +++ b/var/spack/repos/builtin/packages/r-diffusionmap/package.py @@ -11,16 +11,17 @@ class RDiffusionmap(RPackage): computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.""" - homepage = "https://cran.r-project.org/web/packages/diffusionMap/index.html" - url = "https://cran.r-project.org/src/contrib/diffusionMap_1.1-0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/diffusionMap" + homepage = "https://cloud.r-project.org/package=diffusionMap" + url = "https://cloud.r-project.org/src/contrib/diffusionMap_1.1-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/diffusionMap" + version('1.1-0.1', sha256='b24cf841af2566ac36f4ede2885f2ff355a7905398444d6d89747315d99a8486') version('1.1-0', 'cc7d728087ba08d9299ae3a64a8d8919') version('1.0-0', 'bca462e6efe45c5eaa48d38621f0bd6f') version('0.0-2', 'b599f47ebf30127e34ce2219dc3e43ae') version('0.0-1', '20c2cc2fffb5237d5c0216207016c2a1') - depends_on('r@3.4.0:3.4.9') + depends_on('r@2.4.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) depends_on('r-scatterplot3d', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py index d69645f7ee..feb608e7f4 100644 --- a/var/spack/repos/builtin/packages/r-digest/package.py +++ b/var/spack/repos/builtin/packages/r-digest/package.py @@ -25,11 +25,14 @@ class RDigest(RPackage): used.""" homepage = "http://dirk.eddelbuettel.com/code/digest.html" - url = "https://cran.r-project.org/src/contrib/digest_0.6.12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/digest" + url = "https://cloud.r-project.org/src/contrib/digest_0.6.12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/digest" + version('0.6.20', sha256='05674b0b5d888461ff770176c67b10a11be062b0fee5dbd9298f25a9a49830c7') + version('0.6.19', sha256='28d159bd589ecbd01b8da0826eaed417f5c1bf5a11b79e76bf67ce8d935cccf4') version('0.6.12', '738efd4d9a37c5a4001ae66e954ce07e') version('0.6.11', '52a864f55846b48b3cab0b5d0304a82a') version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') - depends_on('r@2.4.1:') + depends_on('r@2.4.1:', when='@:0.6.15', type=('build', 'run')) + depends_on('r@3.1.0:', when='@0.6.16:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-diptest/package.py b/var/spack/repos/builtin/packages/r-diptest/package.py index b7b25d8215..0e5edc21ef 100644 --- a/var/spack/repos/builtin/packages/r-diptest/package.py +++ b/var/spack/repos/builtin/packages/r-diptest/package.py @@ -9,8 +9,8 @@ from spack import * class RDiptest(RPackage): """diptest: Hartigan's Dip Test Statistic for Unimodality - Corrected""" - homepage = "https://CRAN.R-project.org/package=diptest" - url = "https://cran.r-project.org/src/contrib/diptest_0.75-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/diptest" + homepage = "https://cloud.r-project.org/package=diptest" + url = "https://cloud.r-project.org/src/contrib/diptest_0.75-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/diptest" version('0.75-7', '1a4a958fda763f7c99cb485dbe5954ab') diff --git a/var/spack/repos/builtin/packages/r-dismo/package.py b/var/spack/repos/builtin/packages/r-dismo/package.py index 3876f1aa85..4fb5e5e321 100644 --- a/var/spack/repos/builtin/packages/r-dismo/package.py +++ b/var/spack/repos/builtin/packages/r-dismo/package.py @@ -11,8 +11,9 @@ class RDismo(RPackage): entire geographic distributions form occurrences at a number of sites and the environment at these sites.""" - homepage = "https://cran.r-project.org/package=dismo" - url = "https://cran.r-project.org/src/contrib/dismo_1.1-4.tar.gz" + homepage = "https://cloud.r-project.org/package=dismo" + url = "https://cloud.r-project.org/src/contrib/dismo_1.1-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dismo" version('1.1-4', sha256='f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8') diff --git a/var/spack/repos/builtin/packages/r-diversitree/package.py b/var/spack/repos/builtin/packages/r-diversitree/package.py index 9578bbb4ec..bb2c27dac6 100644 --- a/var/spack/repos/builtin/packages/r-diversitree/package.py +++ b/var/spack/repos/builtin/packages/r-diversitree/package.py @@ -19,9 +19,10 @@ class RDiversitree(RPackage): rate 'speciation' and extinction.""" homepage = "http://www.zoology.ubc.ca/prog/diversitree" - url = "https://cran.r-project.org/src/contrib/diversitree_0.9-10.tar.gz" + url = "https://cloud.r-project.org/src/contrib/diversitree_0.9-10.tar.gz" list_url = "https://cron.r-project.org/src/contrib/Archive/diversitree" + version('0.9-11', sha256='4caa6a468f93de9f1c8c30e4457f34bb8346e1acdaf74f684005bfa86a950ecb') version('0.9-10', sha256='e7df5910c8508a5c2c2d6d3deea53dd3f947bb762196901094c32a7033cb043e') depends_on('r@2.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-domc/package.py b/var/spack/repos/builtin/packages/r-domc/package.py index 8228866515..9488d31952 100644 --- a/var/spack/repos/builtin/packages/r-domc/package.py +++ b/var/spack/repos/builtin/packages/r-domc/package.py @@ -10,13 +10,13 @@ class RDomc(RPackage): """Provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.""" - homepage = "https://cran.r-project.org/package=doMC" - url = "https://cran.r-project.org/src/contrib/doMC_1.3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/doMC" + homepage = "https://cloud.r-project.org/package=doMC" + url = "https://cloud.r-project.org/src/contrib/doMC_1.3.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/doMC" + version('1.3.6', sha256='2977fc9e2dc54d85d45b4a36cd286dff72834fbc73f38b6ee45a6eb8557fc9b2') version('1.3.4', 'f965b09add9056e84f99a831dc3af7d1') - depends_on('r@2.14.0:') - + depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-foreach@1.2.0:', type=('build', 'run')) depends_on('r-iterators@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py index 5db870b699..250e396dfb 100644 --- a/var/spack/repos/builtin/packages/r-doparallel/package.py +++ b/var/spack/repos/builtin/packages/r-doparallel/package.py @@ -10,12 +10,14 @@ class RDoparallel(RPackage): """Provides a parallel backend for the %dopar% function using the parallel package.""" - homepage = "https://cran.r-project.org/web/packages/doParallel/index.html" - url = "https://cran.r-project.org/src/contrib/doParallel_1.0.10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/doParallel" + homepage = "https://cloud.r-project.org/package=doParallel" + url = "https://cloud.r-project.org/src/contrib/doParallel_1.0.10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/doParallel" + version('1.0.15', sha256='71ad7ea69616468996aefdd8d02a4a234759a21ddde9ed1657e3c537145cd86e') version('1.0.11', 'd7822f0efd7bdf7582d8b43c986be86c') version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43') - depends_on('r-foreach', type=('build', 'run')) - depends_on('r-iterators', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-foreach@1.2.0:', type=('build', 'run')) + depends_on('r-iterators@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dorng/package.py b/var/spack/repos/builtin/packages/r-dorng/package.py index 9e8baa6a77..a493805a36 100644 --- a/var/spack/repos/builtin/packages/r-dorng/package.py +++ b/var/spack/repos/builtin/packages/r-dorng/package.py @@ -15,13 +15,15 @@ class RDorng(RPackage): independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.""" - homepage = "https://cran.rstudio.com/web/packages/doRNG/index.html" - url = "https://cran.rstudio.com/src/contrib/doRNG_1.6.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/doRNG" + homepage = "https://cloud.r-project.org/package=doRNG" + url = "https://cloud.r-project.org/src/contrib/doRNG_1.6.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/doRNG" + version('1.7.1', sha256='27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9') version('1.6.6', 'ffb26024c58c8c99229470293fbf35cf') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) - depends_on('r-rngtools', type=('build', 'run')) + depends_on('r-rngtools@1.3:', type=('build', 'run')) depends_on('r-iterators', type=('build', 'run')) - depends_on('r-pkgmaker', type=('build', 'run')) + depends_on('r-pkgmaker@0.20:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dosnow/package.py b/var/spack/repos/builtin/packages/r-dosnow/package.py new file mode 100644 index 0000000000..7ad841b431 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dosnow/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDosnow(RPackage): + """Provides a parallel backend for the %dopar% function using the snow + package of Tierney, Rossini, Li, and Sevcikova.""" + + homepage = "https://cloud.r-project.org/package=doSNOW" + url = "https://cloud.r-project.org/src/contrib/doSNOW_1.0.18.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/doSNOW" + + version('1.0.18', sha256='70e7bd82186e477e3d1610676d4c6a75258ac08f104ecf0dcc971550ca174766') + + depends_on('r@2.5.0:', type=('build', 'run')) + depends_on('r-foreach@1.2.0:', type=('build', 'run')) + depends_on('r-iterators@1.0.0:', type=('build', 'run')) + depends_on('r-snow@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-downloader/package.py b/var/spack/repos/builtin/packages/r-downloader/package.py index 9a410e7972..7b59089be6 100644 --- a/var/spack/repos/builtin/packages/r-downloader/package.py +++ b/var/spack/repos/builtin/packages/r-downloader/package.py @@ -14,9 +14,9 @@ class RDownloader(RPackage): compiled with external dependencies. This package has no external dependencies, so it is much easier to install.""" - homepage = "https://cran.rstudio.com/web/packages/downloader/index.html" - url = "https://cran.rstudio.com/src/contrib/downloader_0.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/downloader" + homepage = "https://cloud.r-project.org/package=downloader" + url = "https://cloud.r-project.org/src/contrib/downloader_0.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/downloader" version('0.4', 'f26daf8fbeb29a1882bf102f62008594') diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py index b2aed2c626..a7ed7868d7 100644 --- a/var/spack/repos/builtin/packages/r-dplyr/package.py +++ b/var/spack/repos/builtin/packages/r-dplyr/package.py @@ -10,10 +10,12 @@ class RDplyr(RPackage): """A fast, consistent tool for working with data frame like objects, both in memory and out of memory.""" - homepage = "https://cran.r-project.org/package=dplyr" - url = "https://cran.r-project.org/src/contrib/dplyr_0.7.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dplyr" + homepage = "https://cloud.r-project.org/package=dplyr" + url = "https://cloud.r-project.org/src/contrib/dplyr_0.7.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dplyr" + version('0.8.3', sha256='68b4aac65a69ea6390e90991d9c7ce7a011a07e5db439d60cce911a078424c0c') + version('0.8.2', sha256='e2b6d5b30d04d86f270374623da426541cee8e33ce446fcab6cd7862abf8e18b') version('0.7.7', sha256='0553db5a55f0e6f5d2d111e88422c6d26e9d54cb36b860ad2ca28e3826e3d4a4') version('0.7.6', sha256='d489cc8b53854ec30737bb7d39b331b67ca35f4275ad19e97420d7a247808330') version('0.7.5', sha256='2fbd8f316a59670076d43a0fe854654621941ee5f621ea5f0185a3f5daafda50') @@ -24,14 +26,17 @@ class RDplyr(RPackage): version('0.7.0', sha256='27b3593c09da5e99c0c4fb19ea826edd2cab619f8aaefd0cfd2a4140a0bd9410') version('0.5.0', sha256='93d3b829f1c2d38e14a4f2fa7d6398fc6c1a9e4189b3e78bc38a0eb0e864454f') + depends_on('r@3.1.2:', when='@:0.8.0.1', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.8.1:', type=('build', 'run')) depends_on('r-assertthat@0.2.0:', type=('build', 'run')) - depends_on('r-bindrcpp@0.2.0:', type=('build', 'run')) - depends_on('r-glue@1.1.1:', type=('build', 'run')) + depends_on('r-bindrcpp@0.2.0:', when='@:0.7.9', type=('build', 'run')) + depends_on('r-glue@1.3.0:', type=('build', 'run')) depends_on('r-magrittr@1.5:', type=('build', 'run')) - depends_on('r-pkgconfig@2.0.1:', type=('build', 'run')) - depends_on('r-r6@2.2.2:', type=('build', 'run')) - depends_on('r-rcpp@0.12.19:', type=('build', 'run')) - depends_on('r-rlang@0.3.0:', type=('build', 'run')) - depends_on('r-tibble@1.4.2:', type=('build', 'run')) - depends_on('r-tidyselect@0.2.3:', type=('build', 'run')) - depends_on('r-bh@1.58.0-1:', type=('build', 'run')) + depends_on('r-pkgconfig', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-rcpp@1.0.1:', type=('build', 'run')) + depends_on('r-rlang@0.4.0:', type=('build', 'run')) + depends_on('r-tibble@2.0.0:', type=('build', 'run')) + depends_on('r-tidyselect@0.2.5:', type=('build', 'run')) + depends_on('r-bh', type=('build', 'run')) + depends_on('r-plogr@0.2.0:', when='@0.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dqrng/package.py b/var/spack/repos/builtin/packages/r-dqrng/package.py new file mode 100644 index 0000000000..ebb82b942c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dqrng/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RDqrng(RPackage): + """Several fast random number generators are provided as C++ header only + libraries: The PCG family by O'Neill (2014 + <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as Xoroshiro128+ + and Xoshiro256+ by Blackman and Vigna (2018 <arXiv:1805.01407>). In + addition fast functions for generating random numbers according to a + uniform, normal and exponential distribution are included. The latter two + use the Ziggurat algorithm originally proposed by Marsaglia and Tsang + (2000, <doi:10.18637/jss.v005.i08>). These functions are exported to R and + as a C++ interface and are enabled for use with the default 64 bit + generator from the PCG family, Xoroshiro128+ and Xoshiro256+ as well as the + 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011 + <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.""" + + homepage = "https://www.daqana.org/dqrng" + url = "https://cloud.r-project.org/src/contrib/dqrng_0.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dqrng" + + version('0.2.1', sha256='e149c105b1db31e7f46b1aebf31d911a109e380923f3696fc56a53197fc1e866') + + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.16:', type=('build', 'run')) + depends_on('r-bh@1.64.0-1:', type=('build', 'run')) + depends_on('r-sitmo@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py index b419985173..141b40006b 100644 --- a/var/spack/repos/builtin/packages/r-dt/package.py +++ b/var/spack/repos/builtin/packages/r-dt/package.py @@ -13,9 +13,12 @@ class RDt(RPackage): abbreviation of 'DataTables'.""" homepage = "http://rstudio.github.io/DT" - url = "https://cran.r-project.org/src/contrib/DT_0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/DT" + url = "https://cloud.r-project.org/src/contrib/DT_0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/DT" + version('0.8', sha256='90195054148806cf31c7db5c41f72d5389c75adc0b1183606a9babd2c6ae8e21') + version('0.7', sha256='1de3f170deccd9e3aaefc057dd87c498e3b3f7f88eff645cf165ac34ffe3de2c') + version('0.6', sha256='2ed68e9d161559171fa74b6105eee87b98acf755eae072b38ada60a83d427916') version('0.4', sha256='3daa96b819ca54e5fbc2c7d78cb3637982a2d44be58cea0683663b71cfc7fa19') version('0.3', sha256='ef42b24c9ea6cfa1ce089687bf858d773ac495dc80756d4475234e979bd437eb') version('0.2', sha256='a1b7f9e5c31a241fdf78ac582499f346e915ff948554980bbc2262c924b806bd') @@ -25,3 +28,5 @@ class RDt(RPackage): depends_on('r-htmlwidgets@1.3:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-crosstalk', type=('build', 'run')) + depends_on('r-promises', when='@0.5:', type=('build', 'run')) + depends_on('r-jsonlite@0.9.16:', when='@0.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dtw/package.py b/var/spack/repos/builtin/packages/r-dtw/package.py index bb82035897..f963965161 100644 --- a/var/spack/repos/builtin/packages/r-dtw/package.py +++ b/var/spack/repos/builtin/packages/r-dtw/package.py @@ -11,15 +11,16 @@ class RDtw(RPackage): in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series.""" - homepage = "https://cran.r-project.org/web/packages/dtw/index.html" - url = "https://cran.r-project.org/src/contrib/dtw_1.18-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dtw" + homepage = "https://cloud.r-project.org/package=dtw" + url = "https://cloud.r-project.org/src/contrib/dtw_1.18-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dtw" + version('1.20-1', sha256='43ca1a47a7c81a2b5d5054da1be8b8af79a85d6f9ce7b4512e9ed91f790f60f0') version('1.18-1', '5e9995a198a62f28045c29461265d536') version('1.17-1', 'e8be988fe528acd6b44afdf5aa06b745') version('1.16', '260bd22d9db429394eb39739db4a4686') version('1.15', 'd3b6fdb0b866ff2e5b178c37bcfc7c55') version('1.14-3', 'a7b878e8dda7a61df22356d0a81540c5') - depends_on('r@3.4.0:3.4.9') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-proxy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py index ce17c9dd6d..f286e5363f 100644 --- a/var/spack/repos/builtin/packages/r-dygraphs/package.py +++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py @@ -13,13 +13,17 @@ class RDygraphs(RPackage): axis-display and interactive features like zoom/pan and series/point highlighting.""" - homepage = "https://cran.r-project.org/web/packages/dygraphs/index.html" - url = "https://cran.r-project.org/src/contrib/dygraphs_0.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dygraphs" + homepage = "https://cloud.r-project.org/package=dygraphs" + url = "https://cloud.r-project.org/src/contrib/dygraphs_0.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dygraphs" + version('1.1.1.6', sha256='c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208') + version('1.1.1.5', sha256='274035988fdd6833121fd5831692355d383acc828d540788dbcecaf88eb2d72d') version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833') + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-htmlwidgets', type=('build', 'run')) - depends_on('r-zoo', type=('build', 'run')) - depends_on('r-xts', type=('build', 'run')) + depends_on('r-htmlwidgets@0.6:', type=('build', 'run')) + depends_on('r-zoo@1.7-10:', type=('build', 'run')) + depends_on('r-xts@0.9-7:', type=('build', 'run')) + depends_on('r-htmltools@0.3.5:', when='@1.1.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-dynamictreecut/package.py b/var/spack/repos/builtin/packages/r-dynamictreecut/package.py index 39e3dde227..856e6efb89 100644 --- a/var/spack/repos/builtin/packages/r-dynamictreecut/package.py +++ b/var/spack/repos/builtin/packages/r-dynamictreecut/package.py @@ -10,9 +10,9 @@ class RDynamictreecut(RPackage): """dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms""" - homepage = "https://cran.r-project.org/package=dynamicTreeCut" - url = "https://cran.r-project.org/src/contrib/dynamicTreeCut_1.63-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/dynamicTreeCut/" + homepage = "https://cloud.r-project.org/package=dynamicTreeCut" + url = "https://cloud.r-project.org/src/contrib/dynamicTreeCut_1.63-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/dynamicTreeCut/" version('1.63-1', sha256='831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9') diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py index c09473fe79..41ada9809e 100644 --- a/var/spack/repos/builtin/packages/r-e1071/package.py +++ b/var/spack/repos/builtin/packages/r-e1071/package.py @@ -11,10 +11,12 @@ class RE1071(RPackage): clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...""" - homepage = "https://cran.r-project.org/package=e1071" - url = "https://cran.r-project.org/src/contrib/e1071_1.6-7.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/e1071" + homepage = "https://cloud.r-project.org/package=e1071" + url = "https://cloud.r-project.org/src/contrib/e1071_1.6-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/e1071" + version('1.7-2', sha256='721c299ce83047312acfa3e0c4b3d4c223d84a4c53400c73465cca2c92913752') + version('1.7-1', sha256='5c5f04a51c1cd2c7dbdf69987adef9bc07116804c63992cd36d804a1daf89dfe') version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a') depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ellipse/package.py b/var/spack/repos/builtin/packages/r-ellipse/package.py index 5dd67a3415..abd9783b0f 100644 --- a/var/spack/repos/builtin/packages/r-ellipse/package.py +++ b/var/spack/repos/builtin/packages/r-ellipse/package.py @@ -10,10 +10,11 @@ class REllipse(RPackage): """This package contains various routines for drawing ellipses and ellipse-like confidence regions.""" - homepage = "https://cran.r-project.org/package=ellipse" - url = "https://cran.r-project.org/src/contrib/ellipse_0.3-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ellipse" + homepage = "https://cloud.r-project.org/package=ellipse" + url = "https://cloud.r-project.org/src/contrib/ellipse_0.3-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ellipse" + version('0.4.1', sha256='1a9a9c52195b26c2b4d51ad159ab98aff7aa8ca25fdc6b2198818d1a0adb023d') version('0.3-8', '385f5ec5e49bcda4317ca9dffd33f771') - depends_on('r@2.0.0:') + depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ellipsis/package.py b/var/spack/repos/builtin/packages/r-ellipsis/package.py new file mode 100644 index 0000000000..8945722068 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ellipsis/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class REllipsis(RPackage): + """The ellipsis is a powerful tool for extending functions. Unfortunately + this power comes at a cost: misspelled arguments will be silently ignored. + The ellipsis package provides a collection of functions to catch problems + and alert the user.""" + + homepage = "https://github.com/r-lib/ellipsis" + url = "https://cloud.r-project.org/src/contrib/ellipsis_0.2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ellipsis" + + version('0.2.0.1', sha256='0e6528c5e8016c3617cc1cfcdb5a4bfeb073e0bd5ea76b43e56b0c3208a0a943') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-emmli/package.py b/var/spack/repos/builtin/packages/r-emmli/package.py index 249f3c3f6d..974bb81c8b 100644 --- a/var/spack/repos/builtin/packages/r-emmli/package.py +++ b/var/spack/repos/builtin/packages/r-emmli/package.py @@ -11,8 +11,8 @@ class REmmli(RPackage): on results. Fit models with a single within-module correlation or with separate within-module correlations fitted to each module.""" - homepage = "https://cran.r-project.org/package=EMMLi" - url = "https://cran.r-project.org/src/contrib/EMMLi_0.0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/EMMLi" + homepage = "https://cloud.r-project.org/package=EMMLi" + url = "https://cloud.r-project.org/src/contrib/EMMLi_0.0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/EMMLi" version('0.0.3', sha256='57c04953200d2253bc90b0035dc590179d1b959768bfa7fdac92b6bcbf9f66ac') diff --git a/var/spack/repos/builtin/packages/r-energy/package.py b/var/spack/repos/builtin/packages/r-energy/package.py index 897e96a8ad..ab2ef621de 100644 --- a/var/spack/repos/builtin/packages/r-energy/package.py +++ b/var/spack/repos/builtin/packages/r-energy/package.py @@ -9,11 +9,13 @@ from spack import * class REnergy(RPackage): """E-Statistics: Multivariate Inference via the Energy of Data""" - homepage = "https://cran.r-project.org/web/packages/energy/index.html" - url = "https://cran.r-project.org/src/contrib/energy_1.7-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/energy" + homepage = "https://cloud.r-project.org/package=energy" + url = "https://cloud.r-project.org/src/contrib/energy_1.7-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/energy" + version('1.7-6', sha256='900edbb28e1f1bccd78580828470628cf75eb6333b63e1a58e4da7fc5c5fa89a') version('1.7-5', 'd13c76c26b5221ba29aade6a824f32d6') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rcpp@0.12.6:', type=('build', 'run')) depends_on('r-boot', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ergm/package.py b/var/spack/repos/builtin/packages/r-ergm/package.py index 36c251cfa0..9fedc0c078 100644 --- a/var/spack/repos/builtin/packages/r-ergm/package.py +++ b/var/spack/repos/builtin/packages/r-ergm/package.py @@ -12,16 +12,26 @@ class RErgm(RPackage): part of the "statnet" suite of packages for network analysis.""" homepage = "http://statnet.org" - url = "https://cran.r-project.org/src/contrib/ergm_3.7.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ergm" + url = "https://cloud.r-project.org/src/contrib/ergm_3.7.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ergm" + version('3.10.4', sha256='885f0b1a23c5a2c1947962350cfab66683dfdfd1db173c115e90396d00831f22') + version('3.10.1', sha256='a2ac249ff07ba55b3359242f20389a892543b4fff5956d74143d2d41fa6d4beb') version('3.7.1', '431ae430c76b2408988f469831d80126') - depends_on('r-robustbase@0.9-10:', type=('build', 'run')) - depends_on('r-coda@0.18-1:', type=('build', 'run')) - depends_on('r-trust', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-lpsolve', type=('build', 'run')) - depends_on('r-mass', type=('build', 'run')) - depends_on('r-statnet-common@3.3:', type=('build', 'run')) - depends_on('r-network@1.13:', type=('build', 'run')) + depends_on('r-robustbase@0.93-5:', type=('build', 'run')) + depends_on('r-coda@0.19-2:', type=('build', 'run')) + depends_on('r-trust@0.1.7:', type=('build', 'run')) + depends_on('r-matrix@1.2-17:', type=('build', 'run')) + depends_on('r-lpsolve@5.6.13:', type=('build', 'run')) + depends_on('r-mass@7.3-51.4:', type=('build', 'run')) + depends_on('r-statnet-common@4.3.0:', type=('build', 'run')) + depends_on('r-network@1.15:', type=('build', 'run')) + depends_on('r-purrr@0.3.2:', when='@3.10.0:', type=('build', 'run')) + depends_on('r-rlang@0.3.4:', when='@3.10.0:', type=('build', 'run')) + depends_on('r-tibble@2.1.1:', when='@3.10.0:', type=('build', 'run')) + depends_on('r-dplyr@0.8.0.1:', when='@3.10.0:', type=('build', 'run')) + # The CRAN page list OpenMPI as a dependency but this is not a dependency + # for using the package. If one wishes to use MPI, simply load an MPI + # package, along with r-dosnow and r-rmpi when using r-ergm, and set the + # appropriate options in the R script. diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py index 4df731967b..c56425716d 100644 --- a/var/spack/repos/builtin/packages/r-evaluate/package.py +++ b/var/spack/repos/builtin/packages/r-evaluate/package.py @@ -10,14 +10,14 @@ class REvaluate(RPackage): """Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.""" - homepage = "https://cran.r-project.org/package=evaluate" - url = "https://cran.rstudio.com/src/contrib/evaluate_0.10.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/evaluate" + homepage = "https://cloud.r-project.org/package=evaluate" + url = "https://cloud.r-project.org/src/contrib/evaluate_0.10.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/evaluate" + version('0.14', sha256='a8c88bdbe4e60046d95ddf7e181ee15a6f41cdf92127c9678f6f3d328a3c5e28') version('0.10.1', '1dde5a35e2b9d57f1b1bb16791b35ff5') version('0.10', 'c49326babf984a8b36e7e276da370ad2') version('0.9', '877d89ce8a9ef7f403b1089ca1021775') - depends_on('r@3.0.2:') - - depends_on('r-stringr@0.6.2:', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-stringr@0.6.2:', when='@:0.11', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-expint/package.py b/var/spack/repos/builtin/packages/r-expint/package.py index 39d01fe50d..4bce63d28a 100644 --- a/var/spack/repos/builtin/packages/r-expint/package.py +++ b/var/spack/repos/builtin/packages/r-expint/package.py @@ -10,9 +10,9 @@ from spack import * class RExpint(RPackage): """expint: Exponential Integral and Incomplete Gamma Function""" - homepage = "https://cran.r-project.org/package=expint" - url = "https://cran.r-project.org/src/contrib/expint_0.1-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/expint" + homepage = "https://cloud.r-project.org/package=expint" + url = "https://cloud.r-project.org/src/contrib/expint_0.1-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/expint" version('0.1-5', sha256='b03d60938cd6cf615aa3a02b1bf73436785eca89eaff56059ee0807b8244718a') diff --git a/var/spack/repos/builtin/packages/r-expm/package.py b/var/spack/repos/builtin/packages/r-expm/package.py index c576ec912f..f7e5588e4e 100644 --- a/var/spack/repos/builtin/packages/r-expm/package.py +++ b/var/spack/repos/builtin/packages/r-expm/package.py @@ -10,8 +10,12 @@ class RExpm(RPackage): """Computation of the matrix exponential, logarithm, sqrt, and related quantities.""" - homepage = "http://R-Forge.R-project.org/projects/expm" - url = "https://cran.r-project.org/src/contrib/expm_0.999-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/expm" + homepage = "http://r-forge.r-project.org/projects/expm" + url = "https://cloud.r-project.org/src/contrib/expm_0.999-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/expm" + version('0.999-4', sha256='58d06427a08c9442462b00a5531e2575800be13ed450c5a1546261251e536096') + version('0.999-3', sha256='511bac5860cc5b3888bca626cdf23241b6118eabcc82d100935386039e516412') version('0.999-2', 'e05fa3f995754af92bd03227625da984') + + depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-factoextra/package.py b/var/spack/repos/builtin/packages/r-factoextra/package.py index 47e442cbc7..562dc81c95 100644 --- a/var/spack/repos/builtin/packages/r-factoextra/package.py +++ b/var/spack/repos/builtin/packages/r-factoextra/package.py @@ -11,18 +11,19 @@ class RFactoextra(RPackage): Analyses""" homepage = "http://www.sthda.com/english/rpkgs/factoextra" - url = "https://cran.r-project.org/src/contrib/factoextra_1.0.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/factoextra" + url = "https://cloud.r-project.org/src/contrib/factoextra_1.0.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/factoextra" + version('1.0.5', sha256='8177a3f5107883ae248b2cd0afa388a1794741f5155a9455b3883788cf44d5d0') version('1.0.4', 'aa4c81ca610f17fdee0c9f3379e35429') - depends_on('r@3.1.0:') + depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) depends_on('r-abind', type=('build', 'run')) - # depends_on('r-cluster', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) depends_on('r-dendextend', type=('build', 'run')) depends_on('r-factominer', type=('build', 'run')) - depends_on('r-ggpubr', type=('build', 'run')) + depends_on('r-ggpubr@0.1.5:', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) depends_on('r-ggrepel', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-factominer/package.py b/var/spack/repos/builtin/packages/r-factominer/package.py index 71d6f34415..a5723eff14 100644 --- a/var/spack/repos/builtin/packages/r-factominer/package.py +++ b/var/spack/repos/builtin/packages/r-factominer/package.py @@ -10,9 +10,10 @@ class RFactominer(RPackage): """FactoMineR: Multivariate Exploratory Data Analysis and Data Mining""" homepage = "http://factominer.free.fr" - url = "https://cran.r-project.org/src/contrib/FactoMineR_1.35.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/FactoMineR" + url = "https://cloud.r-project.org/src/contrib/FactoMineR_1.35.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/FactoMineR" + version('1.42', sha256='4cd9efb3681767c3bd48ddc3504ebead1493fcbbc0a9f759a00955b16c3481fa') version('1.41', sha256='a9889d69e298b8a01e8d0a5a54260730e742c95681e367d759829aad9a8740c0') version('1.40', sha256='68cb778fe7581b55666a5ae4aa7a5e7fa3ecbd133ae8cff1b2371a737b6d95e8') version('1.39', sha256='b0bb1d6d7d1f3cb11a4b63c377321e10078a36f29bc78dfa3b80c7c149f4a08a') @@ -20,7 +21,7 @@ class RFactominer(RPackage): version('1.36', sha256='2198c3facaa41a23df6f9373d4ccb636b98a8810896e379e5deb686ab31b36de') version('1.35', sha256='afe176fe561d1d16c5965ecb2b80ec90a56d0fbcd75c43ec8025a401a5b715a9') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-car', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) depends_on('r-ellipse', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fansi/package.py b/var/spack/repos/builtin/packages/r-fansi/package.py index 41695ebc72..ff24e351bf 100644 --- a/var/spack/repos/builtin/packages/r-fansi/package.py +++ b/var/spack/repos/builtin/packages/r-fansi/package.py @@ -10,12 +10,14 @@ class RFansi(RPackage): """Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.""" - homepage = "https://cran.r-project.org/package=fansi" - url = "https://cran.r-project.org/src/contrib/fansi_0.4.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fansi" + homepage = "https://cloud.r-project.org/package=fansi" + url = "https://cloud.r-project.org/src/contrib/fansi_0.4.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fansi" version('0.4.0', sha256='e104e9d01c7ff8a847f6b332ef544c0ef912859f9c6a514fe2e6f3b34fcfc209') version('0.3.0', sha256='dd6401d5c91ff4c45d752cceddd5379d1ae39a8a1196f236b0bc0ec6d691b88c') version('0.2.3', sha256='db6dfef8bfe6682d58b654b6a6a1d59cb07225ca41755176b465ab8611fd96c9') version('0.2.2', sha256='71dfdda467985a4d630ecf93d4bc60446a8a78d69dbd7ac24cc45822329d4bce') version('0.2.1', sha256='abe709d69ddd6610aaa24e049c7a97c16a2c2dbe0873d4e3b8af57e486ef05c5') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fastcluster/package.py b/var/spack/repos/builtin/packages/r-fastcluster/package.py index 0ec80c7207..d08a5ddb66 100644 --- a/var/spack/repos/builtin/packages/r-fastcluster/package.py +++ b/var/spack/repos/builtin/packages/r-fastcluster/package.py @@ -19,8 +19,8 @@ class RFastcluster(RPackage): the 'Python' files, see the file INSTALL in the source distribution.""" homepage = "http://danifold.net/fastcluster.html" - url = "https://cran.r-project.org/src/contrib/fastcluster_1.1.25.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fastcluster/" + url = "https://cloud.r-project.org/src/contrib/fastcluster_1.1.25.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fastcluster/" version('1.1.25', sha256='f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205') diff --git a/var/spack/repos/builtin/packages/r-fastmatch/package.py b/var/spack/repos/builtin/packages/r-fastmatch/package.py index 0257a475de..88ef290d70 100644 --- a/var/spack/repos/builtin/packages/r-fastmatch/package.py +++ b/var/spack/repos/builtin/packages/r-fastmatch/package.py @@ -13,7 +13,7 @@ class RFastmatch(RPackage): subsequent lookup as it keeps the hash table in memory.""" homepage = "http://www.rforge.net/fastmatch" - url = "https://cran.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fastmatch" + url = "https://cloud.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fastmatch" version('1.1-0', '900c2363c15059ac9d63c4c71ea2d6b2') diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py index 76056bca94..6b352a2008 100644 --- a/var/spack/repos/builtin/packages/r-ff/package.py +++ b/var/spack/repos/builtin/packages/r-ff/package.py @@ -11,9 +11,11 @@ class RFf(RPackage): fast access functions.""" homepage = "http://ff.r-forge.r-project.org/" - url = "https://cran.rstudio.com/src/contrib/ff_2.2-13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ff" + url = "https://cloud.r-project.org/src/contrib/ff_2.2-13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ff" + version('2.2-14', sha256='1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0') version('2.2-13', '4adf8840d24cb6e2927a3ef885c86fcd') - depends_on('r-bit', type=('build', 'run')) + depends_on('r@2.10.1:', type=('build', 'run')) + depends_on('r-bit@1.1-13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fftwtools/package.py b/var/spack/repos/builtin/packages/r-fftwtools/package.py index 9d0a427a3e..418347cd8e 100644 --- a/var/spack/repos/builtin/packages/r-fftwtools/package.py +++ b/var/spack/repos/builtin/packages/r-fftwtools/package.py @@ -16,9 +16,10 @@ class RFftwtools(RPackage): the redundant complex conjugate when the input is real data.""" homepage = "https://github.com/krahim/fftwtools" - url = "https://cran.r-project.org/src/contrib/fftwtools_0.9-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fftwtools" + url = "https://cloud.r-project.org/src/contrib/fftwtools_0.9-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fftwtools" version('0.9-8', '2d1258fbaf0940b57ed61c8d6cd6694d') - depends_on('fftw') + depends_on('r@2.15.2:', type=('build', 'run')) + depends_on('fftw@3.1.2:') diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index e2c6b42ddc..8a44c29f70 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -17,8 +17,12 @@ class RFilehash(RPackage): are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.""" - homepage = 'https://cran.r-project.org/' - url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/filehash" + homepage = "https://cloud.r-project.org/package=filehash" + url = "https://cloud.r-project.org/src/contrib/filehash_2.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/filehash" + version('2.4-2', sha256='b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93') + version('2.4-1', sha256='d0e087d338d89372c251c18fc93b53fb24b1750ea154833216ff16aff3b1eaf4') version('2.3', '01fffafe09b148ccadc9814c103bdc2f') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-findpython/package.py b/var/spack/repos/builtin/packages/r-findpython/package.py index 736ff0cb4c..acfc903c33 100644 --- a/var/spack/repos/builtin/packages/r-findpython/package.py +++ b/var/spack/repos/builtin/packages/r-findpython/package.py @@ -10,9 +10,11 @@ class RFindpython(RPackage): """Package designed to find an acceptable python binary.""" homepage = "https://github.com/trevorld/findpython" - url = "https://cran.r-project.org/src/contrib/findpython_1.0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/findpython" + url = "https://cloud.r-project.org/src/contrib/findpython_1.0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/findpython" + version('1.0.5', sha256='3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145') + version('1.0.4', sha256='a58fb46d53d3bdea1e00b2f4f9bdb5e98be9329ea9d8e2fe150d91462e6bccfd') version('1.0.3', sha256='5486535ae2f0a123b630d8eabf93a61b730765f55dfcc8ef4f6e56e7c49408f8') depends_on('python', type='run') diff --git a/var/spack/repos/builtin/packages/r-fit-models/package.py b/var/spack/repos/builtin/packages/r-fit-models/package.py index c15c7701e7..3f1619d2e2 100644 --- a/var/spack/repos/builtin/packages/r-fit-models/package.py +++ b/var/spack/repos/builtin/packages/r-fit-models/package.py @@ -9,9 +9,9 @@ from spack import * class RFitModels(RPackage): """Compare Fitted Models""" - homepage = "https://cran.r-project.org/package=fit.models" - url = "https://cran.r-project.org/src/contrib/fit.models_0.5-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fit.models" + homepage = "https://cloud.r-project.org/package=fit.models" + url = "https://cloud.r-project.org/src/contrib/fit.models_0.5-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fit.models" version('0.5-14', '159b5c57953db4c917bc186ddacdff51') version('0.5-13', 'c9ff87e98189bcc3be597e3833408497') diff --git a/var/spack/repos/builtin/packages/r-fitdistrplus/package.py b/var/spack/repos/builtin/packages/r-fitdistrplus/package.py new file mode 100644 index 0000000000..7a0cdfb107 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fitdistrplus/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFitdistrplus(RPackage): + """Extends the fitdistr() function (of the MASS package) with several + functions to help the fit of a parametric distribution to non-censored or + censored data. Censored data may contain left censored, right censored and + interval censored values, with several lower and upper bounds. In addition + to maximum likelihood estimation (MLE), the package provides moment + matching (MME), quantile matching (QME) and maximum goodness-of-fit + estimation (MGE) methods (available only for non-censored data). Weighted + versions of MLE, MME and QME are available. See e.g. Casella & Berger + (2002). Statistical inference. Pacific Grove.""" + + homepage = "https://lbbe.univ-lyon1.fr/fitdistrplus.html" + url = "https://cloud.r-project.org/src/contrib/fitdistrplus_1.0-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fitdistrplus" + + version('1.0-14', sha256='85082590f62aa08d99048ea3414c5cc1e5b780d97b3779d2397c6cb435470083') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) + depends_on('r-npsurv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flashclust/package.py b/var/spack/repos/builtin/packages/r-flashclust/package.py index 4b32218943..6564e50a2b 100644 --- a/var/spack/repos/builtin/packages/r-flashclust/package.py +++ b/var/spack/repos/builtin/packages/r-flashclust/package.py @@ -9,10 +9,10 @@ from spack import * class RFlashclust(RPackage): """flashClust: Implementation of optimal hierarchical clustering""" - homepage = "https://CRAN.R-project.org/package=flashClust" - url = "https://cran.r-project.org/src/contrib/flashClust_1.01-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/flashClust" + homepage = "https://cloud.r-project.org/package=flashClust" + url = "https://cloud.r-project.org/src/contrib/flashClust_1.01-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/flashClust" version('1.01-2', '23409aeeef98bf35d0b3d5dd755fdeff') - depends_on('r@2.3.0:') + depends_on('r@2.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flexclust/package.py b/var/spack/repos/builtin/packages/r-flexclust/package.py index b37f42e906..324839aa7d 100644 --- a/var/spack/repos/builtin/packages/r-flexclust/package.py +++ b/var/spack/repos/builtin/packages/r-flexclust/package.py @@ -15,11 +15,14 @@ class RFlexclust(RPackage): centroids, ...), and bootstrap methods for the analysis of cluster stability.""" - homepage = "https://cran.r-project.org/package=flexclust" - url = "https://cran.rstudio.com/src/contrib/flexclust_1.3-5.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/flexclust" + homepage = "https://cloud.r-project.org/package=flexclust" + url = "https://cloud.r-project.org/src/contrib/flexclust_1.3-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/flexclust" + version('1.4-0', sha256='82fe445075a795c724644864c7ee803c5dd332a89ea9e6ccf7cd1ae2d1ecfc74') version('1.3-5', '90226a0e3a4f256f392a278e9543f8f4') + depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-modeltools', type=('build', 'run')) + depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-flexmix/package.py b/var/spack/repos/builtin/packages/r-flexmix/package.py index 6eb90aa44b..a8d3e03d9a 100644 --- a/var/spack/repos/builtin/packages/r-flexmix/package.py +++ b/var/spack/repos/builtin/packages/r-flexmix/package.py @@ -9,13 +9,14 @@ from spack import * class RFlexmix(RPackage): """flexmix: Flexible Mixture Modeling""" - homepage = "https://CRAN.R-project.org/package=flexmix" - url = "https://cran.r-project.org/src/contrib/flexmix_2.3-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/flexmix" + homepage = "https://cloud.r-project.org/package=flexmix" + url = "https://cloud.r-project.org/src/contrib/flexmix_2.3-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/flexmix" + version('2.3-15', sha256='ba444c0bfe33ab87d440ab590c06b03605710acd75811c1622253171bb123f43') version('2.3-14', '5be4f7764e6a697f4586e60c2bf6e960') - depends_on('r@2.15.0:') - # depends_on('r-lattice', type=('build', 'run')) + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) depends_on('r-modeltools@0.2-16:', type=('build', 'run')) - # depends_on('r-nnet', type=('build', 'run')) + depends_on('r-nnet', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fnn/package.py b/var/spack/repos/builtin/packages/r-fnn/package.py index 4061e49108..02afb622d2 100644 --- a/var/spack/repos/builtin/packages/r-fnn/package.py +++ b/var/spack/repos/builtin/packages/r-fnn/package.py @@ -11,10 +11,12 @@ class RFnn(RPackage): related applications including KNN classification, regression and information measures are implemented.""" - homepage = "https://cran.r-project.org/web/packages/FNN/index.html" - url = "https://cran.r-project.org/src/contrib/FNN_1.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/FNN" + homepage = "https://cloud.r-project.org/package=FNN" + url = "https://cloud.r-project.org/src/contrib/FNN_1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/FNN" + version('1.1.3', sha256='de763a25c9cfbd19d144586b9ed158135ec49cf7b812938954be54eb2dc59432') + version('1.1.2.2', sha256='b51a60fbbeff58c48cc90c2023c48972d5082d68efd02284c17ccd9820986326') version('1.1', '8ba8f5b8be271785593e13eae7b8c393') version('1.0', 'e9a47dc69d1ba55165be0877b8443fe0') version('0.6-4', '1c105df9763ceb7b13989cdbcb542fcc') @@ -22,5 +24,3 @@ class RFnn(RPackage): version('0.6-2', '20648ba934ea32b1b00dafb75e1a830c') depends_on('r@3.0.0:', type=('build', 'run')) - depends_on('r-mvtnorm', type=('build', 'run')) - depends_on('r-chemometrics', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-forcats/package.py b/var/spack/repos/builtin/packages/r-forcats/package.py index 769bbe4797..e6cf5b73e2 100644 --- a/var/spack/repos/builtin/packages/r-forcats/package.py +++ b/var/spack/repos/builtin/packages/r-forcats/package.py @@ -13,10 +13,15 @@ class RForcats(RPackage): rare levels into other, 'anonymising', and manually 'recoding').""" homepage = "http://forcats.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/forcats_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/forcats" + url = "https://cloud.r-project.org/src/contrib/forcats_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/forcats" + version('0.4.0', sha256='7c83cb576aa6fe1379d7506dcc332f7560068b2025f9e3ab5cd0a5f28780d2b2') + version('0.3.0', sha256='95814610ec18b8a8830eba63751954387f9d21400d6ab40394ed0ff22c0cb657') version('0.2.0', 'e4ba2c0a59dcdfcc02274c519bf3dbfc') + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-ellipsis', when='@0.4.0:', type=('build', 'run')) + depends_on('r-rlang', when='@0.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py index 091b970299..37baf00b4b 100644 --- a/var/spack/repos/builtin/packages/r-foreach/package.py +++ b/var/spack/repos/builtin/packages/r-foreach/package.py @@ -15,11 +15,13 @@ class RForeach(RPackage): evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.""" - homepage = "https://cran.r-project.org/web/packages/foreach/index.html" - url = "https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/foreach" + homepage = "https://cloud.r-project.org/package=foreach" + url = "https://cloud.r-project.org/src/contrib/foreach_1.4.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/foreach" + version('1.4.7', sha256='95632c0b1182fc01490718d82fa3b2bce864f2a011ae53282431c7c2a3f5f160') version('1.4.3', 'ef45768126661b259f9b8994462c49a0') + depends_on('r@2.5.0:', type=('build', 'run')) depends_on('r-codetools', type=('build', 'run')) depends_on('r-iterators', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-forecast/package.py b/var/spack/repos/builtin/packages/r-forecast/package.py index b1d32d5710..6b33bdd1eb 100644 --- a/var/spack/repos/builtin/packages/r-forecast/package.py +++ b/var/spack/repos/builtin/packages/r-forecast/package.py @@ -11,20 +11,24 @@ class RForecast(RPackage): series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.""" - homepage = "https://cran.r-project.org/package=forecast" - url = "https://cran.r-project.org/src/contrib/forecast_8.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/forecast" + homepage = "https://cloud.r-project.org/package=forecast" + url = "https://cloud.r-project.org/src/contrib/forecast_8.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/forecast" + version('8.8', sha256='d077074d77d3ea00e9215c828b3689a8c841a16af1e6859bb2dfdede081c2c1d') + version('8.6', sha256='4279e4f700e26310bae39419ab4a9b5918a850148667a5e577a4807d53eb4d02') version('8.2', '3ef095258984364c100b771b3c90d15e') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggplot2@2.2.1:', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) depends_on('r-nnet', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-fracdiff', type=('build', 'run')) depends_on('r-tseries', type=('build', 'run')) depends_on('r-lmtest', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) depends_on('r-timedate', type=('build', 'run')) - depends_on('r-rcpparmadillo', type=('build', 'run')) + depends_on('r-rcpparmadillo@0.2.35:', type=('build', 'run')) + depends_on('r-urca', when='@8.6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py index 928d9df0ce..9bba9e81a0 100644 --- a/var/spack/repos/builtin/packages/r-foreign/package.py +++ b/var/spack/repos/builtin/packages/r-foreign/package.py @@ -11,8 +11,12 @@ class RForeign(RPackage): Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.""" - homepage = "https://cran.r-project.org/web/packages/foreign/index.html" - url = "https://cran.r-project.org/src/contrib/foreign_0.8-66.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/foreign" + homepage = "https://cloud.r-project.org/package=foreign" + url = "https://cloud.r-project.org/src/contrib/foreign_0.8-66.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/foreign" + version('0.8-72', sha256='439c17c9cd387e180b1bb640efff3ed1696b1016d0f7b3b3b884e89884488c88') + version('0.8-70.2', sha256='ae82fad68159860b8ca75b49538406ef3d2522818e649d7ccc209c18085ef179') version('0.8-66', 'ff12190f4631dca31e30ca786c2c8f62') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py index 8d55e6c96c..15914e209f 100644 --- a/var/spack/repos/builtin/packages/r-formatr/package.py +++ b/var/spack/repos/builtin/packages/r-formatr/package.py @@ -14,14 +14,13 @@ class RFormatr(RPackage): human-readable and tidy. There is also a Shiny app as a user interface in this package.""" - homepage = "https://cran.r-project.org/package=formatR" - url = "https://cran.r-project.org/src/contrib/formatR_1.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/formatR" + homepage = "https://cloud.r-project.org/package=formatR" + url = "https://cloud.r-project.org/src/contrib/formatR_1.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/formatR" + version('1.7', sha256='a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb') + version('1.6', sha256='f5c98f0c3506ca51599671a2cdbc17738d0f326e8e3bb18b7a38e9f172122229') version('1.5', 'ac735515b8e4c32097154f1b68c5ecc7') version('1.4', '98b9b64b2785b35f9df403e1aab6c73c') - depends_on('r-codetools', type=('build', 'run')) - depends_on('r-shiny', type=('build', 'run')) - depends_on('r-testit', type=('build', 'run')) - # depends_on('r-knitr', type=('build', 'run')) - mutual dependency + depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py index cbe9071086..38b50015d9 100644 --- a/var/spack/repos/builtin/packages/r-formula/package.py +++ b/var/spack/repos/builtin/packages/r-formula/package.py @@ -11,9 +11,12 @@ class RFormula(RPackage): """Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side.""" - homepage = "https://cran.r-project.org/package=Formula" - url = "https://cran.rstudio.com/src/contrib/Formula_1.2-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Formula" + homepage = "https://cloud.r-project.org/package=Formula" + url = "https://cloud.r-project.org/src/contrib/Formula_1.2-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Formula" + version('1.2-3', sha256='1411349b20bd09611a9fd0ee6d15f780c758ad2b0e490e908facb49433823872') version('1.2-2', 'c69bb0522811cf8eb9f1cc6c3d182b6e') version('1.2-1', '2afb31e637cecd0c1106317aca1e4849') + + depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fpc/package.py b/var/spack/repos/builtin/packages/r-fpc/package.py index ddc3ea3fea..fd20c495dc 100644 --- a/var/spack/repos/builtin/packages/r-fpc/package.py +++ b/var/spack/repos/builtin/packages/r-fpc/package.py @@ -10,20 +10,22 @@ class RFpc(RPackage): """fpc: Flexible Procedures for Clustering""" homepage = "http://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cran.r-project.org/src/contrib/fpc_2.1-10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fpc" + url = "https://cloud.r-project.org/src/contrib/fpc_2.1-10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fpc" + version('2.2-3', sha256='8100a74e6ff96b1cd65fd22494f2d200e54ea5ea533cfca321fa494914bdc3b7') + version('2.2-2', sha256='b6907019eb161d5c8c814cf02a4663cc8aae6322699932881ce5b02f45ecf8d3') version('2.1-10', '75e5340e416cd13d7751e06f1c07866b') - depends_on('r@2.0.0:') - # depends_on('r-mass', type=('build', 'run')) - # depends_on('r-cluster', type=('build', 'run')) + depends_on('r@2.0.0:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) depends_on('r-flexmix', type=('build', 'run')) depends_on('r-prabclus', type=('build', 'run')) - # depends_on('r-class', type=('build', 'run')) + depends_on('r-class', type=('build', 'run')) depends_on('r-diptest', type=('build', 'run')) - depends_on('r-mvtnorm', type=('build', 'run')) + depends_on('r-mvtnorm', when='@:2.2-2', type=('build', 'run')) depends_on('r-robustbase', type=('build', 'run')) depends_on('r-kernlab', type=('build', 'run')) - depends_on('r-trimcluster', type=('build', 'run')) + depends_on('r-trimcluster', when='@:2.1-10', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-fracdiff/package.py b/var/spack/repos/builtin/packages/r-fracdiff/package.py index 5f947244ed..8f902428ec 100644 --- a/var/spack/repos/builtin/packages/r-fracdiff/package.py +++ b/var/spack/repos/builtin/packages/r-fracdiff/package.py @@ -11,8 +11,8 @@ class RFracdiff(RPackage): fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989).""" - homepage = "https://cran.r-project.org/package=fracdiff" - url = "https://cran.r-project.org/src/contrib/fracdiff_1.4-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/fracdiff" + homepage = "https://cloud.r-project.org/package=fracdiff" + url = "https://cloud.r-project.org/src/contrib/fracdiff_1.4-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fracdiff" version('1.4-2', '6a6977d175ad963d9675736a8f8d41f7') diff --git a/var/spack/repos/builtin/packages/r-fs/package.py b/var/spack/repos/builtin/packages/r-fs/package.py new file mode 100644 index 0000000000..59d581838e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-fs/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFs(RPackage): + """A cross-platform interface to file system operations, built on top of + the 'libuv' C library.""" + + homepage = "http://fs.r-lib.org/" + url = "https://cloud.r-project.org/src/contrib/fs_1.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/fs" + + version('1.3.1', sha256='d6934dca8f835d8173e3fb9fd4d5e2740c8c04348dd2bcc57df1b711facb46bc') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-futile-logger/package.py b/var/spack/repos/builtin/packages/r-futile-logger/package.py index 88a9471526..d45418aa72 100644 --- a/var/spack/repos/builtin/packages/r-futile-logger/package.py +++ b/var/spack/repos/builtin/packages/r-futile-logger/package.py @@ -11,11 +11,12 @@ class RFutileLogger(RPackage): futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.""" - homepage = "https://cran.rstudio.com/web/packages/futile.logger/index.html" - url = "https://cran.rstudio.com/src/contrib/futile.logger_1.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/futile.logger" + homepage = "https://cloud.r-project.org/package=futile.logger" + url = "https://cloud.r-project.org/src/contrib/futile.logger_1.4.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/futile.logger" version('1.4.3', 'ba0e8d2dfb5a970b51c21907bbf8bfc2') - depends_on('r-lambda-r', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-lambda-r@1.1.0:', type=('build', 'run')) depends_on('r-futile-options', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-futile-options/package.py b/var/spack/repos/builtin/packages/r-futile-options/package.py index 0325508c09..c493ac0ea6 100644 --- a/var/spack/repos/builtin/packages/r-futile-options/package.py +++ b/var/spack/repos/builtin/packages/r-futile-options/package.py @@ -9,8 +9,11 @@ from spack import * class RFutileOptions(RPackage): """A scoped options management framework""" - homepage = "https://cran.rstudio.com/web/packages/futile.options/index.html" - url = "https://cran.rstudio.com/src/contrib/futile.options_1.0.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/futile.options" + homepage = "https://cloud.r-project.org/package=futile.options" + url = "https://cloud.r-project.org/src/contrib/futile.options_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/futile.options" + version('1.0.1', sha256='7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570') version('1.0.0', '8fd845774bbce56f41f7c43c3b4c13ba') + + depends_on('r@2.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-future-apply/package.py b/var/spack/repos/builtin/packages/r-future-apply/package.py new file mode 100644 index 0000000000..a0fd59e473 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-future-apply/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFutureApply(RPackage): + """Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(), + replicate(), sapply(), tapply(), and vapply() that can be resolved using + any future-supported backend, e.g. parallel on the local machine or + distributed on a compute cluster. These future_*apply() functions come with + the same pros and cons as the corresponding base-R *apply() functions but + with the additional feature of being able to be processed via the future + framework.""" + + homepage = "https://github.com/HenrikBengtsson/future.apply" + url = "https://cloud.r-project.org/src/contrib/future.apply_1.3.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/future.apply" + + version('1.3.0', sha256='6374eca49bb81e05c013509c8e324cf9c5d023f9f8217b29ce7b7e12025ca371') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-future@1.13.0:', type=('build', 'run')) + depends_on('r-globals@0.12.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-future/package.py b/var/spack/repos/builtin/packages/r-future/package.py new file mode 100644 index 0000000000..d3778bb2c2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-future/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RFuture(RPackage): + """The purpose of this package is to provide a lightweight and unified + Future API for sequential and parallel processing of R expression via + futures. The simplest way to evaluate an expression in parallel is to use + 'x %<-% { expression }' with 'plan(multiprocess)'. This package implements + sequential, multicore, multisession, and cluster futures. With these, R + expressions can be evaluated on the local machine, in parallel a set of + local machines, or distributed on a mix of local and remote machines. + Extensions to this package implement additional backends for processing + futures via compute cluster schedulers etc. Because of its unified API, + there is no need to modify any code in order switch from sequential on the + local machine to, say, distributed processing on a remote compute cluster. + Another strength of this package is that global variables and functions are + automatically identified and exported as needed, making it straightforward + to tweak existing code to make use of futures.""" + + homepage = "https://github.com/HenrikBengtsson/future" + url = "https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/future" + + version('1.14.0', sha256='0a535010d97a01b21aaf9d863603e44359335e273019c1e1980bbb5b2917dbcb') + + depends_on('r-digest', type=('build', 'run')) + depends_on('r-globals@0.12.4:', type=('build', 'run')) + depends_on('r-listenv@0.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gamlss-data/package.py b/var/spack/repos/builtin/packages/r-gamlss-data/package.py index 186654cc17..25b9fde1a5 100644 --- a/var/spack/repos/builtin/packages/r-gamlss-data/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss-data/package.py @@ -9,10 +9,12 @@ from spack import * class RGamlssData(RPackage): """gamlss.data: GAMLSS Data""" - homepage = "https://cran.r-project.org/package=gamlss.data" - url = "https://cran.r-project.org/src/contrib/gamlss.data_5.1-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gamlss.data/" + homepage = "https://cloud.r-project.org/package=gamlss.data" + url = "https://cloud.r-project.org/src/contrib/gamlss.data_5.1-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gamlss.data/" + version('5.1-4', sha256='0d3777d8c3cd76cef273aa6bde40a91688719be401195ed9bfd1e85bd7d5eeb5') + version('5.1-3', sha256='4941180e7eebe97678ba02ca24c2a797bcb69d92cd34600215a94110e2a70470') version('5.1-0', sha256='0aad438ea1aa6395677e52cd2cb496f9f4c9ba2d39edc92c8cb42e7fc91fe6c1') depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gamlss-dist/package.py b/var/spack/repos/builtin/packages/r-gamlss-dist/package.py index 4f08a15657..107dacdea6 100644 --- a/var/spack/repos/builtin/packages/r-gamlss-dist/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss-dist/package.py @@ -10,10 +10,12 @@ class RGamlssDist(RPackage): """gamlss.dist: Distributions for Generalized Additive Models for Location Scale and Shape""" - homepage = "https://cran.r-project.org/package=gamlss.dist" - url = "https://cran.r-project.org/src/contrib/gamlss.dist_5.1-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gamlss.dist/" + homepage = "https://cloud.r-project.org/package=gamlss.dist" + url = "https://cloud.r-project.org/src/contrib/gamlss.dist_5.1-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gamlss.dist/" + version('5.1-4', sha256='343c6ca0fd8a1c1dfdf9ffc65c95d4dae0c6c80b3e60fccba003e5171f3d287e') + version('5.1-3', sha256='87fd643c82579519b67c66c1d87383fa1e203e8b09f607649ee7bce142bda404') version('5.1-1', sha256='44f999ff74ee516757eb39c8308c48aa850523aad2f38e622268313a13dda0b1') depends_on('r@2.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gamlss/package.py b/var/spack/repos/builtin/packages/r-gamlss/package.py index 0b04d2af53..0215a7fc19 100644 --- a/var/spack/repos/builtin/packages/r-gamlss/package.py +++ b/var/spack/repos/builtin/packages/r-gamlss/package.py @@ -9,10 +9,12 @@ from spack import * class RGamlss(RPackage): """gamlss: Generalised Additive Models for Location Scale and Shape""" - homepage = "https://cran.r-project.org/package=gamlss" - url = "https://cran.r-project.org/src/contrib/gamlss_5.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gamlss/" + homepage = "https://cloud.r-project.org/package=gamlss" + url = "https://cloud.r-project.org/src/contrib/gamlss_5.1-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gamlss/" + version('5.1-4', sha256='e2fc36fe6ca3a69d69cdafd9533a4ff35090fdfb01df126f6a49156f4aa3376c') + version('5.1-3', sha256='d37d121bc2acdbacc20cea04a1ed4489a575079e2a7b17b4a9823ee283857317') version('5.1-2', sha256='0d404e74768a8f98c6a5e9a48bd2cf4280125831a5dcd8c7f7b57922f57e016b') depends_on('r@3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gbm/package.py b/var/spack/repos/builtin/packages/r-gbm/package.py index 2c5b4e8f91..1846290c44 100644 --- a/var/spack/repos/builtin/packages/r-gbm/package.py +++ b/var/spack/repos/builtin/packages/r-gbm/package.py @@ -9,10 +9,14 @@ from spack import * class RGbm(RPackage): """Generalized Boosted Regression Models.""" - homepage = "https://cran.rstudio.com/web/packages/gbm/index.html" - url = "https://cran.rstudio.com/src/contrib/gbm_2.1.3.tar.gz" + homepage = "https://cloud.r-project.org/package=gbm" + url = "https://cloud.r-project.org/src/contrib/gbm_2.1.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gbm" + version('2.1.5', sha256='06fbde10639dfa886554379b40a7402d1f1236a9152eca517e97738895a4466f') version('2.1.3', '9b2f32c892c6e31b01c1162e3b16b3f4') + depends_on('r@2.9.0:', type=('build', 'run')) + depends_on('r-gridextra', when='@2.1.5:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gbrd/package.py b/var/spack/repos/builtin/packages/r-gbrd/package.py new file mode 100644 index 0000000000..0dfe6081db --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gbrd/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGbrd(RPackage): + """Provides utilities for processing Rd objects and files. Extract argument + descriptions and other parts of the help pages of functions.""" + + homepage = "https://cloud.r-project.org/package=gbRd" + url = "https://cloud.r-project.org/src/contrib/gbRd_0.4-11.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gbRd" + + version('0.4-11', sha256='0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b') diff --git a/var/spack/repos/builtin/packages/r-gdalutils/package.py b/var/spack/repos/builtin/packages/r-gdalutils/package.py index d8adeae443..96f5e2f59b 100644 --- a/var/spack/repos/builtin/packages/r-gdalutils/package.py +++ b/var/spack/repos/builtin/packages/r-gdalutils/package.py @@ -9,15 +9,16 @@ from spack import * class RGdalutils(RPackage): """gdalUtils: Wrappers for the Geospatial Data Abstraction Library""" - homepage = "https://cran.r-project.org/package=gdalUtils" - url = "https://cran.r-project.org/src/contrib/gdalUtils_2.0.1.14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gdalUtils" + homepage = "https://cloud.r-project.org/package=gdalUtils" + url = "https://cloud.r-project.org/src/contrib/gdalUtils_2.0.1.14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gdalUtils" version('2.0.1.14', sha256='890a502b2eb5f1b23655fab94caad5d32adca05b93f5db1d96d9dcde3f0e7737') depends_on('r@2.14.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) - depends_on('r-utils', type=('build', 'run')) + depends_on('r-r-utils', type=('build', 'run')) depends_on('r-raster', type=('build', 'run')) depends_on('r-rgdal', type=('build', 'run')) + depends_on('gdal') diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py index f23f96165f..40f27d4e00 100644 --- a/var/spack/repos/builtin/packages/r-gdata/package.py +++ b/var/spack/repos/builtin/packages/r-gdata/package.py @@ -25,11 +25,13 @@ class RGdata(RPackage): ('ans'), and - wrapper for 'sample' that ensures consistent behavior for both scalar and vector arguments ('resample').""" - homepage = "https://cran.r-project.org/package=gdata" - url = "https://cran.r-project.org/src/contrib/gdata_2.18.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gdata" + homepage = "https://cloud.r-project.org/package=gdata" + url = "https://cloud.r-project.org/src/contrib/gdata_2.18.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gdata" version('2.18.0', 'f831019aa743fe11dcf0a051e4280921') version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f') + depends_on('r@2.3.0:', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) + depends_on('perl@5.10.0:') diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py index 23453b776c..2225c7051e 100644 --- a/var/spack/repos/builtin/packages/r-geiger/package.py +++ b/var/spack/repos/builtin/packages/r-geiger/package.py @@ -9,18 +9,21 @@ from spack import * class RGeiger(RPackage): """Methods for fitting macroevolutionary models to phylogenetic trees.""" - homepage = "https://cran.r-project.org/package=geiger" - url = "https://cran.r-project.org/src/contrib/geiger_2.0.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geiger" + homepage = "https://cloud.r-project.org/package=geiger" + url = "https://cloud.r-project.org/src/contrib/geiger_2.0.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/geiger" + version('2.0.6.2', sha256='9153047b608d652821251206d1450bb3f517c8884379f498a695315574ae001d') + version('2.0.6.1', sha256='2a95e20a3a90c096343b014344dd97e699e954da99c151c17fc6c245c77dba0b') version('2.0.6', 'e5e1a407ea56805227d0f91bf6d95afc') - depends_on('r-ape@3.0:', type=('build', 'run')) + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-ape@3.0-6:', type=('build', 'run')) depends_on('r-mvtnorm', type=('build', 'run')) depends_on('r-subplex', type=('build', 'run')) depends_on('r-desolve@1.7:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-rcpp@0.9.0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-coda', type=('build', 'run')) depends_on('r-ncbit', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-generics/package.py b/var/spack/repos/builtin/packages/r-generics/package.py new file mode 100644 index 0000000000..0b9e1f681e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-generics/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGenerics(RPackage): + """In order to reduce potential package dependencies and conflicts, + generics provides a number of commonly used S3 generics.""" + + homepage = "https://github.com/r-lib/generics" + url = "https://cloud.r-project.org/src/contrib/generics_0.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/generics" + + version('0.0.2', sha256='71b3d1b719ce89e71dd396ac8bc6aa5f1cd99bbbf03faff61dfbbee32fec6176') + + depends_on('r@3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gensa/package.py b/var/spack/repos/builtin/packages/r-gensa/package.py index e8dc639494..e93e9ce9cb 100644 --- a/var/spack/repos/builtin/packages/r-gensa/package.py +++ b/var/spack/repos/builtin/packages/r-gensa/package.py @@ -12,9 +12,9 @@ class RGensa(RPackage): Performs search for global minimum of a very complex non-linear objective function with a very large number of optima.""" - homepage = "https://cran.r-project.org/package=GenSA" - url = "https://cran.r-project.org/src/contrib/GenSA_1.1.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GenSA/" + homepage = "https://cloud.r-project.org/package=GenSA" + url = "https://cloud.r-project.org/src/contrib/GenSA_1.1.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/GenSA/" version('1.1.7', sha256='9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f') diff --git a/var/spack/repos/builtin/packages/r-geomorph/package.py b/var/spack/repos/builtin/packages/r-geomorph/package.py index 3d33e64837..32049e61e3 100644 --- a/var/spack/repos/builtin/packages/r-geomorph/package.py +++ b/var/spack/repos/builtin/packages/r-geomorph/package.py @@ -12,10 +12,11 @@ class RGeomorph(RPackage): analyses, and provide graphical depictions of shapes and patterns of shape variation.""" - homepage = "https://cran.r-project.org/package=geomorph" - url = "https://cran.r-project.org/src/contrib/geomorph_3.0.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geomorph" + homepage = "https://cloud.r-project.org/package=geomorph" + url = "https://cloud.r-project.org/src/contrib/geomorph_3.0.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/geomorph" + version('3.1.2', sha256='29cf1c484f756cb44808cfdbc20137a6fbc4bd0c5c6f98c6c3f397c5aebda8f1') version('3.1.1', sha256='8eb222011433100860b308beef6f02ade7c421785f575ab4461ee25e38dfa1bd') version('3.0.7', sha256='68f8942e1a5bc3f0298c9f5b8f69c4702c8e12ecb2275d740fda4d04d66d38e1') version('3.0.5', '240e69fe260ca3ef4d84b4281d61396c') @@ -24,6 +25,6 @@ class RGeomorph(RPackage): depends_on('r-rgl', type=('build', 'run')) depends_on('r-ape', type=('build', 'run')) depends_on('r-jpeg', type=('build', 'run')) - depends_on('r-geiger', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) + depends_on('r-geiger', when='@:3.1.1', type=('build', 'run')) + depends_on('r-matrix', when='@:3.1.1', type=('build', 'run')) depends_on('r-rrpp', type=('build', 'run'), when='@3.0.7:') diff --git a/var/spack/repos/builtin/packages/r-geonames/package.py b/var/spack/repos/builtin/packages/r-geonames/package.py index 1d138cfc16..c8de77d062 100644 --- a/var/spack/repos/builtin/packages/r-geonames/package.py +++ b/var/spack/repos/builtin/packages/r-geonames/package.py @@ -9,9 +9,9 @@ from spack import * class RGeonames(RPackage): """geonames: Interface to the "Geonames" Spatial Query Web Service""" - homepage = "https://cran.r-project.org/package=geonames" - url = "https://cran.r-project.org/src/contrib/geonames_0.999.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geonames" + homepage = "https://cloud.r-project.org/package=geonames" + url = "https://cloud.r-project.org/src/contrib/geonames_0.999.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/geonames" version('0.999', sha256='1dd7bbd82d9425d14eb36f8e5bf431feaccfe3b0c4e70bf38f44f13dfc59e17b') diff --git a/var/spack/repos/builtin/packages/r-geor/package.py b/var/spack/repos/builtin/packages/r-geor/package.py index daa827c939..2c499a19b8 100644 --- a/var/spack/repos/builtin/packages/r-geor/package.py +++ b/var/spack/repos/builtin/packages/r-geor/package.py @@ -10,9 +10,9 @@ class RGeor(RPackage): """Geostatistical analysis including traditional, likelihood-based and Bayesian methods.""" - homepage = "https://cran.r-project.org/web/packages/geoR/" - url = "https://cran.r-project.org/src/contrib/geoR_1.7-5.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geoR" + homepage = "https://cloud.r-project.org/package=geoR" + url = "https://cloud.r-project.org/src/contrib/geoR_1.7-5.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/geoR" version('1.7-5.2.1', 'a50f477bea1bec9070a4de01f69b831c') diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py index 58d3da5aea..689e2f3c1d 100644 --- a/var/spack/repos/builtin/packages/r-geosphere/package.py +++ b/var/spack/repos/builtin/packages/r-geosphere/package.py @@ -11,10 +11,13 @@ class RGeosphere(RPackage): distances and related measures for angular (longitude/latitude) locations.""" - homepage = "https://cran.r-project.org/package=geosphere" - url = "https://cran.r-project.org/src/contrib/geosphere_1.5-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/geosphere" + homepage = "https://cloud.r-project.org/package=geosphere" + url = "https://cloud.r-project.org/src/contrib/geosphere_1.5-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/geosphere" + version('1.5-10', sha256='56cd4f787101e2e18f19ddb83794154b58697e63cad81168f0936f60ab7eb497') + version('1.5-7', sha256='9d9b555e2d59a5ae174ae654652121f169fbc3e9cf66c2491bfbe0684b6dd8a0') version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-getopt/package.py b/var/spack/repos/builtin/packages/r-getopt/package.py index 302f1f145c..08c8b97611 100644 --- a/var/spack/repos/builtin/packages/r-getopt/package.py +++ b/var/spack/repos/builtin/packages/r-getopt/package.py @@ -14,8 +14,9 @@ class RGetopt(RPackage): values, positional argument support, etc.""" homepage = "https://github.com/trevorld/getopt" - url = "https://cran.r-project.org/src/contrib/getopt_1.20.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/getopt" + url = "https://cloud.r-project.org/src/contrib/getopt_1.20.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/getopt" + version('1.20.3', sha256='531f5fdfdcd6b96a73df2b39928418de342160ac1b0043861e9ea844f9fbf57f') version('1.20.2', sha256='3d6c12d32d6cd4b2909be626e570e158b3ed960e4739510e3a251e7f172de38e') version('1.20.1', '323cf2846e306f49236b8174bc3d4e47') diff --git a/var/spack/repos/builtin/packages/r-getoptlong/package.py b/var/spack/repos/builtin/packages/r-getoptlong/package.py index f7726bb23e..e6064611e5 100644 --- a/var/spack/repos/builtin/packages/r-getoptlong/package.py +++ b/var/spack/repos/builtin/packages/r-getoptlong/package.py @@ -12,12 +12,17 @@ class RGetoptlong(RPackage): use in R. It also provides a simple way for variable interpolation in R.""" - homepage = "https://cran.rstudio.com/web/packages/GetoptLong/index.html" - url = "https://cran.rstudio.com/src/contrib/GetoptLong_0.1.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GetoptLong" + homepage = "https://cloud.r-project.org/package=GetoptLong" + url = "https://cloud.r-project.org/src/contrib/GetoptLong_0.1.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/GetoptLong" + version('0.1.7', sha256='b9a98881db407eae9b711c4fa9170168fd5f3be1f8485cd8f28d0a60ace083ba') version('0.1.6', 'e4b964d0817cb6c6a707297b21405749') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-rjson', type=('build', 'run')) - depends_on('r-globaloptions', type=('build', 'run')) + depends_on('r-globaloptions@0.1.0:', type=('build', 'run')) + + # The CRAN site lists SystemRequirments as: Perl, Getopt::Long. The + # Getop::Long package will be installed with Perl so just depend on perl. depends_on('perl') diff --git a/var/spack/repos/builtin/packages/r-ggally/package.py b/var/spack/repos/builtin/packages/r-ggally/package.py index 16f54d4744..7ccb73a128 100644 --- a/var/spack/repos/builtin/packages/r-ggally/package.py +++ b/var/spack/repos/builtin/packages/r-ggally/package.py @@ -14,15 +14,19 @@ class RGgally(RPackage): group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.""" - homepage = "https://cran.r-project.org/package=GGally" - url = "https://cran.r-project.org/src/contrib/GGally_1.3.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GGally" + homepage = "https://cloud.r-project.org/package=GGally" + url = "https://cloud.r-project.org/src/contrib/GGally_1.3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/GGally" + version('1.4.0', sha256='9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe') version('1.3.2', 'efe58133ba8431198af7afb6bcb76264') - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-gtable', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) + depends_on('r-gtable@0.2.0:', type=('build', 'run')) + depends_on('r-plyr@1.8.3:', type=('build', 'run')) depends_on('r-progress', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r-reshape', type=('build', 'run')) + depends_on('r-reshape@0.8.5:', type=('build', 'run')) + depends_on('r-rlang', when='@1.4.0:', type=('build', 'run')) + depends_on('openssl', when='@1.4.0:') diff --git a/var/spack/repos/builtin/packages/r-ggdendro/package.py b/var/spack/repos/builtin/packages/r-ggdendro/package.py index e429a319b8..87052809cc 100644 --- a/var/spack/repos/builtin/packages/r-ggdendro/package.py +++ b/var/spack/repos/builtin/packages/r-ggdendro/package.py @@ -16,11 +16,11 @@ class RGgdendro(RPackage): The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.""" - homepage = "https://cran.r-project.org/package=ggdendro" - url = "https://cran.rstudio.com/src/contrib/ggdendro_0.1-20.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ggdendro" + homepage = "https://cloud.r-project.org/package=ggdendro" + url = "https://cloud.r-project.org/src/contrib/ggdendro_0.1-20.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggdendro" version('0.1-20', '787552e346432c758633d8f4b2675eb6') - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggplot2@0.9.2:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggjoy/package.py b/var/spack/repos/builtin/packages/r-ggjoy/package.py index df34c9513d..3262750b38 100644 --- a/var/spack/repos/builtin/packages/r-ggjoy/package.py +++ b/var/spack/repos/builtin/packages/r-ggjoy/package.py @@ -10,14 +10,15 @@ class RGgjoy(RPackage): """Joyplots provide a convenient way of visualizing changes in distributions over time or space.""" - homepage = "https://cran.r-project.org/web/packages/ggjoy/index.html" - url = "https://cran.r-project.org/src/contrib/ggjoy_0.4.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ggjoy" + homepage = "https://cloud.r-project.org/package=ggjoy" + url = "https://cloud.r-project.org/src/contrib/ggjoy_0.4.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggjoy" + version('0.4.1', sha256='d2f778bc40203d7fbb7c81b40beed8614c36ea10448e911663cc6109aa685504') version('0.4.0', 'c63782e2395a9cfc435d08e078e6596b') version('0.3.0', '59bd34a846270d43f2eeb1e90b03a127') version('0.2.0', '8584cd154e228f8505b324e91d2e50d7') - depends_on('r@3.4.0:3.4.9') + depends_on('r@3.2:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-ggridges', type=('build', 'run')) + depends_on('r-ggridges@0.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py index cc7e0a4e3d..a468f4b18c 100644 --- a/var/spack/repos/builtin/packages/r-ggmap/package.py +++ b/var/spack/repos/builtin/packages/r-ggmap/package.py @@ -13,20 +13,32 @@ class RGgmap(RPackage): geolocation and routing.""" homepage = "https://github.com/dkahle/ggmap" - url = "https://cran.r-project.org/src/contrib/ggmap_2.6.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggmap" + url = "https://cloud.r-project.org/src/contrib/ggmap_2.6.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggmap" + version('3.0.0', sha256='96c24ffdc0710d0633ac4721d599d2c06f43a29c59d1e85c94ff0af30dfdb58d') + version('2.6.2', sha256='4e9cf53ab108fc70805d971dadb69b26fe67ea289c23c38adf6e30b198379d90') version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a') - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-proto', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) + depends_on('r-proto', when='@:2.6.2', type=('build', 'run')) depends_on('r-rgooglemaps', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) - depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-reshape2', when='@:2.6.2', type=('build', 'run')) depends_on('r-rjson', type=('build', 'run')) - depends_on('r-mapproj', type=('build', 'run')) + depends_on('r-mapproj', when='@:2.6.2', type=('build', 'run')) depends_on('r-jpeg', type=('build', 'run')) - depends_on('r-geosphere', type=('build', 'run')) + depends_on('r-geosphere', when='@:2.6.2', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) + depends_on('r-dplyr', when='@3.0.0:', type=('build', 'run')) + depends_on('r-bitops', when='@3.0.0:', type=('build', 'run')) + depends_on('r-glue', when='@3.0.0:', type=('build', 'run')) + depends_on('r-httr', when='@3.0.0:', type=('build', 'run')) + depends_on('r-stringr', when='@3.0.0:', type=('build', 'run')) + depends_on('r-purrr', when='@3.0.0:', type=('build', 'run')) + depends_on('r-magrittr', when='@3.0.0:', type=('build', 'run')) + depends_on('r-tibble', when='@3.0.0:', type=('build', 'run')) + depends_on('r-tidyr', when='@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py index 1d0591e85b..59e9b46b35 100644 --- a/var/spack/repos/builtin/packages/r-ggplot2/package.py +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -16,19 +16,25 @@ class RGgplot2(RPackage): documentation and examples.""" homepage = "http://ggplot2.org/" - url = "https://cran.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggplot2" + url = "https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggplot2" + version('3.2.0', sha256='31b6897fb65acb37913ff6e2bdc1b57f652360098ae3aa660abdcf54f84d73b3') + version('3.1.1', sha256='bfde297f3b4732e7f560078f4ce131812a70877e6b5b1d41a772c394939e0c79') version('2.2.1', '14c5a3507bc123c6e7e9ad3bef7cee5c') version('2.1.0', '771928cfb97c649c720423deb3ec7fd3') - depends_on('r@3.1:') - + depends_on('r@3.1:', when='@:3.1.1', type=('build', 'run')) + depends_on('r@3.2:', when='@3.2.0:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-gtable@0.1.1:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) - depends_on('r-plyr@1.7.1:', type=('build', 'run')) + depends_on('r-plyr@1.7.1:', when='@:3.1.1', type=('build', 'run')) depends_on('r-reshape2', type=('build', 'run')) - depends_on('r-scales@0.4.1:', type=('build', 'run')) + depends_on('r-scales@0.5.0:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-lazyeval', type=('build', 'run')) + depends_on('r-mgcv', when='@3.2.0:', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', when='@3.0.0:', type=('build', 'run')) + depends_on('r-viridislite', when='@3.0.0:', type=('build', 'run')) + depends_on('r-withr@2.0.0:', when='@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggpubr/package.py b/var/spack/repos/builtin/packages/r-ggpubr/package.py index 4184d2e4e3..fcd2fc9e93 100644 --- a/var/spack/repos/builtin/packages/r-ggpubr/package.py +++ b/var/spack/repos/builtin/packages/r-ggpubr/package.py @@ -10,13 +10,27 @@ class RGgpubr(RPackage): """ggpubr: 'ggplot2' Based Publication Ready Plots""" homepage = "http://www.sthda.com/english/rpkgs/ggpubr" - url = "https://cran.r-project.org/src/contrib/ggpubr_0.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggpubr" + url = "https://cloud.r-project.org/src/contrib/ggpubr_0.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggpubr" + version('0.2.2', sha256='1c93dc6d1f08680dd00a10b6842445700d1fccb11f18599fbdf51e70c6b6b364') + version('0.2.1', sha256='611e650da9bd15d7157fdcdc4e926fee3b88df3aba87410fdb1c8a7294d98d28') + version('0.2', sha256='06c3075d8c452840662f5d041c3d966494b87254a52a858c849b9e1e96647766') version('0.1.2', '42a5749ae44121597ef511a7424429d1') - depends_on('r@3.1.0:') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) depends_on('r-ggrepel', type=('build', 'run')) depends_on('r-ggsci', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) + depends_on('r-plyr', when='@:0.1.2', type=('build', 'run')) + depends_on('r-tidyr', when='@0.2:', type=('build', 'run')) + depends_on('r-purrr', when='@0.2:', type=('build', 'run')) + depends_on('r-dplyr@0.7.1:', when='@0.2:', type=('build', 'run')) + depends_on('r-cowplot', when='@0.2:', type=('build', 'run')) + depends_on('r-ggsignif', when='@0.2:', type=('build', 'run')) + depends_on('r-scales', when='@0.2:', type=('build', 'run')) + depends_on('r-gridextra', when='@0.2:', type=('build', 'run')) + depends_on('r-glue', when='@0.2:', type=('build', 'run')) + depends_on('r-polynom', when='@0.2:', type=('build', 'run')) + depends_on('r-rlang', when='@0.2.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggrepel/package.py b/var/spack/repos/builtin/packages/r-ggrepel/package.py index 84f811e28b..aca5c2fee3 100644 --- a/var/spack/repos/builtin/packages/r-ggrepel/package.py +++ b/var/spack/repos/builtin/packages/r-ggrepel/package.py @@ -10,12 +10,14 @@ class RGgrepel(RPackage): """ggrepel: Repulsive Text and Label Geoms for 'ggplot2'""" homepage = "http://github.com/slowkow/ggrepel" - url = "https://cran.r-project.org/src/contrib/ggrepel_0.6.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggrepel" + url = "https://cloud.r-project.org/src/contrib/ggrepel_0.6.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggrepel" + version('0.8.1', sha256='d5d03a77ab6d8c831934bc46e840cc4e3df487272ab591fa72767ad42bcb7283') + version('0.8.0', sha256='6386606e716d326354a29fcb6cd09f9b3d3b5e7c5ba0d5f7ff35416b1a4177d4') version('0.6.5', '7e2732cd4840efe2dc9e4bc689cf1ee5') - depends_on('r@3.0.0:') - depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-scales@0.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggridges/package.py b/var/spack/repos/builtin/packages/r-ggridges/package.py index 5968ced805..c63fc86b41 100644 --- a/var/spack/repos/builtin/packages/r-ggridges/package.py +++ b/var/spack/repos/builtin/packages/r-ggridges/package.py @@ -10,12 +10,17 @@ class RGgridges(RPackage): """Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space.""" - homepage = "https://cran.r-project.org/web/packages/ggridges/index.html" - url = "https://cran.r-project.org/src/contrib/ggridges_0.4.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ggridges" + homepage = "https://cloud.r-project.org/package=ggridges" + url = "https://cloud.r-project.org/src/contrib/ggridges_0.4.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggridges" + version('0.5.1', sha256='01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36') + version('0.5.0', sha256='124bc84044e56728fa965682f8232fc868f2af7d3eb7276f6b0df53be8d2dbfe') version('0.4.1', '21d53b3f7263beb17f629f0ebfb7b67a') version('0.4.0', 'da94ed1ee856a7fa5fb87712c84ec4c9') - depends_on('r@3.4.0:3.4.9') - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-ggplot2@2.2.0:', type=('build', 'run')) + depends_on('r-plyr@1.8.0:', type=('build', 'run')) + depends_on('r-scales@0.4.1:', type=('build', 'run')) + depends_on('r-withr@2.1.1:', when='@0.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggsci/package.py b/var/spack/repos/builtin/packages/r-ggsci/package.py index d7f263c38b..fa4fe4130f 100644 --- a/var/spack/repos/builtin/packages/r-ggsci/package.py +++ b/var/spack/repos/builtin/packages/r-ggsci/package.py @@ -11,11 +11,13 @@ class RGgsci(RPackage): 'ggplot2'""" homepage = "https://github.com/road2stat/ggsci" - url = "https://cran.r-project.org/src/contrib/ggsci_2.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggsci" + url = "https://cloud.r-project.org/src/contrib/ggsci_2.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggsci" + version('2.9', sha256='4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c') + version('2.8', sha256='b4ce7adce7ef23edf777866086f98e29b2b45b58fed085bbd1ffe6ab52d74ae8') version('2.4', '8e5dc2fcf84352cacbb91363e26c7175') - depends_on('r@3.0.2:') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-scales', type=('build', 'run')) depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggsignif/package.py b/var/spack/repos/builtin/packages/r-ggsignif/package.py new file mode 100644 index 0000000000..4a2e8cb544 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggsignif/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGgsignif(RPackage): + """Enrich your 'ggplots' with group-wise comparisons. This package provides + an easy way to indicate if two groups are significantly different. Commonly + this is shown by a bracket on top connecting the groups of interest which + itself is annotated with the level of significance (NS, *, **, ***). The + package provides a single layer (geom_signif()) that takes the groups for + comparison and the test (t.test(), wilcox.text() etc.) as arguments and + adds the annotation to the plot.""" + + homepage = "https://github.com/const-ae/ggsignif" + url = "https://cloud.r-project.org/src/contrib/ggsignif_0.6.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggsignif" + + version('0.6.0', sha256='6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e') + + depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py index 1543f23dd2..bf4b902e1d 100644 --- a/var/spack/repos/builtin/packages/r-ggvis/package.py +++ b/var/spack/repos/builtin/packages/r-ggvis/package.py @@ -12,16 +12,18 @@ class RGgvis(RPackage): and web graphics from 'vega'.""" homepage = "http://ggvis.rstudio.com/" - url = "https://cran.rstudio.com/src/contrib/ggvis_0.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ggvis" + url = "https://cloud.r-project.org/src/contrib/ggvis_0.4.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ggvis" + version('0.4.4', sha256='1332ea122b768688c8a407a483be80febc4576de0ec8929077738421b27cafaf') version('0.4.3', '30297d464278a7974fb125bcc7d84e77') version('0.4.2', '039f45e5c7f1e0652779163d7d99f922') + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-shiny', type=('build', 'run')) + depends_on('r-jsonlite@0.9.11:', type=('build', 'run')) + depends_on('r-shiny@0.11.1:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-dplyr@0.4.0:', type=('build', 'run')) depends_on('r-lazyeval', type=('build', 'run')) - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-htmltools@0.2.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gh/package.py b/var/spack/repos/builtin/packages/r-gh/package.py new file mode 100644 index 0000000000..779e3e649e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gh/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGh(RPackage): + """Minimal client to access the 'GitHub' 'API'.""" + + homepage = "https://github.com/r-lib/gh#readme" + url = "https://cloud.r-project.org/src/contrib/gh_1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gh" + + version('1.0.1', sha256='f3c02b16637ae390c3599265852d94b3de3ef585818b260d00e7812595b391d2') + + depends_on('r-ini', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-httr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py index a5769db25f..ca1d6127ca 100644 --- a/var/spack/repos/builtin/packages/r-gistr/package.py +++ b/var/spack/repos/builtin/packages/r-gistr/package.py @@ -16,13 +16,15 @@ class RGistr(RPackage): requests require authentication and some do not.""" homepage = "https://github.com/ropensci/gistr" - url = "https://cran.r-project.org/src/contrib/gistr_0.3.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gistr" + url = "https://cloud.r-project.org/src/contrib/gistr_0.3.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gistr" + version('0.4.2', sha256='43c00c7f565732125f45f6c067724771ba1b337d6dd3a6e301639fe16e11032e') + version('0.4.0', sha256='51771a257379a17552d0c88ada72ca6263954bbe896997f8a66cde3bf0b83ce0') version('0.3.6', '49d548cb3eca0e66711aece37757a2c0') - depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-httr', type=('build', 'run')) + depends_on('r-jsonlite@1.4:', type=('build', 'run')) + depends_on('r-httr@1.2.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-assertthat', type=('build', 'run')) depends_on('r-knitr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py index 2306bf9b08..0e6ce00871 100644 --- a/var/spack/repos/builtin/packages/r-git2r/package.py +++ b/var/spack/repos/builtin/packages/r-git2r/package.py @@ -12,13 +12,15 @@ class RGit2r(RPackage): data and running some basic 'Git' commands.""" homepage = "https://github.com/ropensci/git2r" - url = "https://cran.r-project.org/src/contrib/git2r_0.18.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/git2r" + url = "https://cloud.r-project.org/src/contrib/git2r_0.18.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/git2r" + version('0.26.1', sha256='13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435') + version('0.26.0', sha256='56671389c3a50591e1dae3be8c3b0112d06d291f897d7fe14db17aea175616cf') version('0.18.0', 'fb5741eb490c3d6e23a751a72336f24d') version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1') - depends_on('r@3.0.2:') - + depends_on('r@3.1:', type=('build', 'run')) depends_on('zlib') depends_on('openssl') + depends_on('libgit2') diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py index 21cb2a5986..0e98d4ff0d 100644 --- a/var/spack/repos/builtin/packages/r-glmnet/package.py +++ b/var/spack/repos/builtin/packages/r-glmnet/package.py @@ -14,11 +14,13 @@ class RGlmnet(RPackage): multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.""" - homepage = "https://cran.rstudio.com/web/packages/glmnet/index.html" - url = "https://cran.rstudio.com/src/contrib/glmnet_2.0-13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/glmnet" + homepage = "https://cloud.r-project.org/package=glmnet" + url = "https://cloud.r-project.org/src/contrib/glmnet_2.0-13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/glmnet" + + version('2.0-18', sha256='e8dce9d7b8105f9cc18ba981d420de64a53b09abee219660d3612915d554256b') version('2.0-13', '1dd5636388df5c3a29207d0bf1253343') version('2.0-5', '049b18caa29529614cd684db3beaec2a') - depends_on('r-matrix', type=('build', 'run')) + depends_on('r-matrix@1.0-6:', type=('build', 'run')) depends_on('r-foreach', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-globaloptions/package.py b/var/spack/repos/builtin/packages/r-globaloptions/package.py index d1b0d3d8a0..6831b436bf 100644 --- a/var/spack/repos/builtin/packages/r-globaloptions/package.py +++ b/var/spack/repos/builtin/packages/r-globaloptions/package.py @@ -10,12 +10,12 @@ class RGlobaloptions(RPackage): """It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.""" - homepage = "https://cran.r-project.org/package=GlobalOptions" - url = "https://cran.rstudio.com/src/contrib/GlobalOptions_0.0.12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GlobalOptions" + homepage = "https://cloud.r-project.org/package=GlobalOptions" + url = "https://cloud.r-project.org/src/contrib/GlobalOptions_0.0.12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/GlobalOptions" + version('0.1.0', sha256='567a0a51f6b7b14127302f00e6e4944befd4964c069f96a9e61256e8c3c79ef2') version('0.0.12', '6c268b3b27874918ba62eb0f6aa0a3e5') - depends_on('r-testthat', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-markdown', type=('build', 'run')) + depends_on('r@2.10:', when='@:0.0.12', type=('build', 'run')) + depends_on('r@3.3.0:', when='@0.0.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-globals/package.py b/var/spack/repos/builtin/packages/r-globals/package.py new file mode 100644 index 0000000000..cb3eaad818 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-globals/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGlobals(RPackage): + """Identifies global ("unknown" or "free") objects in R expressions by code + inspection using various strategies, e.g. conservative or liberal. The + objective of this package is to make it as simple as possible to identify + global objects for the purpose of exporting them in distributed compute + environments.""" + + homepage = "https://github.com/HenrikBengtsson/globals" + url = "https://cloud.r-project.org/src/contrib/globals_0.12.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/globals" + + version('0.12.4', sha256='7985356ad75afa1f795f8267a20dee847020c0207252dc075c614cef55d8fe6b') + + depends_on('r@3.1.2:', type=('build', 'run')) + depends_on('r-codetools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-glue/package.py b/var/spack/repos/builtin/packages/r-glue/package.py index 7e60a323fb..c4886be7a4 100644 --- a/var/spack/repos/builtin/packages/r-glue/package.py +++ b/var/spack/repos/builtin/packages/r-glue/package.py @@ -14,7 +14,11 @@ class RGlue(RPackage): manual/strings/#triple-quoted-string-literals>.""" homepage = "https://github.com/tidyverse/glue" - url = "https://cran.r-project.org/src/contrib/glue_1.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/glue" + url = "https://cloud.r-project.org/src/contrib/glue_1.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/glue" + version('1.3.1', sha256='4fc1f2899d71a634e1f0adb7942772feb5ac73223891abe30ea9bd91d3633ea8') + version('1.3.0', sha256='789e5a44c3635c3d3db26666e635e88adcf61cd02b75465125d95d7a12291cee') version('1.2.0', '77d06b6d86abc882fa1c0599e457c5e2') + + depends_on('r@3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gmodels/package.py b/var/spack/repos/builtin/packages/r-gmodels/package.py index 3baa8c7358..6eee528156 100644 --- a/var/spack/repos/builtin/packages/r-gmodels/package.py +++ b/var/spack/repos/builtin/packages/r-gmodels/package.py @@ -10,10 +10,12 @@ class RGmodels(RPackage): """Various R programming tools for model fitting.""" homepage = "http://www.sf.net/projects/r-gregmisc" - url = "https://cran.r-project.org/src/contrib/gmodels_2.16.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gmodels" + url = "https://cloud.r-project.org/src/contrib/gmodels_2.16.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gmodels" + version('2.18.1', sha256='626140a34eb8c53dd0a06511a76c71bc61c48777fa76fcc5e6934c9c276a1369') version('2.16.2', 'f13e5feb2a8b9f0cd47fdf25ddc74228') - depends_on('r@1.9:') + depends_on('r@1.9.0:', type=('build', 'run')) depends_on('r-gdata', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gmp/package.py b/var/spack/repos/builtin/packages/r-gmp/package.py index c3c99c7676..0070a61fdf 100644 --- a/var/spack/repos/builtin/packages/r-gmp/package.py +++ b/var/spack/repos/builtin/packages/r-gmp/package.py @@ -12,9 +12,12 @@ class RGmp(RPackage): using the C library GMP (GNU Multiple Precision Arithmetic).""" homepage = "http://mulcyber.toulouse.inra.fr/projects/gmp" - url = "https://cran.r-project.org/src/contrib/gmp_0.5-13.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gmp" + url = "https://cloud.r-project.org/src/contrib/gmp_0.5-13.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gmp" + version('0.5-13.5', sha256='f681ab2ff3d1e379ba8ac44a8abddd08d08170723e885abc0b469b6fa8fe5510') + version('0.5-13.4', sha256='f05605b40fc39fc589e3a4d2f526a591a649faa45eef7f95c096e1bff8775196') version('0.5-13.1', '4a45d45e53bf7140720bd44f10b075ed') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('gmp@4.2.3:') diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py index 8077403912..5ac11e6a7a 100644 --- a/var/spack/repos/builtin/packages/r-googlevis/package.py +++ b/var/spack/repos/builtin/packages/r-googlevis/package.py @@ -14,9 +14,12 @@ class RGooglevis(RPackage): to Google.""" homepage = "https://github.com/mages/googleVis#googlevis" - url = "https://cran.r-project.org/src/contrib/googleVis_0.6.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/googleVis" + url = "https://cloud.r-project.org/src/contrib/googleVis_0.6.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/googleVis" + version('0.6.4', sha256='7dcaf0e9d5e5598c17e8bd474141708de37eeb2578b09788431b9d871edb7eb8') + version('0.6.3', sha256='17d104c5d4e6ab7b984df229cd51be19681e4726077afec7c61a33f6e4c0b6ef') version('0.6.0', 'ec36fd2a6884ddc7baa894007d0d0468') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-goplot/package.py b/var/spack/repos/builtin/packages/r-goplot/package.py index 4e41bcc8c3..fb94c72f3e 100644 --- a/var/spack/repos/builtin/packages/r-goplot/package.py +++ b/var/spack/repos/builtin/packages/r-goplot/package.py @@ -17,8 +17,8 @@ class RGoplot(RPackage): (circle plot, chord plot, cluster plot, Venn diagram, heatmap).""" homepage = "https://github.com/wencke/wencke.github.io/issues" - url = "https://cran.r-project.org/src/contrib/GOplot_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GOplot" + url = "https://cloud.r-project.org/src/contrib/GOplot_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/GOplot" version('1.0.2', sha256='3ddaa2b6d1297ad6daad30d18af708adf43d86e8804b1b92fa29dfbf26d80df9') diff --git a/var/spack/repos/builtin/packages/r-gower/package.py b/var/spack/repos/builtin/packages/r-gower/package.py new file mode 100644 index 0000000000..72393b714b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gower/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGower(RPackage): + """Compute Gower's distance (or similarity) coefficient between records. + Compute the top-n matches between records. Core algorithms are executed in + parallel on systems supporting OpenMP.""" + + homepage = "https://github.com/markvanderloo/gower" + url = "https://cloud.r-project.org/src/contrib/gower_0.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gower" + + version('0.2.1', sha256='af3fbe91cf818c0841b2c0ec4ddf282c182a588031228c8d88f7291b2cdff100') diff --git a/var/spack/repos/builtin/packages/r-gplots/package.py b/var/spack/repos/builtin/packages/r-gplots/package.py index 6b61f87f90..3ba000a5dd 100644 --- a/var/spack/repos/builtin/packages/r-gplots/package.py +++ b/var/spack/repos/builtin/packages/r-gplots/package.py @@ -11,10 +11,14 @@ from spack import * class RGplots(RPackage): """Various R Programming Tools for Plotting Data.""" - homepage = "https://cran.r-project.org/package=gplots" - url = "https://cran.rstudio.com/src/contrib/gplots_3.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gplots" + homepage = "https://cloud.r-project.org/package=gplots" + url = "https://cloud.r-project.org/src/contrib/gplots_3.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gplots" + + version('3.0.1.1', sha256='7db103f903a25d174cddcdfc7b946039b61e236c95084b90ad17f1a41da3770c') version('3.0.1', '6116822401d55add044beb120ca93d14') + + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) depends_on('r-gdata', type=('build', 'run')) depends_on('r-catools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-grbase/package.py b/var/spack/repos/builtin/packages/r-grbase/package.py index e1f00f410c..cb057aef3c 100644 --- a/var/spack/repos/builtin/packages/r-grbase/package.py +++ b/var/spack/repos/builtin/packages/r-grbase/package.py @@ -10,8 +10,8 @@ class RGrbase(RPackage): """gRbase: A Package for Graphical Modelling in R""" homepage = "http://people.math.aau.dk/~sorenh/software/gR/" - url = "https://cran.r-project.org/src/contrib/gRbase_1.8-3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gRbase" + url = "https://cloud.r-project.org/src/contrib/gRbase_1.8-3.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gRbase" version('1.8-3.4', sha256='d35f94c2fb7cbd4ce3991570424dfe6723a849658da32e13df29f53b6ea2cc2c') diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py index 6c2acf087d..38d7b684a2 100644 --- a/var/spack/repos/builtin/packages/r-gridbase/package.py +++ b/var/spack/repos/builtin/packages/r-gridbase/package.py @@ -9,8 +9,10 @@ from spack import * class RGridbase(RPackage): """Integration of base and grid graphics.""" - homepage = "https://cran.r-project.org/web/packages/gridBase/index.html" - url = "https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gridBase" + homepage = "https://cloud.r-project.org/package=gridBase" + url = "https://cloud.r-project.org/src/contrib/gridBase_0.4-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gridBase" version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f') + + depends_on('r@2.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py index 8486e2c23d..3f26f2ef56 100644 --- a/var/spack/repos/builtin/packages/r-gridextra/package.py +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -10,9 +10,9 @@ class RGridextra(RPackage): """Provides a number of user-level functions to work with "grid" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.""" - homepage = "https://cran.r-project.org/package=gridExtra" - url = "https://cran.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gridExtras" + homepage = "https://cloud.r-project.org/package=gridExtra" + url = "https://cloud.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gridExtras" version('2.3', '01e0ea88610756a0fd3b260e83c9bd43') version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2') diff --git a/var/spack/repos/builtin/packages/r-gsa/package.py b/var/spack/repos/builtin/packages/r-gsa/package.py new file mode 100644 index 0000000000..aa27d7a228 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gsa/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RGsa(RPackage): + """Gene Set Analysis.""" + + homepage = "http://www-stat.stanford.edu/~tibs/GSA" + url = "https://cloud.r-project.org/src/contrib/GSA_1.03.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/GSA" + + version('1.03.1', sha256='e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917') diff --git a/var/spack/repos/builtin/packages/r-gss/package.py b/var/spack/repos/builtin/packages/r-gss/package.py index 26018c242e..0c652099fc 100644 --- a/var/spack/repos/builtin/packages/r-gss/package.py +++ b/var/spack/repos/builtin/packages/r-gss/package.py @@ -10,8 +10,11 @@ class RGss(RPackage): """A comprehensive package for structural multivariate function estimation using smoothing splines.""" - homepage = "https://cran.r-project.org/package=gss" - url = "https://cran.rstudio.com/src/contrib/gss_2.1-7.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/gss" + homepage = "https://cloud.r-project.org/package=gss" + url = "https://cloud.r-project.org/src/contrib/gss_2.1-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gss" + version('2.1-10', sha256='26c47ecae6a9b7854a1b531c09f869cf8b813462bd8093e3618e1091ace61ee2') version('2.1-7', '4a6bd96339d22b40c932895b64504fb2') + + depends_on('r@2.14.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gsubfn/package.py b/var/spack/repos/builtin/packages/r-gsubfn/package.py index 1a7ecb919f..b5c9d95eff 100644 --- a/var/spack/repos/builtin/packages/r-gsubfn/package.py +++ b/var/spack/repos/builtin/packages/r-gsubfn/package.py @@ -21,10 +21,11 @@ class RGsubfn(RPackage): sql calls that may involve strings where substitution is desirable.""" - homepage = "https://cran.r-project.org/package=gsubfn" - url = "https://cran.r-project.org/src/contrib/gsubfn_0.6-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gsubfn" + homepage = "https://cloud.r-project.org/package=gsubfn" + url = "https://cloud.r-project.org/src/contrib/gsubfn_0.6-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gsubfn" + version('0.7', sha256='89351df9e65722d2862f26a0a3985666de3c86e8400808ced8a6eb6e165a4602') version('0.6-6', '94195ff3502706c736d9c593c07252bc') depends_on('r-proto', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py index fec5fdbb75..6df80edc58 100644 --- a/var/spack/repos/builtin/packages/r-gtable/package.py +++ b/var/spack/repos/builtin/packages/r-gtable/package.py @@ -9,8 +9,11 @@ from spack import * class RGtable(RPackage): """Tools to make it easier to work with "tables" of 'grobs'.""" - homepage = "https://cran.r-project.org/web/packages/gtable/index.html" - url = "https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gtable" + homepage = "https://cloud.r-project.org/package=gtable" + url = "https://cloud.r-project.org/src/contrib/gtable_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gtable" + version('0.3.0', sha256='fd386cc4610b1cc7627dac34dba8367f7efe114b968503027fb2e1265c67d6d3') version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab') + + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py index 2103df512f..752dd44437 100644 --- a/var/spack/repos/builtin/packages/r-gtools/package.py +++ b/var/spack/repos/builtin/packages/r-gtools/package.py @@ -40,8 +40,9 @@ class RGtools(RPackage): """ - homepage = "https://cran.r-project.org/package=gtools" - url = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/gtools" + homepage = "https://cloud.r-project.org/package=gtools" + url = "https://cloud.r-project.org/src/contrib/gtools_3.5.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/gtools" + version('3.8.1', sha256='051484459bd8ad1b03425b8843d24f6828fea18f7357cfa1c192198cc3f4ba38') version('3.5.0', '45f8800c0336d35046641fbacc56bdbb') diff --git a/var/spack/repos/builtin/packages/r-gwmodel/package.py b/var/spack/repos/builtin/packages/r-gwmodel/package.py index dfbcaf9b89..08e1cb9c1b 100644 --- a/var/spack/repos/builtin/packages/r-gwmodel/package.py +++ b/var/spack/repos/builtin/packages/r-gwmodel/package.py @@ -10,9 +10,11 @@ class RGwmodel(RPackage): """GWmodel: Geographically-Weighted Models""" homepage = "http://gwr.nuim.ie/" - url = "https://cran.r-project.org/src/contrib/GWmodel_2.0-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/GWmodel" + url = "https://cloud.r-project.org/src/contrib/GWmodel_2.0-9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/GWmodel" + version('2.1-3', sha256='3e1a36fddf8e64f61d548067bb043216f8d12069d814a4cbf07a9cae0b310af6') + version('2.1-1', sha256='91241b4e26d423a54c7c6784ef5159759058a5dafdff18a1ea8451faf979d1f3') version('2.0-9', sha256='b479af2c19d4aec30f1883d00193d52e342c609c1badcb51cc0344e4404cffa7') depends_on('r@3.0.0:', type=('build', 'run')) @@ -24,3 +26,4 @@ class RGwmodel(RPackage): depends_on('r-spacetime', type=('build', 'run')) depends_on('r-spatialreg', type=('build', 'run')) depends_on('r-spdep', type=('build', 'run')) + depends_on('r-fnn', when='@2.1-1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-haven/package.py b/var/spack/repos/builtin/packages/r-haven/package.py index e825ac5f79..1ddb4e0bff 100644 --- a/var/spack/repos/builtin/packages/r-haven/package.py +++ b/var/spack/repos/builtin/packages/r-haven/package.py @@ -11,13 +11,18 @@ class RHaven(RPackage): library, <https://github.com/WizardMac/ReadStat>.""" homepage = "http://haven.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/haven_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/haven" + url = "https://cloud.r-project.org/src/contrib/haven_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/haven" + version('2.1.1', sha256='90bcb4e7f24960e7aa3e15c06b95cd897f08de149cec43fd8ba110b14526068a') + version('2.1.0', sha256='c0a1cf1b039549fb3ad833f9644ed3f142790236ad755d2ee7bd3d8109e3ae74') version('1.1.0', '8edd4b7683f8c36b5bb68582ac1b8733') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-readr', type=('build', 'run')) + depends_on('r@3.1:', when='@:2.1.0', type=('build', 'run')) + depends_on('r@3.2:', when='@2.1.1:', type=('build', 'run')) + depends_on('r-rcpp@0.11.4:', type=('build', 'run')) + depends_on('r-readr@0.1.0:', type=('build', 'run')) depends_on('r-hms', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) - depends_on('r-forcats', type=('build', 'run')) + depends_on('r-forcats@0.2.0:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-hdf5r/package.py b/var/spack/repos/builtin/packages/r-hdf5r/package.py new file mode 100644 index 0000000000..670d1acb63 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-hdf5r/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RHdf5r(RPackage): + """'HDF5' is a data model, library and file format for storing and managing + large amounts of data. This package provides a nearly feature complete, + object oriented wrapper for the 'HDF5' API + <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6 + classes. Additionally, functionality is added so that 'HDF5' objects behave + very similar to their corresponding R counterparts.""" + + homepage = "https://hhoeflin.github.io/hdf5r" + url = "https://cloud.r-project.org/src/contrib/hdf5r_1.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/hdf5r" + + version('1.2.0', sha256='58813e334fd3f9040038345a7186e5cb02090898883ac192477a76a5b8b4fe81') + + depends_on('r@3.2.2:', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-bit64', type=('build', 'run')) + depends_on('hdf5@1.8.13:') + + def configure_args(self): + if 'mpi' in self.spec: + args = [ + '--with-hdf5={0}/h5pcc'.format(self.spec['hdf5'].prefix.bin), + ] + else: + args = [ + '--with-hdf5={0}/h5cc'.format(self.spec['hdf5'].prefix.bin), + ] + return args diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py index 2f2a39554d..adfec4c76b 100644 --- a/var/spack/repos/builtin/packages/r-hexbin/package.py +++ b/var/spack/repos/builtin/packages/r-hexbin/package.py @@ -12,9 +12,12 @@ class RHexbin(RPackage): on grid graphics and formal (S4) classes and methods.""" homepage = "http://github.com/edzer/hexbin" - url = "https://cran.r-project.org/src/contrib/hexbin_1.27.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/hexbin" + url = "https://cloud.r-project.org/src/contrib/hexbin_1.27.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/hexbin" + version('1.27.3', sha256='7ea422a76542c2fc2840df601af1b7803aa96df4fee6d51dec456ac36940c191') + version('1.27.2', sha256='46d47b1efef75d6f126af686a4dd614228b60418b9a5bde9e9e5d11200a0ee52') version('1.27.1', '7590ed158f8a57a71901bf6ca26f81be') + depends_on('r@2.0.1:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py index 9824c1e55d..fb600dc567 100644 --- a/var/spack/repos/builtin/packages/r-highr/package.py +++ b/var/spack/repos/builtin/packages/r-highr/package.py @@ -13,7 +13,12 @@ class RHighr(RPackage): Andre Simon's highlight package.""" homepage = "https://github.com/yihui/highr" - url = "https://cran.r-project.org/src/contrib/highr_0.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/highr" + url = "https://cloud.r-project.org/src/contrib/highr_0.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/highr" + version('0.8', sha256='4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657') + version('0.7', sha256='cabba5b6f2ea82024a49c5ced5f1aa476f864bc52bc129038e319e4e26b6f3b7') version('0.6', 'bf47388c5f57dc61962362fb7e1d8b16') + + depends_on('r@3.0.2:', when='@:0.7', type=('build', 'run')) + depends_on('r@3.2.3:', when='@0.8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py index a7f4c5e4df..1ef0b1aa91 100644 --- a/var/spack/repos/builtin/packages/r-hmisc/package.py +++ b/var/spack/repos/builtin/packages/r-hmisc/package.py @@ -15,21 +15,27 @@ class RHmisc(RPackage): code, and recoding variables.""" homepage = "http://biostat.mc.vanderbilt.edu/Hmisc" - url = "https://cran.rstudio.com/src/contrib/Hmisc_4.1-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Hmisc" + url = "https://cloud.r-project.org/src/contrib/Hmisc_4.1-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Hmisc" + version('4.2-0', sha256='9e9614673288dd00295f250fa0bf96fc9e9fed692c69bf97691081c1a01411d9') version('4.1-1', 'd255611f2b108d3cc0212b8a98fef6e3') version('4.0-3', '7091924db1e473419d8116c3335f82da') depends_on('r-lattice', type=('build', 'run')) - depends_on('r-survival', type=('build', 'run')) + depends_on('r-survival@2.40-1:', type=('build', 'run')) depends_on('r-formula', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-ggplot2@2.2:', type=('build', 'run')) depends_on('r-latticeextra', type=('build', 'run')) depends_on('r-acepack', type=('build', 'run')) depends_on('r-gridextra', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-htmltable', type=('build', 'run')) + depends_on('r-htmltable@1.11.0:', type=('build', 'run')) depends_on('r-viridis', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) + depends_on('r-rpart', type=('build', 'run')) + depends_on('r-nnet', type=('build', 'run')) + depends_on('r-foreign', type=('build', 'run')) + depends_on('r-gtable', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hms/package.py b/var/spack/repos/builtin/packages/r-hms/package.py index 6e4b513799..b39d7f4ee5 100644 --- a/var/spack/repos/builtin/packages/r-hms/package.py +++ b/var/spack/repos/builtin/packages/r-hms/package.py @@ -10,8 +10,13 @@ class RHms(RPackage): """Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.""" - homepage = "https://cran.rstudio.com/web/packages/hms/index.html" - url = "https://cran.rstudio.com/src/contrib/hms_0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/hms" + homepage = "https://cloud.r-project.org/package=hms" + url = "https://cloud.r-project.org/src/contrib/hms_0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/hms" + version('0.5.0', sha256='a87872665c3bf3901f597d78c152e7805f7129e4dbe27397051de4cf1a76561b') version('0.3', '92c4a0cf0c402a35145b5bb57212873e') + + depends_on('r-pkgconfig', when='@0.5.0:', type=('build', 'run')) + depends_on('r-rlang', when='@0.5.0:', type=('build', 'run')) + depends_on('r-vctrs@0.2.0:', when='@0.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hoardr/package.py b/var/spack/repos/builtin/packages/r-hoardr/package.py index 2e00826bbe..cbc9806c3e 100644 --- a/var/spack/repos/builtin/packages/r-hoardr/package.py +++ b/var/spack/repos/builtin/packages/r-hoardr/package.py @@ -9,16 +9,12 @@ from spack import * class RHoardr(RPackage): """hoardr: Manage Cached Files""" - homepage = "https://cran.r-project.org/package=hoardr" - url = "https://cran.r-project.org/src/contrib/hoardr_0.5.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/hoardr/" + homepage = "https://cloud.r-project.org/package=hoardr" + url = "https://cloud.r-project.org/src/contrib/hoardr_0.5.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/hoardr/" version('0.5.2', sha256='819113f0e25da105f120a676b5173872a4144f2f6f354cad14b35f898e76dc54') depends_on('r-r6@2.2.0:', type=('build', 'run')) depends_on('r-rappdirs@0.3.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-roxygen2@6.0.1:', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-rmarkdown', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-htmltable/package.py b/var/spack/repos/builtin/packages/r-htmltable/package.py index 09c77875bb..8693a8d8cc 100644 --- a/var/spack/repos/builtin/packages/r-htmltable/package.py +++ b/var/spack/repos/builtin/packages/r-htmltable/package.py @@ -15,10 +15,11 @@ class RHtmltable(RPackage): few text formatting functions that help outputting text compatible with HTML/'LaTeX'.""" - homepage = "https://CRAN.R-project.org/package=htmlTable" - url = "https://cran.rstudio.com/src/contrib/htmlTable_1.11.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/htmlTable" + homepage = "https://cloud.r-project.org/package=htmlTable" + url = "https://cloud.r-project.org/src/contrib/htmlTable_1.11.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/htmlTable" + version('1.13.1', sha256='689f32b65da6a57ad500e8d9ef3309d346401dca277c6b264a46c8d7c75884d0') version('1.11.2', '473e6d486e7714f8dd7f16a31480c896') version('1.9', '08c62c19e1ffe570e7d8fa57db5094b9') @@ -27,4 +28,5 @@ class RHtmltable(RPackage): depends_on('r-magrittr@1.5:', type=('build', 'run')) depends_on('r-checkmate', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r-htmltools', type=('build', 'run'), when="@1.11.0:") depends_on('r-rstudioapi@0.6:', type=('build', 'run'), when="@1.11.0:") diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py index 0f23d8df4e..866f20fe56 100644 --- a/var/spack/repos/builtin/packages/r-htmltools/package.py +++ b/var/spack/repos/builtin/packages/r-htmltools/package.py @@ -10,11 +10,12 @@ class RHtmltools(RPackage): """Tools for HTML generation and output.""" homepage = "https://github.com/rstudio/htmltools" - url = "https://cran.rstudio.com/src/contrib/htmltools_0.3.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/htmltools" + url = "https://cloud.r-project.org/src/contrib/htmltools_0.3.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/htmltools" version('0.3.6', '336419c2143f958862e01ef1bbc9c253') version('0.3.5', '5f001aff4a39e329f7342dcec5139724') + depends_on('r@2.14.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py index f6a42ac733..aed9faa579 100644 --- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py +++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py @@ -11,14 +11,15 @@ class RHtmlwidgets(RPackage): including the R console, 'R Markdown' documents, and 'Shiny' web applications.""" - homepage = "https://cran.r-project.org/package=htmlTable" - url = "https://cran.rstudio.com/src/contrib/htmlwidgets_0.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/htmlwidgets" + homepage = "https://cloud.r-project.org/package=htmlwidgets" + url = "https://cloud.r-project.org/src/contrib/htmlwidgets_0.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/htmlwidgets" + version('1.3', sha256='f1e4ffabc29e6cfe857f627da095be3cfcbe0e1f02ae75e572f10b4a026c5a12') version('0.9', 'b42730691eca8fc9a28903c272d11605') version('0.8', '06b0404a00e25736946607a36ee5351d') version('0.6', '7fa522d2eda97593978021bda9670c0e') - depends_on('r-htmltools', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-htmltools@0.3:', type=('build', 'run')) + depends_on('r-jsonlite@0.9.16:', type=('build', 'run')) depends_on('r-yaml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-httpcode/package.py b/var/spack/repos/builtin/packages/r-httpcode/package.py index edbed0d232..ffd772eee7 100644 --- a/var/spack/repos/builtin/packages/r-httpcode/package.py +++ b/var/spack/repos/builtin/packages/r-httpcode/package.py @@ -10,7 +10,7 @@ class RHttpcode(RPackage): """httpcode: 'HTTP' Status Code Helper""" homepage = "https://github.com/sckott/httpcode" - url = "https://cran.r-project.org/src/contrib/httpcode_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/httpcode" + url = "https://cloud.r-project.org/src/contrib/httpcode_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/httpcode" version('0.2.0', sha256='fbc1853db742a2cc1df11285cf27ce2ea43bc0ba5f7d393ee96c7e0ee328681a') diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py index ea9461773e..9bc6326d95 100644 --- a/var/spack/repos/builtin/packages/r-httpuv/package.py +++ b/var/spack/repos/builtin/packages/r-httpuv/package.py @@ -16,12 +16,16 @@ class RHttpuv(RPackage): information.)""" homepage = "https://github.com/rstudio/httpuv" - url = "https://cran.rstudio.com/src/contrib/httpuv_1.3.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/httpuv" + url = "https://cloud.r-project.org/src/contrib/httpuv_1.3.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/httpuv" + version('1.5.1', sha256='b5bb6b3b2f1a6d792568a70f3f357d6b3a35a5e26dd0c668c61a31f2ae8f5710') version('1.3.5', '48d894ff0067148f41a651634fbb2012') version('1.3.3', 'c78ae068cf59e949b9791be987bb4489') - depends_on('r@2.15.1:') - + depends_on('r@2.15.1:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-r6', when='@1.5.0:', type=('build', 'run')) + depends_on('r-promises', when='@1.5.0:', type=('build', 'run')) + depends_on('r-later@0.8.0:', when='@1.5.0:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py index e1ba98698e..7f79836f9a 100644 --- a/var/spack/repos/builtin/packages/r-httr/package.py +++ b/var/spack/repos/builtin/packages/r-httr/package.py @@ -12,17 +12,20 @@ class RHttr(RPackage): request components (authenticate(), add_headers() and so on).""" homepage = "https://github.com/hadley/httr" - url = "https://cran.r-project.org/src/contrib/httr_1.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/httr" + url = "https://cloud.r-project.org/src/contrib/httr_1.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/httr" + version('1.4.1', sha256='675c7e07bbe82c48284ee1ab929bb14a6e653abae2860d854dc41a3c028de156') + version('1.4.0', sha256='d633f1425da514f65f3b8c034ae0a8b6911995009840c6bb9657ceedb99ddb48') version('1.3.1', '5acfb6b2a6f2f26cd6dfad0458fe3351') version('1.2.1', 'c469948dedac9ab3926f23cf484b33d9') version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600') - depends_on('r@3.0.0:') - + depends_on('r@3.0.0:', when='@:1.3.1', type=('build', 'run')) + depends_on('r@3.1:', when='@1.4.0', type=('build', 'run')) + depends_on('r@3.2:', when='@1.4.1:', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-mime', type=('build', 'run')) - depends_on('r-curl@0.9.1:', type=('build', 'run')) - depends_on('r-openssl', type=('build', 'run')) + depends_on('r-curl@3.0.0:', type=('build', 'run')) + depends_on('r-openssl@0.8:', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-hwriter/package.py b/var/spack/repos/builtin/packages/r-hwriter/package.py index 9fa89f91d6..de980bb2d5 100644 --- a/var/spack/repos/builtin/packages/r-hwriter/package.py +++ b/var/spack/repos/builtin/packages/r-hwriter/package.py @@ -10,7 +10,10 @@ class RHwriter(RPackage): """Easy-to-use and versatile functions to output R objects in HTML format.""" - homepage = "https://cran.rstudio.com/web/packages/hwriter/index.html" - url = "https://cran.rstudio.com/src/contrib/hwriter_1.3.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/hwriter" + homepage = "https://cloud.r-project.org/package=hwriter" + url = "https://cloud.r-project.org/src/contrib/hwriter_1.3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/hwriter" + version('1.3.2', '9eef49df2eb68bbf3a16b5860d933517') + + depends_on('r@2.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ica/package.py b/var/spack/repos/builtin/packages/r-ica/package.py index ef882eb51e..aea4b44ead 100644 --- a/var/spack/repos/builtin/packages/r-ica/package.py +++ b/var/spack/repos/builtin/packages/r-ica/package.py @@ -11,10 +11,10 @@ class RIca(RPackage): Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).""" - homepage = "https://cran.r-project.org/web/packages/ica/index.html" - url = "https://cran.r-project.org/src/contrib/ica_1.0-1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ica" + homepage = "https://cloud.r-project.org/package=ica" + url = "https://cloud.r-project.org/src/contrib/ica_1.0-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ica" - depends_on('r@3.4.0:3.4.9') + version('1.0-2', sha256='e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179') version('1.0-1', '15c8d5afeec2804beec55dd14abc585d') version('1.0-0', '3ade2b3b00eb39c348d802f24d2afd1d') diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py index 69c1d161e1..2dbc16b173 100644 --- a/var/spack/repos/builtin/packages/r-igraph/package.py +++ b/var/spack/repos/builtin/packages/r-igraph/package.py @@ -12,15 +12,18 @@ class RIgraph(RPackage): graphs, graph visualization, centrality methods and much more.""" homepage = "http://igraph.org/" - url = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/igraph" + url = "https://cloud.r-project.org/src/contrib/igraph_1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/igraph" + version('1.2.4.1', sha256='891acc763b5a4a4a245358a95dee69280f4013c342f14dd6a438e7bb2bf2e480') + version('1.2.4', sha256='1048eb26ab6b592815bc269c1d91e974c86c9ab827ccb80ae0a40042019592cb') version('1.1.2', 'ca1617aea272852d2856c4661ad1c7d8') version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065') depends_on('r-matrix', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-pkgconfig', type=('build', 'run')) - depends_on('r-irlba', type=('build', 'run')) + depends_on('r-pkgconfig@2.0.0:', type=('build', 'run')) + depends_on('r-irlba', when='@:1.1.9', type=('build', 'run')) depends_on('gmp') depends_on('libxml2') + depends_on('glpk', when='@1.2.0:') diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py index b6f2c7eb62..5144761850 100644 --- a/var/spack/repos/builtin/packages/r-influencer/package.py +++ b/var/spack/repos/builtin/packages/r-influencer/package.py @@ -17,10 +17,11 @@ class RInfluencer(RPackage): configured.""" homepage = "https://github.com/rcc-uchicago/influenceR" - url = "https://cran.r-project.org/src/contrib/influenceR_0.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/influenceR" + url = "https://cloud.r-project.org/src/contrib/influenceR_0.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/influenceR" version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5') - depends_on('r-igraph', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-igraph@1.0.1:', type=('build', 'run')) + depends_on('r-matrix@1.1-4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ini/package.py b/var/spack/repos/builtin/packages/r-ini/package.py new file mode 100644 index 0000000000..67edc74e65 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ini/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RIni(RPackage): + """Parse simple '.ini' configuration files to an structured list. Users can + manipulate this resulting list with lapply() functions. This same + structured list can be used to write back to file after modifications.""" + + homepage = "https://github.com/dvdscripter/ini" + url = "https://cloud.r-project.org/src/contrib/ini_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ini" + + version('0.3.1', sha256='7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813') diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py index 88cb95a696..6083319dbd 100644 --- a/var/spack/repos/builtin/packages/r-inline/package.py +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -11,8 +11,11 @@ class RInline(RPackage): inlined C, C++ or Fortran code supporting .C and .Call calling conventions.""" - homepage = "https://cran.r-project.org/web/packages/inline/index.html" - url = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/inline" + homepage = "https://cloud.r-project.org/package=inline" + url = "https://cloud.r-project.org/src/contrib/inline_0.3.14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/inline" + version('0.3.15', sha256='ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68') version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca') + + depends_on('r@2.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-intervals/package.py b/var/spack/repos/builtin/packages/r-intervals/package.py index 3b384f772c..52ce3e8ccf 100644 --- a/var/spack/repos/builtin/packages/r-intervals/package.py +++ b/var/spack/repos/builtin/packages/r-intervals/package.py @@ -10,8 +10,8 @@ class RIntervals(RPackage): """intervals: Tools for Working with Points and Intervals""" homepage = "http://github.com/edzer/intervals" - url = "https://cran.r-project.org/src/contrib/intervals_0.15.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/intervals" + url = "https://cloud.r-project.org/src/contrib/intervals_0.15.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/intervals" version('0.15.1', sha256='9a8b3854300f2055e1492c71932cc808b02feac8c4d3dbf6cba1c7dbd09f4ae4') diff --git a/var/spack/repos/builtin/packages/r-inum/package.py b/var/spack/repos/builtin/packages/r-inum/package.py new file mode 100644 index 0000000000..7376f998ff --- /dev/null +++ b/var/spack/repos/builtin/packages/r-inum/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RInum(RPackage): + """Enum-type representation of vectors and representation of intervals, + including a method of coercing variables in data frames.""" + + homepage = "https://cloud.r-project.org/package=inum" + url = "https://cloud.r-project.org/src/contrib/inum_1.0-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/inum" + + version('1.0-1', sha256='3c2f94c13c03607e05817e4859595592068b55e810fed94e29bc181ad248a099') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-libcoin@1.0-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ipred/package.py b/var/spack/repos/builtin/packages/r-ipred/package.py index edd42b5645..43d9153092 100644 --- a/var/spack/repos/builtin/packages/r-ipred/package.py +++ b/var/spack/repos/builtin/packages/r-ipred/package.py @@ -11,14 +11,15 @@ class RIpred(RPackage): classification, regression and survival problems as well as resampling based estimators of prediction error.""" - homepage = "https://cran.r-project.org/package=ipred" - url = "https://cran.r-project.org/src/contrib/ipred_0.9-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ipred" + homepage = "https://cloud.r-project.org/package=ipred" + url = "https://cloud.r-project.org/src/contrib/ipred_0.9-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ipred" + version('0.9-9', sha256='0da87a70730d5a60b97e46b2421088765e7d6a7cc2695757eba0f9d31d86416f') + version('0.9-8', sha256='9c1d11c3cb0d72be7870e70a216e589e403bbfee38c796fe75cd0611d878ac07') version('0.9-5', 'ce8768547a7aa9554ad3650b18ea3cbd') - depends_on('r@2.10:') - + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-rpart@3.1-8:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py index f908fff778..c246abbae0 100644 --- a/var/spack/repos/builtin/packages/r-irdisplay/package.py +++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py @@ -13,8 +13,11 @@ class RIrdisplay(RPackage): session""" homepage = "https://irkernel.github.io" - url = "https://cran.rstudio.com/src/contrib/IRdisplay_0.4.4.tar.gz" + url = "https://cloud.r-project.org/src/contrib/IRdisplay_0.4.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/IRdisplay" + version('0.7.0', sha256='91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089') version('0.4.4', '5be672fb82185b90f23bd99ac1e1cdb6') + depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-repr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py index 466e75ee45..46a5d712dc 100644 --- a/var/spack/repos/builtin/packages/r-irlba/package.py +++ b/var/spack/repos/builtin/packages/r-irlba/package.py @@ -11,10 +11,12 @@ class RIrlba(RPackage): decompositions and principal component analysis of large sparse or dense matrices.""" - homepage = "https://cran.r-project.org/web/packages/irlba/index.html" - url = "https://cran.r-project.org/src/contrib/irlba_2.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/irlba" + homepage = "https://cloud.r-project.org/package=irlba" + url = "https://cloud.r-project.org/src/contrib/irlba_2.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/irlba" + version('2.3.3', sha256='6ee233697bcd579813bd0af5e1f4e6dd1eea971e8919c748408130d970fef5c0') + version('2.3.2', sha256='3fdf2d8fefa6ab14cd0992740de7958f9f501c71aca93229f5eb03c54558fc38') version('2.1.2', '290940abf6662ed10c0c5a8db1bc6e88') version('2.0.0', '557674cf8b68fea5b9f231058c324d26') diff --git a/var/spack/repos/builtin/packages/r-isdparser/package.py b/var/spack/repos/builtin/packages/r-isdparser/package.py index 83e9d92a84..bb5e038d04 100644 --- a/var/spack/repos/builtin/packages/r-isdparser/package.py +++ b/var/spack/repos/builtin/packages/r-isdparser/package.py @@ -10,8 +10,8 @@ class RIsdparser(RPackage): """isdparser: Parse 'NOAA' Integrated Surface Data Files""" homepage = "https://github.com/ropensci/isdparser" - url = "https://cran.r-project.org/src/contrib/isdparser_0.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/isdparser" + url = "https://cloud.r-project.org/src/contrib/isdparser_0.3.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/isdparser" version('0.3.0', sha256='6c9e1d7f3661802838010d659d7c77b964423dcc9a6623402df1fe3be627b7b9') diff --git a/var/spack/repos/builtin/packages/r-iso/package.py b/var/spack/repos/builtin/packages/r-iso/package.py index 4bbca3b0b6..9640af6cbf 100644 --- a/var/spack/repos/builtin/packages/r-iso/package.py +++ b/var/spack/repos/builtin/packages/r-iso/package.py @@ -10,8 +10,11 @@ class RIso(RPackage): """Linear order and unimodal order (univariate) isotonic regression; bivariate isotonic regression with linear order on both variables.""" - homepage = "https://cran.r-project.org/package=Iso" - url = "https://cran.rstudio.com/src/contrib/Iso_0.0-17.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/Iso" + homepage = "https://cloud.r-project.org/package=Iso" + url = "https://cloud.r-project.org/src/contrib/Iso_0.0-17.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Iso" + version('0.0-18', sha256='2d7e8c4452653364ee086d95cea620c50378e30acfcff129b7261e1756a99504') version('0.0-17', 'bf99821efb6a44fa75fdbf5e5c4c91e4') + + depends_on('r@1.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py index 397ba24644..da880c792f 100644 --- a/var/spack/repos/builtin/packages/r-iterators/package.py +++ b/var/spack/repos/builtin/packages/r-iterators/package.py @@ -10,8 +10,12 @@ class RIterators(RPackage): """Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.""" - homepage = "https://cran.r-project.org/web/packages/iterators/index.html" - url = "https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/iterators" + homepage = "https://cloud.r-project.org/package=iterators" + url = "https://cloud.r-project.org/src/contrib/iterators_1.0.8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/iterators" + version('1.0.12', sha256='96bf31d60ebd23aefae105d9b7790715e63327eec0deb2ddfb3d543994ea9f4b') + version('1.0.9', sha256='de001e063805fdd124953b571ccb0ed2838c55e40cca2e9d283d8a90b0645e9b') version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee') + + depends_on('r@2.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-janitor/package.py b/var/spack/repos/builtin/packages/r-janitor/package.py index a48d57f851..a754eb61ee 100644 --- a/var/spack/repos/builtin/packages/r-janitor/package.py +++ b/var/spack/repos/builtin/packages/r-janitor/package.py @@ -20,11 +20,17 @@ class RJanitor(RPackage): for the fun stuff.""" homepage = "https://github.com/sfirke/janitor" - url = "https://cran.r-project.org/src/contrib/janitor_0.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/janitor" + url = "https://cloud.r-project.org/src/contrib/janitor_0.3.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/janitor" + version('1.2.0', sha256='5e15a2292c65c5ddd6160289dec2604b05a813651a2be0d7854ace4548a32b8c') + version('1.1.1', sha256='404b41f56e571fab4c95ef62e79cb4f3bb34d5bb6e4ea737e748ff269536176b') version('0.3.0', '76036c54693b91aef19d468107ae066a') - depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-tidyr', type=('build', 'run')) + depends_on('r@3.1.2:', type=('build', 'run')) + depends_on('r-dplyr@0.7.0:', type=('build', 'run')) + depends_on('r-tidyr@0.7.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-snakecase@0.9.2:', when='@1.1.0:', type=('build', 'run')) + depends_on('r-purrr', when='@1.1.0:', type=('build', 'run')) + depends_on('r-rlang', when='@1.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jomo/package.py b/var/spack/repos/builtin/packages/r-jomo/package.py index 39eced1560..8fcbd881b2 100644 --- a/var/spack/repos/builtin/packages/r-jomo/package.py +++ b/var/spack/repos/builtin/packages/r-jomo/package.py @@ -15,11 +15,15 @@ class RJomo(RPackage): with the substantive model. """ - homepage = "https://cran.r-project.org/package=jomo" - url = "https://cran.r-project.org/src/contrib/jomo_2.6-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/jomo" + homepage = "https://cloud.r-project.org/package=jomo" + url = "https://cloud.r-project.org/src/contrib/jomo_2.6-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/jomo" + version('2.6-9', sha256='b90f47071e62b8863b00b1ae710a56ae6efbfe2baeb9963f8a91a10d6183cc9b') + version('2.6-7', sha256='6e83dab51103511038a3e9a3c762e00cc45ae7080c0a0f64e37bcea8c488db53') version('2.6-2', 'eff4a6c1a971708959d65b3224c98a25') depends_on('r-lme4', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) + depends_on('r-mass', when='@2.6-7:', type=('build', 'run')) + depends_on('r-ordinal', when='@2.6-7:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py index ca83414049..53b986d6d6 100644 --- a/var/spack/repos/builtin/packages/r-jpeg/package.py +++ b/var/spack/repos/builtin/packages/r-jpeg/package.py @@ -12,9 +12,10 @@ class RJpeg(RPackage): and in-memory raw vectors.""" homepage = "http://www.rforge.net/jpeg/" - url = "https://cran.r-project.org/src/contrib/jpeg_0.1-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/jpeg" + url = "https://cloud.r-project.org/src/contrib/jpeg_0.1-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/jpeg" version('0.1-8', '696007451d14395b1ed1d0e9af667a57') + depends_on('r@2.9.0:', type=('build', 'run')) depends_on('jpeg') diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index 81601f6dd6..6cbdf132a8 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -19,9 +19,10 @@ class RJsonlite(RPackage): use with dynamic data in systems and applications.""" homepage = "https://github.com/jeroenooms/jsonlite" - url = "https://cran.rstudio.com/src/contrib/jsonlite_1.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite" + url = "https://cloud.r-project.org/src/contrib/jsonlite_1.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/jsonlite" + version('1.6', sha256='88c5b425229966b7409145a6cabc72db9ed04f8c37ee95901af0146bb285db53') version('1.5', '2a81c261a702fccbbd5d2b32df108f76') version('1.2', '80cd2678ae77254be470f5931db71c51') version('1.0', 'c8524e086de22ab39b8ac8000220cc87') diff --git a/var/spack/repos/builtin/packages/r-kernlab/package.py b/var/spack/repos/builtin/packages/r-kernlab/package.py index 6c8694f3c8..3eedaac279 100644 --- a/var/spack/repos/builtin/packages/r-kernlab/package.py +++ b/var/spack/repos/builtin/packages/r-kernlab/package.py @@ -12,10 +12,12 @@ class RKernlab(RPackage): reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.""" - homepage = "https://cran.r-project.org/package=kernlab" - url = "https://cran.r-project.org/src/contrib/kernlab_0.9-25.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/kernlab" + homepage = "https://cloud.r-project.org/package=kernlab" + url = "https://cloud.r-project.org/src/contrib/kernlab_0.9-25.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/kernlab" + version('0.9-27', sha256='f6add50ed4097f04d09411491625f8d46eafc4f003b1c1cff78a6fff8cc31dd4') + version('0.9-26', sha256='954940478c6fcf60433e50e43cf10d70bcb0a809848ca8b9d683bf371cd56077') version('0.9-25', '1182a2a336a79fd2cf70b4bc5a35353f') - depends_on('r@2.10:') + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kernsmooth/package.py b/var/spack/repos/builtin/packages/r-kernsmooth/package.py index 8910c12247..d39ea1e4ff 100644 --- a/var/spack/repos/builtin/packages/r-kernsmooth/package.py +++ b/var/spack/repos/builtin/packages/r-kernsmooth/package.py @@ -9,10 +9,10 @@ from spack import * class RKernsmooth(RPackage): """Functions for kernel smoothing (and density estimation).""" - homepage = "https://cran.r-project.org/package=KernSmooth" - url = "https://cran.r-project.org/src/contrib/KernSmooth_2.23-15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/KernSmooth" + homepage = "https://cloud.r-project.org/package=KernSmooth" + url = "https://cloud.r-project.org/src/contrib/KernSmooth_2.23-15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/KernSmooth" version('2.23-15', '746cdf26dec72004cf19978e87dcc982') - depends_on('r@2.5.0:') + depends_on('r@2.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-kknn/package.py b/var/spack/repos/builtin/packages/r-kknn/package.py index 4729ce905f..c63bbf2d6a 100644 --- a/var/spack/repos/builtin/packages/r-kknn/package.py +++ b/var/spack/repos/builtin/packages/r-kknn/package.py @@ -10,13 +10,12 @@ class RKknn(RPackage): """Weighted k-Nearest Neighbors for Classification, Regression and Clustering.""" - homepage = "https://cran.r-project.org/package=kknn" - url = "https://cran.r-project.org/src/contrib/kknn_1.3.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/kknn" + homepage = "https://cloud.r-project.org/package=kknn" + url = "https://cloud.r-project.org/src/contrib/kknn_1.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/kknn" version('1.3.1', '372cd84f618cd5005f8c4c5721755117') - depends_on('r@2.10:') - + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-igraph@1.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py index f6fcb80398..90f3cbb334 100644 --- a/var/spack/repos/builtin/packages/r-knitr/package.py +++ b/var/spack/repos/builtin/packages/r-knitr/package.py @@ -11,18 +11,25 @@ class RKnitr(RPackage): """Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.""" - homepage = "https://cran.r-project.org/package=knitr" - url = "https://cran.rstudio.com/src/contrib/knitr_1.14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/knitr" + homepage = "https://cloud.r-project.org/package=knitr" + url = "https://cloud.r-project.org/src/contrib/knitr_1.14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/knitr" + version('1.24', sha256='e80c2043b445a7e576b62ae8510cce89322660fe388881d799a706d35cd27b89') + version('1.23', sha256='063bfb3300fc9f3e7d223c346e19b93beced0e6784470b9bef2524868a206a99') version('1.17', '4407ccf8f2a51629800d6d5243cf3e70') version('1.14', 'ef0fbeaa9372f99ffbc57212a7781511') version('0.6', 'c67d6db84cd55594a9e870c90651a3db') - depends_on('r-evaluate', type=('build', 'run')) - depends_on('r-digest', type=('build', 'run')) - depends_on('r-formatr', type=('build', 'run')) + depends_on('r@2.14.1:', when='@:1.9', type=('build', 'run')) + depends_on('r@3.0.2:', when='@1.10:1.14', type=('build', 'run')) + depends_on('r@3.1.0:', when='@1.15:1.22', type=('build', 'run')) + depends_on('r@3.2.3:', when='@1.23:', type=('build', 'run')) + depends_on('r-evaluate@0.10:', type=('build', 'run')) + depends_on('r-digest@:1.17', type=('build', 'run')) + depends_on('r-formatr@:1.14', type=('build', 'run')) depends_on('r-highr', type=('build', 'run')) - depends_on('r-stringr', type=('build', 'run')) + depends_on('r-stringr@0.6:', type=('build', 'run')) depends_on('r-markdown', type=('build', 'run')) - depends_on('r-yaml', type=('build', 'run')) + depends_on('r-yaml@2.1.19:', type=('build', 'run')) + depends_on('r-xfun', when='@1.23:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ks/package.py b/var/spack/repos/builtin/packages/r-ks/package.py index ceab1b8eb0..5ff34544a4 100644 --- a/var/spack/repos/builtin/packages/r-ks/package.py +++ b/var/spack/repos/builtin/packages/r-ks/package.py @@ -9,13 +9,15 @@ from spack import * class RKs(RPackage): """Kernel smoothers for univariate and multivariate data.""" - homepage = "https://cran.r-project.org/package=ks" - url = "https://cran.r-project.org/src/contrib/Archive/ks/ks_1.11.2.tar.gz" + homepage = "https://cloud.r-project.org/package=ks" + url = "https://cloud.r-project.org/src/contrib/ks_1.11.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ks" + version('1.11.5', sha256='4f65565376391b8a6dcce76168ef628fd4859dba8496910cbdd54e4f88e8d51b') + version('1.11.4', sha256='0beffaf8694819fba8c93af07a8782674a15fe00a04ad1d94d31238d0a41b134') version('1.11.2', sha256='9dfd485096e1e67abc7dfcb7b76a83de110dd15bcfeffe5c899605b3a5592961') depends_on('r@2.10:', type=('build', 'run')) - depends_on('r-fnn@1.1:', type=('build', 'run')) depends_on('r-kernlab', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py index 061d10272c..49b481f61c 100644 --- a/var/spack/repos/builtin/packages/r-labeling/package.py +++ b/var/spack/repos/builtin/packages/r-labeling/package.py @@ -9,8 +9,8 @@ from spack import * class RLabeling(RPackage): """Provides a range of axis labeling algorithms.""" - homepage = "https://cran.r-project.org/web/packages/labeling/index.html" - url = "https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/labeling" + homepage = "https://cloud.r-project.org/package=labeling" + url = "https://cloud.r-project.org/src/contrib/labeling_0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/labeling" version('0.3', 'ccd7082ec0b211aba8a89d85176bb534') diff --git a/var/spack/repos/builtin/packages/r-lambda-r/package.py b/var/spack/repos/builtin/packages/r-lambda-r/package.py index bbc6b81ad4..459ac5a341 100644 --- a/var/spack/repos/builtin/packages/r-lambda-r/package.py +++ b/var/spack/repos/builtin/packages/r-lambda-r/package.py @@ -11,8 +11,12 @@ class RLambdaR(RPackage): Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.""" - homepage = "https://cran.rstudio.com/web/packages/lambda.r/index.html" - url = "https://cran.rstudio.com/src/contrib/lambda.r_1.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/lambda.r" + homepage = "https://cloud.r-project.org/package=lambda.r" + url = "https://cloud.r-project.org/src/contrib/lambda.r_1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lambda.r" + version('1.2.3', sha256='0cd8e37ba1a0960888016a85d492da51a57df54bd65ff920b08c79a3bfbe8631') version('1.2', 'bda49898b85ad5902880a31f43b432e2') + + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-formatr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py index a07c84a32c..60bfe0ba76 100644 --- a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py +++ b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py @@ -12,7 +12,11 @@ class RLaplacesdemon(RPackage): describes the history of the package development process.""" homepage = "https://github.com/LaplacesDemonR/LaplacesDemon" - url = "https://cran.r-project.org/src/contrib/LaplacesDemon_16.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/LaplacesDemon" + url = "https://cloud.r-project.org/src/contrib/LaplacesDemon_16.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/LaplacesDemon" + version('16.1.1', sha256='779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77') + version('16.1.0', sha256='41d99261e8fc33c977b43ecf66ebed8ef1c84d9bd46b271609e9aadddc2ca8bb') version('16.0.1', '1e4dab2dd0e27251734d68b0bfdbe911') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lars/package.py b/var/spack/repos/builtin/packages/r-lars/package.py index 82fbc6fd79..e2595d3c3a 100644 --- a/var/spack/repos/builtin/packages/r-lars/package.py +++ b/var/spack/repos/builtin/packages/r-lars/package.py @@ -10,9 +10,9 @@ class RLars(RPackage): """Efficient procedures for fitting an entire lasso sequence with the cost of a single least squares fit.""" - homepage = "https://cran.r-project.org/web/packages/lars/index.html" - url = "https://cran.r-project.org/src/contrib/lars_1.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/lars" + homepage = "https://cloud.r-project.org/package=lars" + url = "https://cloud.r-project.org/src/contrib/lars_1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lars" version('1.2', '2571bae325f6cba1ad0202ea61695b8c') version('1.1', 'e94f6902aade09b13ec25ba2381384e5') diff --git a/var/spack/repos/builtin/packages/r-later/package.py b/var/spack/repos/builtin/packages/r-later/package.py new file mode 100644 index 0000000000..1a1f2fa679 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-later/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RLater(RPackage): + """Executes arbitrary R or C functions some time after the current time, + after the R execution stack has emptied.""" + + homepage = "https://github.com/r-lib/later" + url = "https://cloud.r-project.org/src/contrib/later_0.8.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/later" + + version('0.8.0', sha256='6b2a28b43c619b2c7890840c62145cd3a34a7ed65b31207fdedde52efb00e521') + + depends_on('r-rcpp@0.12.9:', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-bh', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py index 4c040d88e5..c47360d701 100644 --- a/var/spack/repos/builtin/packages/r-lattice/package.py +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -13,8 +13,11 @@ class RLattice(RPackage): handle most nonstandard requirements. See ?Lattice for an introduction.""" homepage = "http://lattice.r-forge.r-project.org/" - url = "https://cran.rstudio.com/src/contrib/lattice_0.20-35.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lattice" + url = "https://cloud.r-project.org/src/contrib/lattice_0.20-35.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lattice" + version('0.20-38', sha256='fdeb5e3e50dbbd9d3c5e2fa3eef865132b3eef30fbe53a10c24c7b7dfe5c0a2d') version('0.20-35', '07f1814623b3da6278ca61554ff7bfe6') version('0.20-34', 'c2a648b22d4206ae7526fb70b8e90fed') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-latticeextra/package.py b/var/spack/repos/builtin/packages/r-latticeextra/package.py index b82f7a9f25..7cf8b7da49 100644 --- a/var/spack/repos/builtin/packages/r-latticeextra/package.py +++ b/var/spack/repos/builtin/packages/r-latticeextra/package.py @@ -13,10 +13,11 @@ class RLatticeextra(RPackage): functions.""" homepage = "http://latticeextra.r-forge.r-project.org/" - url = "https://cran.rstudio.com/src/contrib/latticeExtra_0.6-28.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/latticeExtra" + url = "https://cloud.r-project.org/src/contrib/latticeExtra_0.6-28.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/latticeExtra" version('0.6-28', '771938f25d0983763369b48a1153b26c') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lava/package.py b/var/spack/repos/builtin/packages/r-lava/package.py index 01739d205f..b9daaf2e3a 100644 --- a/var/spack/repos/builtin/packages/r-lava/package.py +++ b/var/spack/repos/builtin/packages/r-lava/package.py @@ -9,13 +9,15 @@ from spack import * class RLava(RPackage): """Estimation and simulation of latent variable models.""" - homepage = "https://cran.r-project.org/package=lava" - url = "https://cran.r-project.org/src/contrib/lava_1.4.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lava" + homepage = "https://cloud.r-project.org/package=lava" + url = "https://cloud.r-project.org/src/contrib/lava_1.4.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lava" + version('1.6.6', sha256='7abc84dd99cce450a45ac4f232812cde3a322e432da3472f43b057fb5c59ca59') + version('1.6.4', sha256='41c6eeb96eaef9e1bfb04b31f7203e250a5ea7e7860be4d95f7f96f2a8644718') version('1.4.7', '28039248a7039ba9281d172e4dbf9543') - depends_on('r@3.0:') - + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-numderiv', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) + depends_on('r-squarem', when='@1.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py index ded81125a8..5650181c56 100644 --- a/var/spack/repos/builtin/packages/r-lazyeval/package.py +++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py @@ -11,8 +11,12 @@ class RLazyeval(RPackage): Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.""" - homepage = "https://cran.r-project.org/web/packages/lazyeval/index.html" - url = "https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lazyeval" + homepage = "https://cloud.r-project.org/package=lazyeval" + url = "https://cloud.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lazyeval" + version('0.2.2', sha256='d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4') + version('0.2.1', sha256='83b3a43e94c40fe7977e43eb607be0a3cd64c02800eae4f2774e7866d1e93f61') version('0.2.0', 'df1daac908dcf02ae7e12f4335b1b13b') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py index 4c88c49712..3a436e009a 100644 --- a/var/spack/repos/builtin/packages/r-leaflet/package.py +++ b/var/spack/repos/builtin/packages/r-leaflet/package.py @@ -12,12 +12,16 @@ class RLeaflet(RPackage): the R console, from 'RStudio', in Shiny apps and R Markdown documents.""" homepage = "http://rstudio.github.io/leaflet/" - url = "https://cran.r-project.org/src/contrib/leaflet_1.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/leaflet" + url = "https://cloud.r-project.org/src/contrib/leaflet_1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/leaflet" + version('2.0.2', sha256='fa448d20940e01e953e0706fc5064b0fa347e69fa967792599eb03c52b2e3114') + version('2.0.1', sha256='9876d5adf3235ea5683db79ec2435d3997c626774e8c4ec4ef14022e24dfcf06') version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) + depends_on('r-crosstalk', when='@2.0.0:', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) @@ -25,5 +29,6 @@ class RLeaflet(RPackage): depends_on('r-png', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) depends_on('r-raster', type=('build', 'run')) - depends_on('r-scales', type=('build', 'run')) + depends_on('r-scales@1.0.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) + depends_on('r-viridis@0.5.1:', when='@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-leaps/package.py b/var/spack/repos/builtin/packages/r-leaps/package.py index ae0e7f7909..b02ab2cfe4 100644 --- a/var/spack/repos/builtin/packages/r-leaps/package.py +++ b/var/spack/repos/builtin/packages/r-leaps/package.py @@ -9,8 +9,8 @@ from spack import * class RLeaps(RPackage): """leaps: Regression Subset Selection""" - homepage = "https://CRAN.R-project.org/package=leaps" - url = "https://cran.r-project.org/src/contrib/leaps_3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/leaps" + homepage = "https://cloud.r-project.org/package=leaps" + url = "https://cloud.r-project.org/src/contrib/leaps_3.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/leaps" version('3.0', '30823138890680e0493d1491c8f43edc') diff --git a/var/spack/repos/builtin/packages/r-learnbayes/package.py b/var/spack/repos/builtin/packages/r-learnbayes/package.py index 5a152d06ef..71644b853b 100644 --- a/var/spack/repos/builtin/packages/r-learnbayes/package.py +++ b/var/spack/repos/builtin/packages/r-learnbayes/package.py @@ -15,8 +15,9 @@ class RLearnbayes(RPackage): for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.""" - homepage = "https://CRAN.R-project.org/package=LearnBayes" - url = "https://cran.r-project.org/src/contrib/LearnBayes_2.15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/LearnBayes" + homepage = "https://cloud.r-project.org/package=LearnBayes" + url = "https://cloud.r-project.org/src/contrib/LearnBayes_2.15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/LearnBayes" + version('2.15.1', sha256='9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532') version('2.15', '213713664707bc79fd6d3a109555ef76') diff --git a/var/spack/repos/builtin/packages/r-leiden/package.py b/var/spack/repos/builtin/packages/r-leiden/package.py new file mode 100644 index 0000000000..3079ce3ba6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-leiden/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RLeiden(RPackage): + """Implements the 'Python leidenalg' module to be called in R. Enables + clustering using the leiden algorithm for partition a graph into + communities. See the 'Python' repository for more details: + <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain + to Leiden: guaranteeing well-connected communities. + <arXiv:1810.08473>.""" + + homepage = "https://github.com/TomKellyGenetics/leiden" + url = "https://cloud.r-project.org/src/contrib/leiden_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/leiden" + + version('0.3.1', sha256='17fa1e49667fdd30ef5166506181c8514ae406f68f0878a026ee111bff11f8a5') + + depends_on('r-reticulate', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lhs/package.py b/var/spack/repos/builtin/packages/r-lhs/package.py index a0b5a7f4df..da10bff658 100644 --- a/var/spack/repos/builtin/packages/r-lhs/package.py +++ b/var/spack/repos/builtin/packages/r-lhs/package.py @@ -11,7 +11,13 @@ class RLhs(RPackage): Samples.""" homepage = "http://lhs.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/lhs_0.16.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lhs" + url = "https://cloud.r-project.org/src/contrib/lhs_0.16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lhs" + version('1.0.1', sha256='a4d5ac0c6f585f2880364c867fa94e6554698beb65d3678ba5938dd84fc6ea53') + version('1.0', sha256='38c53482b360bdea89ddcfadf6d45476c80b99aee8902f97c5e97975903e2745') version('0.16', '088e593e5283414951e7e541a50ec2d1') + + depends_on('r@3.3.0:', when='@:0.16', type=('build', 'run')) + depends_on('r@3.4.0:', when='@1.0:', type=('build', 'run')) + depends_on('r-rcpp', when='@1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-libcoin/package.py b/var/spack/repos/builtin/packages/r-libcoin/package.py new file mode 100644 index 0000000000..69e70f4c8f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-libcoin/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RLibcoin(RPackage): + """Basic infrastructure for linear test statistics and permutation + inference in the framework of Strasser and Weber (1999) + <http://epub.wu.ac.at/102/>. This package must not be used by end-users. + CRAN package 'coin' implements all user interfaces and is ready to be used + by anyone.""" + + homepage = "https://cloud.r-project.org/package=libcoin" + url = "https://cloud.r-project.org/src/contrib/libcoin_1.0-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/libcoin" + + version('1.0-4', sha256='91dcbaa0ab8c2109aa54c3eda29ad0acd67c870efcda208e27acce9d641c09c5') + + depends_on('r@3.4.0:', type=('build', 'run')) + depends_on('r-mvtnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-listenv/package.py b/var/spack/repos/builtin/packages/r-listenv/package.py new file mode 100644 index 0000000000..ef931f2612 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-listenv/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RListenv(RPackage): + """List environments are environments that have list-like properties. For + instance, the elements of a list environment are ordered and can be + accessed and iterated over using index subsetting.""" + + homepage = "https://github.com/HenrikBengtsson/listenv" + url = "https://cloud.r-project.org/src/contrib/listenv_0.7.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/listenv" + + version('0.7.0', sha256='6126020b111870baea08b36afa82777cd578e88c17db5435cd137f11b3964555') + + depends_on('r@3.1.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py index 0f6d6bbb0b..64a021616c 100644 --- a/var/spack/repos/builtin/packages/r-lme4/package.py +++ b/var/spack/repos/builtin/packages/r-lme4/package.py @@ -13,16 +13,21 @@ class RLme4(RPackage): numerical linear algebra and 'RcppEigen' "glue".""" homepage = "https://github.com/lme4/lme4/" - url = "https://cran.r-project.org/src/contrib/lme4_1.1-12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lme4" + url = "https://cloud.r-project.org/src/contrib/lme4_1.1-12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lme4" + version('1.1-21', sha256='7f5554b69ff8ce9bac21e8842131ea940fb7a7dfa2de03684f236d3e3114b20c') + version('1.1-20', sha256='44f45f5cd20ec6a50bf96a939b1db44b1a180dbc871a5e3042baf7a107016b2c') version('1.1-12', 'da8aaebb67477ecb5631851c46207804') - depends_on('r-matrix', type=('build', 'run')) + depends_on('r@3.0.2:', when='@:1.1-15', type=('build', 'run')) + depends_on('r@3.2.0:', when='@1.1-16:', type=('build', 'run')) + depends_on('r-matrix@1.2-1:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) - depends_on('r-nlme', type=('build', 'run')) - depends_on('r-minqa', type=('build', 'run')) - depends_on('r-nloptr', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-nlme@3.1-123:', type=('build', 'run')) + depends_on('r-minqa@1.1.15:', type=('build', 'run')) + depends_on('r-nloptr@1.0.4:', type=('build', 'run')) + depends_on('r-rcpp@0.10.5:', type=('build', 'run')) depends_on('r-rcppeigen', type=('build', 'run')) + depends_on('r-boot', when='@1.1-21:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py index eebc165b3f..ad59ed29c7 100644 --- a/var/spack/repos/builtin/packages/r-lmtest/package.py +++ b/var/spack/repos/builtin/packages/r-lmtest/package.py @@ -11,10 +11,13 @@ class RLmtest(RPackage): in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.""" - homepage = "https://cran.r-project.org/package=lmtest" - url = "https://cran.r-project.org/src/contrib/lmtest_0.9-34.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lmtest" + homepage = "https://cloud.r-project.org/package=lmtest" + url = "https://cloud.r-project.org/src/contrib/lmtest_0.9-34.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lmtest" + version('0.9-37', sha256='ddc929f94bf055974832fa4a20fdd0c1eb3a84ee11f716c287936f2141d5ca0a') + version('0.9-36', sha256='be9f168d6554e9cd2be0f9d8fc3244f055dce90d1fca00f05bcbd01daa4ed56b') version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-locfit/package.py b/var/spack/repos/builtin/packages/r-locfit/package.py index 141b25fbea..ce7536500f 100644 --- a/var/spack/repos/builtin/packages/r-locfit/package.py +++ b/var/spack/repos/builtin/packages/r-locfit/package.py @@ -9,10 +9,11 @@ from spack import * class RLocfit(RPackage): """Local regression, likelihood and density estimation.""" - homepage = "https://cran.rstudio.com/web/packages/locfit/index.html" - url = "https://cran.rstudio.com/src/contrib/locfit_1.5-9.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/locfit" + homepage = "https://cloud.r-project.org/package=locfit" + url = "https://cloud.r-project.org/src/contrib/locfit_1.5-9.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/locfit" version('1.5-9.1', '38af7791c9cda78e2804020e65ac7fb4') + depends_on('r@2.0.1:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-log4r/package.py b/var/spack/repos/builtin/packages/r-log4r/package.py index 66ea6a38cd..82d73f3bf8 100644 --- a/var/spack/repos/builtin/packages/r-log4r/package.py +++ b/var/spack/repos/builtin/packages/r-log4r/package.py @@ -10,10 +10,9 @@ class RLog4r(RPackage): """logr4 provides an object-oriented logging system that uses an API roughly equivalent to log4j and its related variants.""" - homepage = "https://cran.r-project.org/package=log4r" - url = "https://cran.rstudio.com/src/contrib/log4r_0.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/log4r" + homepage = "https://cloud.r-project.org/package=log4r" + url = "https://cloud.r-project.org/src/contrib/log4r_0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/log4r" + version('0.3.0', sha256='8e5d0221298410e48bee9d9a983a23e1834ce88592f9d931471bfdb05f37a691') version('0.2', 'f3fcb7b1f48526c6543b2e00e278ff65') - - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-loo/package.py b/var/spack/repos/builtin/packages/r-loo/package.py index 6135d41ade..9a41eec8bc 100644 --- a/var/spack/repos/builtin/packages/r-loo/package.py +++ b/var/spack/repos/builtin/packages/r-loo/package.py @@ -11,11 +11,12 @@ class RLoo(RPackage): BayesianModels""" homepage = "https://mc-stan.org/loo" - url = "https://cran.r-project.org/src/contrib/loo_2.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/loo" + url = "https://cloud.r-project.org/src/contrib/loo_2.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/loo" version('2.1.0', sha256='1bf4a1ef85d151577ff96d4cf2a29c9ef24370b0b1eb08c70dcf45884350e87d') depends_on('r@3.1.2:', type=('build', 'run')) depends_on('r-checkmate', type=('build', 'run')) depends_on('r-matrixstats@0.52:', type=('build', 'run')) + depends_on('pandoc@1.12.3:') diff --git a/var/spack/repos/builtin/packages/r-lpsolve/package.py b/var/spack/repos/builtin/packages/r-lpsolve/package.py index ef132bc632..c118b4ebfc 100644 --- a/var/spack/repos/builtin/packages/r-lpsolve/package.py +++ b/var/spack/repos/builtin/packages/r-lpsolve/package.py @@ -14,8 +14,10 @@ class RLpsolve(RPackage): problems, and transportation problems. This version calls lp_solve""" - homepage = "https://cran.r-project.org/web/packages/lpSolve/index.html" - url = "https://cran.r-project.org/src/contrib/lpSolve_5.6.13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lpSolve" + homepage = "https://cloud.r-project.org/package=lpSolve" + url = "https://cloud.r-project.org/src/contrib/lpSolve_5.6.13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lpSolve" + version('5.6.13.2', sha256='75f0c0af5cbdc219ac29c792342ecd625903632ad86e581c408879958aa88539') + version('5.6.13.1', sha256='6ad8dc430f72a4698fc4a615bb5ecb73690b3c4520e84d9094af51a528f720b8') version('5.6.13', '8471654d9ae76e0f85ff3449433d4bc1') diff --git a/var/spack/repos/builtin/packages/r-lsei/package.py b/var/spack/repos/builtin/packages/r-lsei/package.py index 59e23c1e0e..e23f0e2033 100644 --- a/var/spack/repos/builtin/packages/r-lsei/package.py +++ b/var/spack/repos/builtin/packages/r-lsei/package.py @@ -15,8 +15,8 @@ class RLsei(RPackage): is public domain and available at <http://www.netlib.org/lawson-hanson>.""" - homepage = "https://cran.r-project.org/package=lsei" - url = "https://cran.rstudio.com/src/contrib/lsei_1.2-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lsei" + homepage = "https://cloud.r-project.org/package=lsei" + url = "https://cloud.r-project.org/src/contrib/lsei_1.2-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lsei" version('1.2-0', '18a9322d7a79ecb86b8788645c4b7e3c') diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py index 34466be118..675cdaf098 100644 --- a/var/spack/repos/builtin/packages/r-lubridate/package.py +++ b/var/spack/repos/builtin/packages/r-lubridate/package.py @@ -14,12 +14,15 @@ class RLubridate(RPackage): a consistent and memorable syntax that makes working with dates easy and fun.""" - homepage = "https://cran.r-project.org/web/packages/lubridate/index.html" - url = "https://cran.r-project.org/src/contrib/lubridate_1.7.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/lubridate" + homepage = "https://cloud.r-project.org/package=lubridate" + url = "https://cloud.r-project.org/src/contrib/lubridate_1.7.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/lubridate" + version('1.7.4', sha256='510ca87bd91631c395655ee5029b291e948b33df09e56f6be5839f43e3104891') + version('1.7.3', sha256='2cffbf54afce1d068e65241fb876a77b10ee907d5a19d2ffa84d5ba8a2c3f3df') version('1.7.1', '17dcb4c6a95189941bbdcffecf61b83b') version('1.5.6', 'a5dc44817548ee219d26a10bae92e611') - depends_on('r-rcpp@0.11:', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.13:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index d65fa443dc..c4a04edc8d 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -12,10 +12,13 @@ class RMagic(RPackage): functions for the manipulation and analysis of arbitrarily dimensioned arrays.""" - homepage = "https://cran.r-project.org/" - url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/magic" + homepage = "https://cloud.r-project.org/package=magic" + url = "https://cloud.r-project.org/src/contrib/magic_1.5-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/magic" + version('1.5-9', sha256='fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a') + version('1.5-8', sha256='7f8bc26e05003168e9d2dadf64eb9a34b51bc41beba482208874803dee7d6c20') version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-abind', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-magick/package.py b/var/spack/repos/builtin/packages/r-magick/package.py new file mode 100644 index 0000000000..66ae049615 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-magick/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RMagick(RPackage): + """Bindings to 'ImageMagick': the most comprehensive open-source image + processing library available. Supports many common formats (png, jpeg, + tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, + etc). All operations are vectorized via the Magick++ STL meaning they + operate either on a single frame or a series of frames for working with + layers, collages, or animation. In RStudio images are automatically + previewed when printed to the console, resulting in an interactive editing + environment. The latest version of the package includes a native graphics + device for creating in-memory graphics or drawing onto images using pixel + coordinates.""" + + homepage = "https://docs.ropensci.org/magick" + url = "https://cloud.r-project.org/src/contrib/magick_2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/magick" + + version('2.1', sha256='ef4fb8fc1c5a9cfcc36b22485a0e17d622f61e55803b1e7423fd15f0550de7df') + + depends_on('r-rcpp@0.12.12:', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-curl', type=('build', 'run')) + depends_on('image-magick') diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py index 2020a11689..5f9cda54b4 100644 --- a/var/spack/repos/builtin/packages/r-magrittr/package.py +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -13,8 +13,8 @@ class RMagrittr(RPackage): support for the type of right-hand side expressions. For more information, see package vignette.""" - homepage = "https://cran.r-project.org/web/packages/magrittr/index.html" - url = "https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/magrittr" + homepage = "https://cloud.r-project.org/package=magrittr" + url = "https://cloud.r-project.org/src/contrib/magrittr_1.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/magrittr" version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a') diff --git a/var/spack/repos/builtin/packages/r-maldiquant/package.py b/var/spack/repos/builtin/packages/r-maldiquant/package.py index 5e2ea009c1..6e596d92b1 100644 --- a/var/spack/repos/builtin/packages/r-maldiquant/package.py +++ b/var/spack/repos/builtin/packages/r-maldiquant/package.py @@ -17,11 +17,12 @@ class RMaldiquant(RPackage): replicated measurements as well as allowing spectra with different resolutions.""" - homepage = "https://cran.r-project.org/package=MALDIquant" - url = "https://cran.r-project.org/src/contrib/MALDIquant_1.16.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MALDIquant" + homepage = "https://cloud.r-project.org/package=MALDIquant" + url = "https://cloud.r-project.org/src/contrib/MALDIquant_1.16.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/MALDIquant" + version('1.19.3', sha256='a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c') + version('1.19.2', sha256='8c6efc4ae4f1af4770b079db29743049f2fd597bcdefeaeb16f623be43ddeb87') version('1.16.4', '83200e7496d05c5a99292e45d2b11c67') - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-manipulatewidget/package.py b/var/spack/repos/builtin/packages/r-manipulatewidget/package.py index fa589df09b..0f04db37d9 100644 --- a/var/spack/repos/builtin/packages/r-manipulatewidget/package.py +++ b/var/spack/repos/builtin/packages/r-manipulatewidget/package.py @@ -13,8 +13,8 @@ class RManipulatewidget(RPackage): chart created with package 'htmlwidgets'.""" homepage = "https://github.com/rte-antares-rpackage/manipulateWidget" - url = "https://cran.r-project.org/src/contrib/manipulateWidget_0.10.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/manipulateWidget/" + url = "https://cloud.r-project.org/src/contrib/manipulateWidget_0.10.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/manipulateWidget/" version('0.10.0', sha256='3d61a3d0cedf5c8a850a3e62ed6af38c600dc3f25b44c4ff07a5093bf9ca4ffd') diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py index 65206ca7bc..a30907c055 100644 --- a/var/spack/repos/builtin/packages/r-mapproj/package.py +++ b/var/spack/repos/builtin/packages/r-mapproj/package.py @@ -9,10 +9,13 @@ from spack import * class RMapproj(RPackage): """Converts latitude/longitude into projected coordinates.""" - homepage = "https://cran.r-project.org/package=mapproj" - url = "https://cran.r-project.org/src/contrib/mapproj_1.2-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mapproj" + homepage = "https://cloud.r-project.org/package=mapproj" + url = "https://cloud.r-project.org/src/contrib/mapproj_1.2-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mapproj" + version('1.2.6', sha256='62a5aa97837ae95ef9f973d95fe45fe43dbbf482dfa922e9df60f3c510e7efe5') + version('1.2-5', sha256='f3026a3a69a550c923b44c18b1ccc60d98e52670a438250d13f3c74cf2195f66') version('1.2-4', '10e22bde1c790e1540672f15ddcaee71') - depends_on('r-maps', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-maps@2.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py index 090fcfec37..4e98fbbff4 100644 --- a/var/spack/repos/builtin/packages/r-maps/package.py +++ b/var/spack/repos/builtin/packages/r-maps/package.py @@ -10,8 +10,12 @@ class RMaps(RPackage): """Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').""" - homepage = "https://cran.r-project.org/" - url = "https://cran.r-project.org/src/contrib/maps_3.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/maps" + homepage = "https://cloud.r-project.org/package=maps" + url = "https://cloud.r-project.org/src/contrib/maps_3.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/maps" + version('3.3.0', sha256='199afe19a4edcef966ae79ef802f5dcc15a022f9c357fcb8cae8925fe8bd2216') + version('3.2.0', sha256='437abeb4fa4ad4a36af6165d319634b89bfc6bf2b1827ca86c478d56d670e714') version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py index fd5e62a93a..131a57bf88 100644 --- a/var/spack/repos/builtin/packages/r-maptools/package.py +++ b/var/spack/repos/builtin/packages/r-maptools/package.py @@ -14,11 +14,14 @@ class RMaptools(RPackage): maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.""" homepage = "http://r-forge.r-project.org/projects/maptools/" - url = "https://cran.r-project.org/src/contrib/maptools_0.8-39.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/maptools" + url = "https://cloud.r-project.org/src/contrib/maptools_0.8-39.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/maptools" + version('0.9-5', sha256='5d9511f09fb49d57a51f28495b02239800596a4fcfad7b03ee1074d793657bdd') + version('0.9-4', sha256='930875f598a516f0f9049fa2fae7391bc9bdf7e3e5db696059ab4ec2fc9ba39c') version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836') - depends_on('r-sp', type=('build', 'run')) - depends_on('r-foreign', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-sp@1.0-11:', type=('build', 'run')) + depends_on('r-foreign@0.8:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py index 9629da7627..b90967ce5a 100644 --- a/var/spack/repos/builtin/packages/r-markdown/package.py +++ b/var/spack/repos/builtin/packages/r-markdown/package.py @@ -13,11 +13,16 @@ class RMarkdown(RPackage): http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.""" - homepage = "https://cran.r-project.org/package=markdown" - url = "https://cran.r-project.org/src/contrib/markdown_0.7.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/markdown" + homepage = "https://cloud.r-project.org/package=markdown" + url = "https://cloud.r-project.org/src/contrib/markdown_0.7.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/markdown" + version('1.1', sha256='8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b') + version('1.0', sha256='172d8072d1829644ee6cdf54282a55718e2cfe9c9915d3589ca5f9a016f8d9a6') + version('0.9', sha256='3068c6a41ca7a76cbedeb93b7371798f4d8437eea69a23c0ed5204c716d1bf23') version('0.8', '5dde829a865ad65bab37a2b9d243b071') version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff') - depends_on('r-mime', type=('build', 'run')) + depends_on('r@2.11.1:', type=('build', 'run')) + depends_on('r-mime@0.3:', type=('build', 'run')) + depends_on('r-xfun', when='@1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py index a5dd34ec2d..35356a6375 100644 --- a/var/spack/repos/builtin/packages/r-mass/package.py +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -10,9 +10,13 @@ class RMass(RPackage): """Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).""" - homepage = "https://cran.r-project.org/web/packages/MASS/index.html" - url = "https://cran.r-project.org/src/contrib/MASS_7.3-47.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MASS" + homepage = "https://cloud.r-project.org/package=MASS" + url = "https://cloud.r-project.org/src/contrib/MASS_7.3-47.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/MASS" + version('7.3-51.4', sha256='9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74') + version('7.3-51.3', sha256='5b0e0e7704d43a94b08dcc4b3fe600b9723d1b3e446dd393e82d39ddf66608b6') version('7.3-47', '2ef69aa9e25c0a445661a9877e117594') version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matr/package.py b/var/spack/repos/builtin/packages/r-matr/package.py index 5277fdb7c4..47e2f782a6 100644 --- a/var/spack/repos/builtin/packages/r-matr/package.py +++ b/var/spack/repos/builtin/packages/r-matr/package.py @@ -15,11 +15,12 @@ class RMatr(RPackage): environment for statistical computing.""" homepage = "https://github.com/MG-RAST/matR" - url = "https://cran.r-project.org/src/contrib/matR_0.9.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/matR/matR_0.9.tar.gz" + url = "https://cloud.r-project.org/src/contrib/matR_0.9.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/matR" version('0.9.1', sha256='554aeff37b27d0f17ddeb62b2e1004aa1f29190300e4946b1bec1d7c2bde82e3') version('0.9', 'e2be8734009f5c5b9c1f6b677a77220a') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mgraster', type=('build', 'run')) depends_on('r-biom-utils', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py index c39e209d0f..c624e1c89e 100644 --- a/var/spack/repos/builtin/packages/r-matrix/package.py +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -11,13 +11,16 @@ class RMatrix(RPackage): using 'LAPACK' and 'SuiteSparse'.""" homepage = "http://matrix.r-forge.r-project.org/" - url = "https://cran.rstudio.com/src/contrib/Matrix_1.2-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix" + url = "https://cloud.r-project.org/src/contrib/Matrix_1.2-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Matrix" + version('1.2-17', sha256='db43e6f0196fd5dfd05a7e88cac193877352c60d771d4ec8772763e645723fcc') version('1.2-14', 'b2babcf1515625196b75592c9b345bba') version('1.2-12', '0ade6e374716f08650cc8b8da99a313c') version('1.2-11', 'b7d2a639aa52228dfde7c3c3ee68b38e') version('1.2-8', '4a6406666bf97d3ec6b698eea5d9c0f5') version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') + depends_on('r@3.0.1:', when='@:1.2-12', type=('build', 'run')) + depends_on('r@3.2.0:', when='@1.2.13:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py index de276c8c90..ced334ea4f 100644 --- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py +++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py @@ -11,9 +11,10 @@ class RMatrixmodels(RPackage): prediction and response module classes.""" homepage = "http://matrix.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MatrixModels" + url = "https://cloud.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/MatrixModels" version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0') - depends_on('r-matrix', type=('build', 'run')) + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r-matrix@1.1-5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py index 5d098bbc48..5918f8b8a5 100644 --- a/var/spack/repos/builtin/packages/r-matrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py @@ -14,8 +14,11 @@ class RMatrixstats(RPackage): vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().""" - homepage = "https://cran.rstudio.com/web/packages/matrixStats/index.html" - url = "https://cran.rstudio.com/src/contrib/matrixStats_0.52.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/matrixStats" + homepage = "https://cloud.r-project.org/package=matrixStats" + url = "https://cloud.r-project.org/src/contrib/matrixStats_0.52.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/matrixStats" + version('0.54.0', sha256='8f0db4e181300a208b9aedbebfdf522a2626e6675d2662656efb8ba71b05a06f') version('0.52.2', '41b987d3ae96ee6895875c413adcba3c') + + depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mclust/package.py b/var/spack/repos/builtin/packages/r-mclust/package.py index 4b748d22d1..aca88d788f 100644 --- a/var/spack/repos/builtin/packages/r-mclust/package.py +++ b/var/spack/repos/builtin/packages/r-mclust/package.py @@ -11,9 +11,11 @@ class RMclust(RPackage): Classification, and Density Estimation""" homepage = "http://www.stat.washington.edu/mclust" - url = "https://cran.r-project.org/src/contrib/mclust_5.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mclust" + url = "https://cloud.r-project.org/src/contrib/mclust_5.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mclust" + version('5.4.5', sha256='75f2963082669485953e4306ffa93db98335ee6afdc1318b95d605d56cb30a72') + version('5.4.4', sha256='ccc31b0ad445e121a447b04988e73232a085c506fcc7ebdf11a3e0754aae3e0d') version('5.3', '74aac9fccdfc78373ce733c1a09176ef') - depends_on('r@3.0.0:') + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py index 79a93688eb..4c952a3271 100644 --- a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py +++ b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py @@ -9,10 +9,12 @@ from spack import * class RMcmcglmm(RPackage): """MCMC Generalised Linear Mixed Models.""" - homepage = "https://cran.r-project.org/web/packages/MCMCglmm/index.html" - url = "https://cran.r-project.org/src/contrib/MCMCglmm_2.25.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MCMCglmm" + homepage = "https://cloud.r-project.org/package=MCMCglmm" + url = "https://cloud.r-project.org/src/contrib/MCMCglmm_2.25.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/MCMCglmm" + version('2.29', sha256='13ba7837ea2049e892c04e7ec5c83d5b599a7e4820b9d875f55ec40fc2cc67b4') + version('2.28', sha256='7d92e6d35638e5e060a590b92c3b1bfc02a11386276a8ab99bceec5d797bfc2a') version('2.25', '260527ef6fecdd87f762fd07406d674a') depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mco/package.py b/var/spack/repos/builtin/packages/r-mco/package.py index 4769f3a879..a6cee70aa3 100644 --- a/var/spack/repos/builtin/packages/r-mco/package.py +++ b/var/spack/repos/builtin/packages/r-mco/package.py @@ -11,8 +11,10 @@ class RMco(RPackage): and related test problems""" homepage = "https://github.com/cran/mco" - url = "https://cran.r-project.org/src/contrib/mco_1.0-15.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mco" + url = "https://cloud.r-project.org/src/contrib/mco_1.0-15.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mco" version('1.0-15.1', '1768dea61d0561d71be2bbc6ac3dccfa') version('1.0-15', '0b444e085c59d919611224e86b5637f8') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mda/package.py b/var/spack/repos/builtin/packages/r-mda/package.py index fcdda3baa2..2568f2fc5b 100644 --- a/var/spack/repos/builtin/packages/r-mda/package.py +++ b/var/spack/repos/builtin/packages/r-mda/package.py @@ -10,12 +10,12 @@ class RMda(RPackage): """Mixture and flexible discriminant analysis, multivariate adaptive regression splines (MARS), BRUTO.""" - homepage = "https://cran.r-project.org/package=mda" - url = "https://cran.r-project.org/src/contrib/mda_0.4-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mda" + homepage = "https://cloud.r-project.org/package=mda" + url = "https://cloud.r-project.org/src/contrib/mda_0.4-9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mda" + version('0.4-10', sha256='7036bc622a8fea5b2de94fc19e6b64f5f0c27e5d743ae7646e116af08c9de6a5') version('0.4-9', '2ce1446c4a013e0ebcc1099a00269ad9') - depends_on('r@1.9.0:') - + depends_on('r@1.9.0:', type=('build', 'run')) depends_on('r-class', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py index ec039cc08f..627b4e1609 100644 --- a/var/spack/repos/builtin/packages/r-memoise/package.py +++ b/var/spack/repos/builtin/packages/r-memoise/package.py @@ -11,9 +11,9 @@ class RMemoise(RPackage): same arguments it returns the pre-computed value.""" homepage = "https://github.com/hadley/memoise" - url = "https://cran.rstudio.com/src/contrib/memoise_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/memoise" + url = "https://cloud.r-project.org/src/contrib/memoise_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/memoise" version('1.1.0', '493209ee04673f0fcab473c3dd80fb8c') version('1.0.0', 'd31145292e2a88ae9a504cab1602e4ac') - depends_on('r-digest', type=('build', 'run')) + depends_on('r-digest@0.6.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-metap/package.py b/var/spack/repos/builtin/packages/r-metap/package.py new file mode 100644 index 0000000000..2b9ee109a6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-metap/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RMetap(RPackage): + """The canonical way to perform meta-analysis involves using effect sizes. + When they are not available this package provides a number of methods for + meta-analysis of significance values including the methods of Edgington, + Fisher, Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets + to replicate published results; and a routine for graphical display.""" + + homepage = "http://www.dewey.myzen.co.uk/meta/meta.html" + url = "https://cloud.r-project.org/src/contrib/metap_1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/metap" + + version('1.1', sha256='20120428672d39dc15829c7e66850fc4350a34df290d48cef0b1cc78d13f7b82') + + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-rdpack', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py index 5938192ddb..c4e2d98b7a 100644 --- a/var/spack/repos/builtin/packages/r-mgcv/package.py +++ b/var/spack/repos/builtin/packages/r-mgcv/package.py @@ -12,10 +12,12 @@ class RMgcv(RPackage): function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.""" - homepage = "https://cran.r-project.org/package=mgcv" - url = "https://cran.r-project.org/src/contrib/mgcv_1.8-16.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv" + homepage = "https://cloud.r-project.org/package=mgcv" + url = "https://cloud.r-project.org/src/contrib/mgcv_1.8-16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mgcv" + version('1.8-28', sha256='b55ea8227cd5c263c266c3885fa3299aa6bd23b54186517f9299bf38a7bdd3ea') + version('1.8-27', sha256='c88b99fb518decd7e9cd17a4c267e74f98a78172f056784194b5b127ca0f7d1b') version('1.8-22', 'b42079b33b46de784f293a74c824b877') version('1.8-21', 'aae8262a07c8698ca8d6213065c4983f') version('1.8-20', '58eb94404aad7ff8a0cf11a2f098f8bf') @@ -25,5 +27,6 @@ class RMgcv(RPackage): version('1.8-16', '4c1d85e0f80b017bccb4b63395842911') version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984') - depends_on('r-nlme', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-nlme@3.1-64:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mgraster/package.py b/var/spack/repos/builtin/packages/r-mgraster/package.py index 25eba17c7d..9aa0023095 100644 --- a/var/spack/repos/builtin/packages/r-mgraster/package.py +++ b/var/spack/repos/builtin/packages/r-mgraster/package.py @@ -12,7 +12,8 @@ class RMgraster(RPackage): (DOE) Systems Biology Knowledge Base (KBase).""" homepage = "https://github.com/braithwaite/MGRASTer/" - url = "https://cran.r-project.org/src/contrib/MGRASTer_0.9.tar.gz" + url = "https://cloud.r-project.org/src/contrib/MGRASTer_0.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/MGRASTer" version('0.9', '902c7ad4180b858d6b6428ea26d7652a') diff --git a/var/spack/repos/builtin/packages/r-mice/package.py b/var/spack/repos/builtin/packages/r-mice/package.py index c785631bc1..daaefe5a9c 100644 --- a/var/spack/repos/builtin/packages/r-mice/package.py +++ b/var/spack/repos/builtin/packages/r-mice/package.py @@ -20,12 +20,15 @@ class RMice(RPackage): variables. Various diagnostic plots are available to inspect the quality of the imputations.""" - homepage = "https://cran.r-project.org/package=mice" - url = "https://cran.r-project.org/src/contrib/mice_3.0.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mice" + homepage = "https://cloud.r-project.org/package=mice" + url = "https://cloud.r-project.org/src/contrib/mice_3.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mice" + version('3.6.0', sha256='7bc72bdb631bc9f67d8f76ffb48a7bb275228d861075e20c24c09c736bebec5d') + version('3.5.0', sha256='4fccecdf9e8d8f9f63558597bfbbf054a873b2d0b0820ceefa7b6911066b9e45') version('3.0.0', 'fb54a29679536c474c756cca4538d7e3') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-broom', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index 41b42a18f7..8c99d8d720 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -11,8 +11,10 @@ class RMime(RPackage): from /etc/mime.types in UNIX-type systems.""" homepage = "https://github.com/yihui/mime" - url = "https://cran.r-project.org/src/contrib/mime_0.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mime" + url = "https://cloud.r-project.org/src/contrib/mime_0.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mime" + version('0.7', sha256='11083ee44c92569aadbb9baf60a2e079ab7a721c849b74d102694975cc8d778b') + version('0.6', sha256='4775b605ab0117406bee7953c8af59eea8b35e67d1bd63f4007686a7097fc401') version('0.5', '87e00b6d57b581465c19ae869a723c4d') version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') diff --git a/var/spack/repos/builtin/packages/r-miniui/package.py b/var/spack/repos/builtin/packages/r-miniui/package.py index 1dc54ed86c..5b7de8ba85 100644 --- a/var/spack/repos/builtin/packages/r-miniui/package.py +++ b/var/spack/repos/builtin/packages/r-miniui/package.py @@ -10,11 +10,11 @@ class RMiniui(RPackage): """Provides UI widget and layout functions for writing Shiny apps that work well on small screens.""" - homepage = "https://cran.r-project.org/package=miniUI" - url = "https://cran.r-project.org/src/contrib/miniUI_0.1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/miniUI/" + homepage = "https://cloud.r-project.org/package=miniUI" + url = "https://cloud.r-project.org/src/contrib/miniUI_0.1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/miniUI/" version('0.1.1.1', sha256='452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0') depends_on('r-shiny@0.13:', type=('build', 'run')) - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-htmltools@0.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py index bb54a7252a..f579dbdf57 100644 --- a/var/spack/repos/builtin/packages/r-minqa/package.py +++ b/var/spack/repos/builtin/packages/r-minqa/package.py @@ -11,9 +11,10 @@ class RMinqa(RPackage): interface to Fortran implementations by M. J. D. Powell.""" homepage = "http://optimizer.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/minqa_1.2.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/minqa" + url = "https://cloud.r-project.org/src/contrib/minqa_1.2.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/minqa" version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.9.10:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-misc3d/package.py b/var/spack/repos/builtin/packages/r-misc3d/package.py index e215a4fcb2..a4043961ae 100644 --- a/var/spack/repos/builtin/packages/r-misc3d/package.py +++ b/var/spack/repos/builtin/packages/r-misc3d/package.py @@ -9,8 +9,8 @@ from spack import * class RMisc3d(RPackage): """A collection of miscellaneous 3d plots, including isosurfaces.""" - homepage = "https://cran.r-project.org/web/packages/misc3d/index.html" - url = "https://cran.r-project.org/src/contrib/misc3d_0.8-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/misc3d" + homepage = "https://cloud.r-project.org/package=misc3d" + url = "https://cloud.r-project.org/src/contrib/misc3d_0.8-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/misc3d" version('0.8-4', 'aefa27e67a243c21a1046868540343fe') diff --git a/var/spack/repos/builtin/packages/r-mitml/package.py b/var/spack/repos/builtin/packages/r-mitml/package.py index 88e6784c4d..4980a9e157 100644 --- a/var/spack/repos/builtin/packages/r-mitml/package.py +++ b/var/spack/repos/builtin/packages/r-mitml/package.py @@ -12,9 +12,12 @@ class RMitml(RPackage): 'jomo', and several functions for visualization, data management and the analysis of multiply imputed data sets.""" - homepage = "https://cran.r-project.org/package=mitml" - url = "https://cran.r-project.org/src/contrib/mitml_0.3-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mitml" + homepage = "https://cloud.r-project.org/package=mitml" + url = "https://cloud.r-project.org/src/contrib/mitml_0.3-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mitml" + + version('0.3-7', sha256='c6f796d0059f1b093b599a89d955982fa257de9c45763ecc2cbbce10fdec1e7b') + version('0.3-6', sha256='bc59bdc802eb882340393752535446560c716f12c6fca2b95f03c6af30d978de') version('0.3-5', '6f8659c33696915bf510241287b2a34d') depends_on('r-pan', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mitools/package.py b/var/spack/repos/builtin/packages/r-mitools/package.py new file mode 100644 index 0000000000..45a9f80c6e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mitools/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RMitools(RPackage): + """Tools to perform analyses and combine results from multiple-imputation + datasets.""" + + homepage = "https://cloud.r-project.org/package=mitools" + url = "https://cloud.r-project.org/src/contrib/mitools_2.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mitools" + + version('2.4', sha256='f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30') + + depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mixtools/package.py b/var/spack/repos/builtin/packages/r-mixtools/package.py index 5b2f9d912e..f818006754 100644 --- a/var/spack/repos/builtin/packages/r-mixtools/package.py +++ b/var/spack/repos/builtin/packages/r-mixtools/package.py @@ -12,14 +12,14 @@ class RMixtools(RPackage): Analyzes finite mixture models for various parametric and semiparametric settings.""" - homepage = "https://cran.r-project.org/web/packages/mixtools/index.html" - url = "https://cran.r-project.org/src/contrib/mixtools_1.1.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/mixtools" + homepage = "https://cloud.r-project.org/package=mixtools" + url = "https://cloud.r-project.org/src/contrib/mixtools_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mixtools" version('1.1.0', 'c7d59110dd42964d40593a05b98acd5f') version('1.0.4', 'c0e6ec44d16ec8914797fb74a651d3e5') - depends_on('r@3.4.0:3.4.9') + depends_on('r@3.2:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-segmented', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlbench/package.py b/var/spack/repos/builtin/packages/r-mlbench/package.py index c0bebc0672..f861d6a547 100644 --- a/var/spack/repos/builtin/packages/r-mlbench/package.py +++ b/var/spack/repos/builtin/packages/r-mlbench/package.py @@ -10,12 +10,10 @@ class RMlbench(RPackage): """A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.""" - homepage = "https://cran.r-project.org/web/packages/mlbench/index.html" - url = "https://cran.r-project.org/src/contrib/mlbench_2.1-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mlbench" + homepage = "https://cloud.r-project.org/package=mlbench" + url = "https://cloud.r-project.org/src/contrib/mlbench_2.1-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mlbench" version('2.1-1', '9f06848b8e137b8a37417c92d8e57f3b') - depends_on('r@2.10:') - - depends_on('r-lattice', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlr/package.py b/var/spack/repos/builtin/packages/r-mlr/package.py index 6994ace5d0..34a8f8f1fd 100644 --- a/var/spack/repos/builtin/packages/r-mlr/package.py +++ b/var/spack/repos/builtin/packages/r-mlr/package.py @@ -19,12 +19,16 @@ class RMlr(RPackage): resampling. Most operations can be parallelized.""" homepage = "https://github.com/mlr-org/mlr/" - url = "https://cran.r-project.org/src/contrib/mlr_2.12.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mlr" + url = "https://cloud.r-project.org/src/contrib/mlr_2.12.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mlr" + version('2.15.0', sha256='a3c2c2bd65a87d90b5e5e877b1ef8e7712e76b4eb1660d3f69672a1860ca5324') + version('2.14.0', sha256='1f72184400678386c7c44297c4c92a448b50148de700df5ba0438d4e486e944a') + version('2.13', sha256='e8729be7acddc1ea124c44f9493a8b903c5f54b97e09c714366553aed733011d') version('2.12.1', 'abddfc9dfe95f290a233ecd97969a4ec') version('2.12', '94ee7495aeafb432c8af5a8bdd26c25f') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-paramhelpers@1.10:', type=('build', 'run')) depends_on('r-bbmisc@1.11:', type=('build', 'run')) depends_on('r-backports@1.1.0:', type=('build', 'run')) @@ -33,4 +37,5 @@ class RMlr(RPackage): depends_on('r-checkmate@1.8.2:', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) depends_on('r-parallelmap@1.3:', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mlrmbo/package.py b/var/spack/repos/builtin/packages/r-mlrmbo/package.py index fcde2d6d8b..3caeec50dc 100644 --- a/var/spack/repos/builtin/packages/r-mlrmbo/package.py +++ b/var/spack/repos/builtin/packages/r-mlrmbo/package.py @@ -22,9 +22,10 @@ class RMlrmbo(RPackage): use cases.""" homepage = "https://github.com/mlr-org/mlrMBO/" - url = "https://cran.r-project.org/src/contrib/mlrMBO_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mlrMBO" + url = "https://cloud.r-project.org/src/contrib/mlrMBO_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mlrMBO" + version('1.1.2', sha256='8e84caaa5d5d443d7019128f88ebb212fb095870b3a128697c9b64fe988f3efe') version('1.1.1', '9a35b41ceb8754111af294dee0ae76e0') version('1.1.0', '9e27ff8498225d24863b8da758d2918e') diff --git a/var/spack/repos/builtin/packages/r-mmwrweek/package.py b/var/spack/repos/builtin/packages/r-mmwrweek/package.py index 83799560ae..cb36d6e6fb 100644 --- a/var/spack/repos/builtin/packages/r-mmwrweek/package.py +++ b/var/spack/repos/builtin/packages/r-mmwrweek/package.py @@ -14,8 +14,8 @@ class RMmwrweek(RPackage): functionality to convert Dates to MMWR day, week, and year and the reverse.""" - homepage = "https://cran.r-project.org/package=MMWRweek" - url = "https://cran.r-project.org/src/contrib/MMWRweek_0.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/MMWRweek" + homepage = "https://cloud.r-project.org/package=MMWRweek" + url = "https://cloud.r-project.org/src/contrib/MMWRweek_0.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/MMWRweek" version('0.1.1', 'a1245025126f8a96c72be8f7b06b0499') diff --git a/var/spack/repos/builtin/packages/r-mnormt/package.py b/var/spack/repos/builtin/packages/r-mnormt/package.py index cdea6845c3..e322a43d12 100644 --- a/var/spack/repos/builtin/packages/r-mnormt/package.py +++ b/var/spack/repos/builtin/packages/r-mnormt/package.py @@ -15,7 +15,9 @@ class RMnormt(RPackage): of dimensions.""" homepage = "http://azzalini.stat.unipd.it/SW/Pkg-mnormt" - url = "https://cran.r-project.org/src/contrib/mnormt_1.5-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mnormt" + url = "https://cloud.r-project.org/src/contrib/mnormt_1.5-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mnormt" version('1.5-5', '19b5be2e9ed33b92d7a716bfcca6b2c7') + + depends_on('r@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-modelmetrics/package.py b/var/spack/repos/builtin/packages/r-modelmetrics/package.py index 106e90e330..47e925e4da 100644 --- a/var/spack/repos/builtin/packages/r-modelmetrics/package.py +++ b/var/spack/repos/builtin/packages/r-modelmetrics/package.py @@ -10,12 +10,14 @@ class RModelmetrics(RPackage): """Collection of metrics for evaluating models written in C++ using 'Rcpp'.""" - homepage = "https://cran.r-project.org/package=ModelMetrics" - url = "https://cran.r-project.org/src/contrib/ModelMetrics_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ModelMetrics" + homepage = "https://cloud.r-project.org/package=ModelMetrics" + url = "https://cloud.r-project.org/src/contrib/ModelMetrics_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ModelMetrics" + version('1.2.2', sha256='66d6fc75658287fdbae4d437b51d26781e138b8baa558345fb9e5a2df86a0d95') + version('1.2.0', sha256='3021ae88733695a35d66e279e8e61861431f14c9916a341f0a562f675cf6ede9') version('1.1.0', 'd43175001f0531b8810d2802d76b7b44') - depends_on('r@3.2.2:') - + depends_on('r@3.2.2:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-data-table', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-modelr/package.py b/var/spack/repos/builtin/packages/r-modelr/package.py index f693fd7b2e..b65d8ec323 100644 --- a/var/spack/repos/builtin/packages/r-modelr/package.py +++ b/var/spack/repos/builtin/packages/r-modelr/package.py @@ -11,15 +11,21 @@ class RModelr(RPackage): into a pipeline of data manipulation and visualisation.""" homepage = "https://github.com/hadley/modelr" - url = "https://cran.r-project.org/src/contrib/modelr_0.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/modelr" + url = "https://cloud.r-project.org/src/contrib/modelr_0.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/modelr" + version('0.1.5', sha256='45bbee387c6ba154f9f8642e9f03ea333cce0863c324ff15d23096f33f85ce5a') + version('0.1.4', sha256='b4da77c1244bbda512ce323751c8338741eeaa195283f172a0feec2917bcfdd9') + version('0.1.3', sha256='e536b247c17d6cacf10565dd8a1b744efc90a8815c70edd54371e413e6d1b423') version('0.1.1', 'ce5fd088fb7850228ab1e34d241a975d') + depends_on('r@3.1:', when='@:0.1.4', type=('build', 'run')) + depends_on('r@3.2:', when='@0.1.5:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-purrr', type=('build', 'run')) - depends_on('r-lazyeval', type=('build', 'run')) + depends_on('r-purrr@0.2.2:', type=('build', 'run')) + depends_on('r-lazyeval@0.2.0:', when='@:0.1.1', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-broom', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-tidyr', type=('build', 'run')) + depends_on('r-tidyr@0.8.0:', type=('build', 'run')) + depends_on('r-rlang@0.2.0:', when='@0.1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-modeltools/package.py b/var/spack/repos/builtin/packages/r-modeltools/package.py index bbcfc99671..16f2c63116 100644 --- a/var/spack/repos/builtin/packages/r-modeltools/package.py +++ b/var/spack/repos/builtin/packages/r-modeltools/package.py @@ -9,8 +9,9 @@ from spack import * class RModeltools(RPackage): """A collection of tools to deal with statistical models.""" - homepage = "https://cran.r-project.org/package=modeltools" - url = "https://cran.r-project.org/src/contrib/modeltools_0.2-21.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/modeltools" + homepage = "https://cloud.r-project.org/package=modeltools" + url = "https://cloud.r-project.org/src/contrib/modeltools_0.2-21.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/modeltools" + version('0.2-22', sha256='256a088fc80b0d9182f984f9bd3d6207fb7c1e743f72e2ecb480e6c1d4ac34e9') version('0.2-21', '3bf56b2e7bf78981444385d87eeccdd7') diff --git a/var/spack/repos/builtin/packages/r-mpm/package.py b/var/spack/repos/builtin/packages/r-mpm/package.py index ce0b0d0e35..ef159313d9 100644 --- a/var/spack/repos/builtin/packages/r-mpm/package.py +++ b/var/spack/repos/builtin/packages/r-mpm/package.py @@ -8,12 +8,15 @@ from spack import * class RMpm(RPackage): """Exploratory graphical analysis of multivariate data, specifically - gene expression data with different projection methods: principal - component analysis, correspondence analysis, spectral map analysis.""" + gene expression data with different projection methods: principal + component analysis, correspondence analysis, spectral map analysis.""" + + homepage = "https://cloud.r-project.org/package=mpm" + url = "https://cloud.r-project.org/src/contrib/mpm_1.0-22.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mpm" - homepage = "https://cran.rstudio.com/web/packages/mpm/index.html" - url = "https://cran.rstudio.com/src/contrib/mpm_1.0-22.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mpm" version('1.0-22', '91885c421cafd89ce8893ccf827165a2') + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) depends_on('r-kernsmooth', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py index 656b55a54d..db2bf15312 100644 --- a/var/spack/repos/builtin/packages/r-multcomp/package.py +++ b/var/spack/repos/builtin/packages/r-multcomp/package.py @@ -14,12 +14,14 @@ class RMultcomp(RPackage): (Bretz, Hothorn, Westfall, 2010, CRC Press).""" homepage = "http://multcomp.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/multcomp_1.4-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/multcomp" + url = "https://cloud.r-project.org/src/contrib/multcomp_1.4-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/multcomp" + version('1.4-10', sha256='29bcc635c0262e304551b139cd9ee655ab25a908d9693e1cacabfc2a936df5cf') + version('1.4-8', sha256='a20876619312310e9523d67e9090af501383ce49dc6113c6b4ca30f9c943a73a') version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88') - depends_on('r-mvtnorm@1.0-3:', type=('build', 'run')) + depends_on('r-mvtnorm@1.0-10:', type=('build', 'run')) depends_on('r-survival@2.39-4:', type=('build', 'run')) depends_on('r-th-data@1.0-2:', type=('build', 'run')) depends_on('r-sandwich@2.3-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-multicool/package.py b/var/spack/repos/builtin/packages/r-multicool/package.py index 5d9548da2b..c4e322f678 100644 --- a/var/spack/repos/builtin/packages/r-multicool/package.py +++ b/var/spack/repos/builtin/packages/r-multicool/package.py @@ -9,8 +9,9 @@ from spack import * class RMulticool(RPackage): """Permutations of multisets in cool-lex order.""" - homepage = "https://cran.r-project.org/package=multicool" - url = "https://cran.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz" + homepage = "https://cloud.r-project.org/package=multicool" + url = "https://cloud.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/multicool/Archive/multicool" version('0.1-9', sha256='bdf92571cef1b649952d155395a92b8683099ee13114f73a9d41fc5d7d49d329') diff --git a/var/spack/repos/builtin/packages/r-multitaper/package.py b/var/spack/repos/builtin/packages/r-multitaper/package.py index 172c24dce5..8e31a39c39 100644 --- a/var/spack/repos/builtin/packages/r-multitaper/package.py +++ b/var/spack/repos/builtin/packages/r-multitaper/package.py @@ -10,9 +10,9 @@ class RMultitaper(RPackage): """multitaper: Spectral Analysis Tools using the Multitaper Method""" homepage = "https://github.com/krahim/multitaper/" - url = "https://cran.r-project.org/src/contrib/multitaper_1.0-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/multitaper/" + url = "https://cloud.r-project.org/src/contrib/multitaper_1.0-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/multitaper/" version('1.0-14', sha256='c84c122541dc2874131446e23b212259b3b00590d701efee49e6740fd74a8d13') - depends_on('r@3.0:', type='build') + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py index 20ba74f6f1..8a0678d5d4 100644 --- a/var/spack/repos/builtin/packages/r-munsell/package.py +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -13,10 +13,11 @@ class RMunsell(RPackage): utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.""" - homepage = "https://cran.r-project.org/web/packages/munsell/index.html" - url = "https://cran.r-project.org/src/contrib/munsell_0.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/munsell" + homepage = "https://cloud.r-project.org/package=munsell" + url = "https://cloud.r-project.org/src/contrib/munsell_0.4.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/munsell" + version('0.5.0', sha256='d0f3a9fb30e2b5d411fa61db56d4be5733a2621c0edf017d090bdfa5e377e199') version('0.4.3', 'ebd205323dc37c948f499ee08be9c476') depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py index db6ef6d65a..bd7b6eab46 100644 --- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py +++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py @@ -11,8 +11,13 @@ class RMvtnorm(RPackage): deviates and densities.""" homepage = "http://mvtnorm.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/mvtnorm" + url = "https://cloud.r-project.org/src/contrib/mvtnorm_1.0-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/mvtnorm" + version('1.0-11', sha256='0321612de99aa9bc75a45c7e029d3372736014223cbdefb80d8cae600cbc7252') + version('1.0-10', sha256='31df19cd8b4cab9d9a70dba00442b7684e625d4ca143a2c023c2c5872b07ad12') version('1.0-6', 'cb69426868fd3e330412b8491901d9d4') version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52') + + depends_on('r@1.9.0:', when='@:1.0-8', type=('build', 'run')) + depends_on('r@3.5.0:', when='@1.0-9:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nanotime/package.py b/var/spack/repos/builtin/packages/r-nanotime/package.py index 40eb209c4d..8d0b6c7cc0 100644 --- a/var/spack/repos/builtin/packages/r-nanotime/package.py +++ b/var/spack/repos/builtin/packages/r-nanotime/package.py @@ -11,12 +11,14 @@ class RNanotime(RPackage): nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type.""" - homepage = "https://cran.r-project.org/package=nanotime" - url = "https://cran.r-project.org/src/contrib/nanotime_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nanotime" + homepage = "https://cloud.r-project.org/package=nanotime" + url = "https://cloud.r-project.org/src/contrib/nanotime_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nanotime" + version('0.2.4', sha256='2dfb7e7435fec59634b87563a215467e7793e2711e302749c0533901c74eb184') + version('0.2.3', sha256='7d6df69a4223ae154f610b650e24ece38ce4aa706edfa38bec27d15473229f5d') version('0.2.0', '796b1f7d0bb43e2f3d98e3cc6f4b0657') depends_on('r-bit64', type=('build', 'run')) - depends_on('r-rcppcctz', type=('build', 'run')) + depends_on('r-rcppcctz@0.2.3:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ncbit/package.py b/var/spack/repos/builtin/packages/r-ncbit/package.py index ad8c2b79cf..f01a2035dd 100644 --- a/var/spack/repos/builtin/packages/r-ncbit/package.py +++ b/var/spack/repos/builtin/packages/r-ncbit/package.py @@ -10,8 +10,10 @@ class RNcbit(RPackage): """Making NCBI taxonomic data locally available and searchable as an R object.""" - homepage = "https://cran.r-project.org/package=ncbit" - url = "https://cran.r-project.org/src/contrib/ncbit_2013.03.29.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ncbit" + homepage = "https://cloud.r-project.org/package=ncbit" + url = "https://cloud.r-project.org/src/contrib/ncbit_2013.03.29.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ncbit" version('2013.03.29', '29582d7e5c8bbf9683c57c4f6ac3e891') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index 21ce037fba..a040454530 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -23,9 +23,11 @@ class RNcdf4(RPackage): package does not provide an interface for netcdf version 4 files.""" homepage = "http://cirrus.ucsd.edu/~pierce/ncdf" - url = "https://cran.r-project.org/src/contrib/ncdf4_1.15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ncdf4" + url = "https://cloud.r-project.org/src/contrib/ncdf4_1.15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ncdf4" + version('1.16.1', sha256='0dde2d6d1e8474f4abd15a61af8a2f7de564f13da00f1a01d7a479ab88587a20') + version('1.16', sha256='edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253') version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a') - depends_on('netcdf') + depends_on('netcdf@4.1:') diff --git a/var/spack/repos/builtin/packages/r-network/package.py b/var/spack/repos/builtin/packages/r-network/package.py index ef59109a02..03f728256f 100644 --- a/var/spack/repos/builtin/packages/r-network/package.py +++ b/var/spack/repos/builtin/packages/r-network/package.py @@ -12,7 +12,13 @@ class RNetwork(RPackage): arbitrary vertex/edge/graph attributes.""" homepage = "https://statnet.org" - url = "https://cran.r-project.org/src/contrib/network_1.13.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/network" + url = "https://cloud.r-project.org/src/contrib/network_1.13.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/network" + version('1.15', sha256='5cbe5c0369e5f8363e33a86f14fd33ce8727166106381627ecd13b7452e14cb3') + version('1.14-377', sha256='013c02f8d97f1f87f2c421760534df9353d2a8c2277f20b46b59fb79822d3e46') version('1.13.0', 'd0b967d6f1aad43b6479d72f29b705de') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-tibble', when='@1.14-377:', type=('build', 'run')) + depends_on('r-magrittr', when='@1.14-377:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py index 4db5c88274..976f313fcd 100644 --- a/var/spack/repos/builtin/packages/r-networkd3/package.py +++ b/var/spack/repos/builtin/packages/r-networkd3/package.py @@ -10,12 +10,15 @@ class RNetworkd3(RPackage): """Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.""" - homepage = "http://cran.r-project.org/package=networkD3" - url = "https://cran.r-project.org/src/contrib/networkD3_0.2.12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/networkD3" + homepage = "https://cloud.r-project.org/package=networkD3" + url = "https://cloud.r-project.org/src/contrib/networkD3_0.2.12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/networkD3" + version('0.4', sha256='33b82585f1eec6233303ec14033a703d0b17def441c7a0a67bf7e6764c9c9d0b') + version('0.3', sha256='6f9d6b35bb1562883df734bef8fbec166dd365e34c6e656da7be5f8a8d42343c') version('0.2.12', '356fe4be59698e6fb052644bd9659d84') - depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-htmlwidgets@0.3.2:', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nleqslv/package.py b/var/spack/repos/builtin/packages/r-nleqslv/package.py index 97d29e4bfc..75dda5930d 100644 --- a/var/spack/repos/builtin/packages/r-nleqslv/package.py +++ b/var/spack/repos/builtin/packages/r-nleqslv/package.py @@ -9,8 +9,8 @@ from spack import * class RNleqslv(RPackage): """nleqslv: Solve Systems of Nonlinear Equations""" - homepage = "https://cran.r-project.org/package=nleqslv" - url = "https://cran.r-project.org/src/contrib/nleqslv_3.3.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nleqslv" + homepage = "https://cloud.r-project.org/package=nleqslv" + url = "https://cloud.r-project.org/src/contrib/nleqslv_3.3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nleqslv" version('3.3.2', sha256='f54956cf67f9970bb3c6803684c84a27ac78165055745e444efc45cfecb63fed') diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py index 1356f73967..bd13d96c20 100644 --- a/var/spack/repos/builtin/packages/r-nlme/package.py +++ b/var/spack/repos/builtin/packages/r-nlme/package.py @@ -9,12 +9,18 @@ from spack import * class RNlme(RPackage): """Fit and compare Gaussian linear and nonlinear mixed-effects models.""" - homepage = "https://cran.r-project.org/package=nlme" - url = "https://cran.r-project.org/src/contrib/nlme_3.1-130.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nlme" + homepage = "https://cloud.r-project.org/package=nlme" + url = "https://cloud.r-project.org/src/contrib/nlme_3.1-130.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nlme" + version('3.1-141', sha256='910046260a03d8f776ac7b0766b5adee91556829d0d8a70165b2c695ce038056') + version('3.1-139', sha256='0460fc69d85122177e7ef01bad665d56bcaf63d31bdbfdbdfdcba2c082085739') version('3.1-131', '0f1215ec4d4e3bca939282d122f4d1fa') version('3.1-130', '1935d6e308a8018ed8e45d25c8731288') version('3.1-128', '3d75ae7380bf123761b95a073eb55008') + depends_on('r@3.0.2:', when='@:3.1-131', type=('build', 'run')) + depends_on('r@3.3.0:', when='@3.1-131.1', type=('build', 'run')) + depends_on('r@3.4.0:', when='@3.1-135.5:', type=('build', 'run')) + depends_on('r@3.5.0:', when='@3.1-134:3.1-135', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py index 13a8469e0e..f6f7502524 100644 --- a/var/spack/repos/builtin/packages/r-nloptr/package.py +++ b/var/spack/repos/builtin/packages/r-nloptr/package.py @@ -16,13 +16,13 @@ class RNloptr(RPackage): During installation on Unix the NLopt code is downloaded and compiled from the NLopt website.""" - homepage = "https://cran.r-project.org/package=nloptr" - url = "https://cran.rstudio.com/src/contrib/nloptr_1.0.4.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/nloptr" + homepage = "https://cloud.r-project.org/package=nloptr" + url = "https://cloud.r-project.org/src/contrib/nloptr_1.0.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nloptr" + version('1.2.1', sha256='1f86e33ecde6c3b0d2098c47591a9cd0fa41fb973ebf5145859677492730df97') version('1.0.4', 'f2775dfb4f7f5552d46937a04c062b0d') - depends_on('r-testthat', type=('build', 'run')) depends_on('nlopt') def configure_args(self): diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index 854aafd636..91c356d794 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -15,16 +15,18 @@ class RNmf(RPackage): computations on multicore machines..""" homepage = "http://renozao.github.io/NMF" - url = "https://cran.r-project.org/src/contrib/NMF_0.20.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/NMF" + url = "https://cloud.r-project.org/src/contrib/NMF_0.20.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF" + version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3') version('0.20.6', '81df07b3bf710a611db5af24730ff3d0') - depends_on('r-pkgmaker', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-pkgmaker@0.20:', type=('build', 'run')) depends_on('r-registry', type=('build', 'run')) - depends_on('r-rngtools', type=('build', 'run')) + depends_on('r-rngtools@1.2.3:', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) - depends_on('r-stringr', type=('build', 'run')) + depends_on('r-stringr@1.0.0:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) depends_on('r-gridbase', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nmof/package.py b/var/spack/repos/builtin/packages/r-nmof/package.py new file mode 100644 index 0000000000..ccd3061f12 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-nmof/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RNmof(RPackage): + """Functions, examples and data from the book "Numerical Methods and + Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2011), + ISBN 978-0123756626. The package provides implementations of several + optimisation heuristics, such as Differential Evolution, Genetic Algorithms + and Threshold Accepting. There are also functions for the valuation of + financial instruments, such as bonds and options, and functions that help + with stochastic simulations.""" + + homepage = "http://nmof.net/" + url = "https://cloud.r-project.org/src/contrib/NMOF_1.6-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/NMOF" + + version('1.6-0', sha256='5484cd43c28aaf23d560c2dde8bcd8dd440a205d2214eb50e02fe0bb42ec2755') + + depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py index 5f5c8cc759..dada76423e 100644 --- a/var/spack/repos/builtin/packages/r-nnet/package.py +++ b/var/spack/repos/builtin/packages/r-nnet/package.py @@ -11,7 +11,9 @@ class RNnet(RPackage): and for multinomial log-linear models.""" homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" - url = "https://cran.r-project.org/src/contrib/nnet_7.3-12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nnet" + url = "https://cloud.r-project.org/src/contrib/nnet_7.3-12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nnet" version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e') + + depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-nnls/package.py b/var/spack/repos/builtin/packages/r-nnls/package.py index 548dc480c9..815f35b925 100644 --- a/var/spack/repos/builtin/packages/r-nnls/package.py +++ b/var/spack/repos/builtin/packages/r-nnls/package.py @@ -11,8 +11,8 @@ class RNnls(RPackage): algorithm for non-negative least squares (NNLS). Also allows the combination of non-negative and non-positive constraints.""" - homepage = "https://cran.r-project.org/package=nnls" - url = "https://cran.rstudio.com/src/contrib/nnls_1.4.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/nnls" + homepage = "https://cloud.r-project.org/package=nnls" + url = "https://cloud.r-project.org/src/contrib/nnls_1.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nnls" version('1.4', 'cdb3640120f73e0ccb6079108e0ef361') diff --git a/var/spack/repos/builtin/packages/r-nor1mix/package.py b/var/spack/repos/builtin/packages/r-nor1mix/package.py index 14543b4571..050252b7e3 100644 --- a/var/spack/repos/builtin/packages/r-nor1mix/package.py +++ b/var/spack/repos/builtin/packages/r-nor1mix/package.py @@ -13,8 +13,9 @@ class RNor1mix(RPackage): generation and graphics; now fitting to data by ML (Maximum Likelihood) or EM estimation.""" - homepage = "https://CRAN.R-project.org/package=nor1mix" - url = "https://cran.rstudio.com/src/contrib/nor1mix_1.2-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nor1mix" + homepage = "https://cloud.r-project.org/package=nor1mix" + url = "https://cloud.r-project.org/src/contrib/nor1mix_1.2-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nor1mix" + version('1.3-0', sha256='9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0') version('1.2-3', '60eb5cc1ea6b366f53042087a080b105') diff --git a/var/spack/repos/builtin/packages/r-nortest/package.py b/var/spack/repos/builtin/packages/r-nortest/package.py index 5407eb9721..c93b8b79bb 100644 --- a/var/spack/repos/builtin/packages/r-nortest/package.py +++ b/var/spack/repos/builtin/packages/r-nortest/package.py @@ -11,8 +11,8 @@ class RNortest(RPackage): Five omnibus tests for testing the composite hypothesis of normality.""" - homepage = "https://cran.r-project.org/package=nortest" - url = "https://cran.r-project.org/src/contrib/nortest_1.0-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/nortest" + homepage = "https://cloud.r-project.org/package=nortest" + url = "https://cloud.r-project.org/src/contrib/nortest_1.0-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/nortest" version('1.0-4', sha256='a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f') diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py index f076e4d808..0a7e983535 100644 --- a/var/spack/repos/builtin/packages/r-np/package.py +++ b/var/spack/repos/builtin/packages/r-np/package.py @@ -16,10 +16,14 @@ class RNp(RPackage): Research Computing Network (SHARCNET:www.sharcnet.ca).""" homepage = "https://github.com/JeffreyRacine/R-Package-np/" - url = "https://cran.r-project.org/src/contrib/np_0.60-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/np" + url = "https://cloud.r-project.org/src/contrib/np_0.60-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/np" + version('0.60-9', sha256='fe31a8985f0b1a576a7775022b7131093b1c9a8337734136d5fcad85fa6592fc') + version('0.60-8', sha256='924c342feb2a862fa3871a45db5f8434dbbfb900cfc40c001a0872108a3a069e') version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389') depends_on('r-boot', type=('build', 'run')) depends_on('r-cubature', type=('build', 'run')) + depends_on('r-quadprog', when='@0.60-8:', type=('build', 'run')) + depends_on('r-quantreg', when='@0.60-8:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-npsurv/package.py b/var/spack/repos/builtin/packages/r-npsurv/package.py new file mode 100644 index 0000000000..6ef60c6345 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-npsurv/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RNpsurv(RPackage): + """Contains functions for non-parametric survival analysis of exact and + interval-censored observations.""" + + homepage = "https://www.stat.auckland.ac.nz/~yongwang" + url = "https://cloud.r-project.org/src/contrib/npsurv_0.4-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/npsurv" + + version('0.4-0', sha256='404cf7135dc40a04e9b81224a543307057a8278e11109ba1fcaa28e87c6204f3') + + depends_on('r-lsei', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-numderiv/package.py b/var/spack/repos/builtin/packages/r-numderiv/package.py index 16342ff5c5..d234dca538 100644 --- a/var/spack/repos/builtin/packages/r-numderiv/package.py +++ b/var/spack/repos/builtin/packages/r-numderiv/package.py @@ -10,10 +10,11 @@ class RNumderiv(RPackage): """Methods for calculating (usually) accurate numerical first and second order derivatives.""" - homepage = "https://cran.r-project.org/package=numDeriv" - url = "https://cran.r-project.org/src/contrib/numDeriv_2016.8-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/numDeriv" + homepage = "https://cloud.r-project.org/package=numDeriv" + url = "https://cloud.r-project.org/src/contrib/numDeriv_2016.8-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/numDeriv" + version('2016.8-1.1', sha256='d8c4d19ff9aeb31b0c628bd4a16378e51c1c9a3813b525469a31fe89af00b345') version('2016.8-1', '30e486298d5126d86560095be8e8aac1') - depends_on('r@2.11.1:') + depends_on('r@2.11.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index a11bb4546a..72ef242667 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -18,12 +18,15 @@ class ROpenssl(RPackage): generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.""" - homepage = "https://CRAN.R-project.org/package=openssl" - url = "https://cran.r-project.org/src/contrib/openssl_0.9.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/openssl" + homepage = "https://cloud.r-project.org/package=openssl" + url = "https://cloud.r-project.org/src/contrib/openssl_0.9.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/openssl" + version('1.4.1', sha256='f7fbecc75254fc43297a95a4338c674ab9ba2ec056b59e027d16d23122161fc6') + version('1.3', sha256='1c83f4d529adc1f5ec40e477c690a8d5b0a42422f3e542f1fc39062dcfaca4bf') version('0.9.7', '86773824dce7d3d79abfef574ce2531a') version('0.9.6', '7ef137929d9dd07db690d35db242ba4b') version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb') + depends_on('r-askpass', when='@1.2:', type=('build', 'run')) depends_on('openssl@1.0.1:') diff --git a/var/spack/repos/builtin/packages/r-openxlsx/package.py b/var/spack/repos/builtin/packages/r-openxlsx/package.py new file mode 100644 index 0000000000..cd375247e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-openxlsx/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class ROpenxlsx(RPackage): + """Simplifies the creation of Excel .xlsx files by providing a high level + interface to writing, styling and editing worksheets. Through the use of + 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' + packages with the added benefit of removing the dependency on Java.""" + + homepage = "https://github.com/awalker89/openxlsx" + url = "https://cloud.r-project.org/src/contrib/openxlsx_4.1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/openxlsx" + + version('4.1.0.1', sha256='8b7011debe14714de035ef42797c8caa923162d5dc3cc3c2a299fc10eff3d4d1') + + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-zip', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-optparse/package.py b/var/spack/repos/builtin/packages/r-optparse/package.py index 6bbe628b6b..be8c989605 100644 --- a/var/spack/repos/builtin/packages/r-optparse/package.py +++ b/var/spack/repos/builtin/packages/r-optparse/package.py @@ -11,10 +11,12 @@ class ROptparse(RPackage): with Rscript to write "#!" shebang scripts that accept short and long flag/options""" - homepage = "https://cran.r-project.org/package=optparse" - url = "https://cran.r-project.org/src/contrib/optparse_1.6.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/optparse" + homepage = "https://cloud.r-project.org/package=optparse" + url = "https://cloud.r-project.org/src/contrib/optparse_1.6.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/optparse" + version('1.6.2', sha256='b5a5a49ae05005f20359868329b73daac83d50f5e088981dcf5c41399534377f') + version('1.6.1', sha256='819be3eff54cb7f3f18703eed9714fc655290ab8e169f87605433d069b597e13') version('1.6.0', '8d0bd89b2e25cc1580437cdeeb1faac2') depends_on('r@2.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ordinal/package.py b/var/spack/repos/builtin/packages/r-ordinal/package.py new file mode 100644 index 0000000000..ad837a3411 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ordinal/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class ROrdinal(RPackage): + """Implementation of cumulative link (mixed) models also known as ordered + regression models, proportional odds models, proportional hazards models + for grouped survival times and ordered logit/probit/... models. Estimation + is via maximum likelihood and mixed models are fitted with the Laplace + approximation and adaptive Gauss-Hermite quadrature. Multiple random effect + terms are allowed and they may be nested, crossed or partially + nested/crossed. Restrictions of symmetry and equidistance can be imposed on + the thresholds (cut-points/intercepts). Standard model methods are + available (summary, anova, drop-methods, step, confint, predict etc.) in + addition to profile methods and slice methods for visualizing the + likelihood function and checking convergence.""" + + homepage = "https://github.com/runehaubo/ordinal" + url = "https://cloud.r-project.org/src/contrib/ordinal_2019.4-25.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ordinal" + + version('2019.4-25', sha256='2812ad7a123cae5dbe053d1fe5f2d9935afc799314077eac185c844e3c9d79df') + + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-ucminf', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-numderiv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py index a871964a0e..427843d080 100644 --- a/var/spack/repos/builtin/packages/r-packrat/package.py +++ b/var/spack/repos/builtin/packages/r-packrat/package.py @@ -11,8 +11,12 @@ class RPackrat(RPackage): and reproducible way.""" homepage = "https://github.com/rstudio/packrat/" - url = "https://cran.r-project.org/src/contrib/packrat_0.4.7-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/packrat" + url = "https://cloud.r-project.org/src/contrib/packrat_0.4.7-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/packrat" + version('0.5.0', sha256='d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7') + version('0.4.9-3', sha256='87299938a751defc54eb00a029aecd3522d6349d900aaa8b3e1aa6bf31e98234') version('0.4.8-1', '14e82feba55fcda923396282fc490038') version('0.4.7-1', '80c2413269b292ade163a70ba5053e84') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pacman/package.py b/var/spack/repos/builtin/packages/r-pacman/package.py index a65db10103..fef678b671 100644 --- a/var/spack/repos/builtin/packages/r-pacman/package.py +++ b/var/spack/repos/builtin/packages/r-pacman/package.py @@ -12,12 +12,15 @@ class RPacman(RPackage): and names them in an intuitive and consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.""" - homepage = "https://cran.r-project.org/package=pacman" - url = "https://cran.r-project.org/src/contrib/pacman_0.4.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pacman" + homepage = "https://cloud.r-project.org/package=pacman" + url = "https://cloud.r-project.org/src/contrib/pacman_0.4.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pacman" + version('0.5.1', sha256='9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c') + version('0.5.0', sha256='61294757212ab0aa0153219d7d031f58be6f30ead88d84859001d58caa76603d') version('0.4.1', 'bf18fe6d1407d31e00b337d9b07fb648') - depends_on('r@3.0.2:') - - depends_on('r-devtools', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r@3.5.0:', when='@0.5.0:', type=('build', 'run')) + depends_on('r-devtools', when='@:0.4.6', type=('build', 'run')) + depends_on('r-remotes', when='@0.5.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-paleotree/package.py b/var/spack/repos/builtin/packages/r-paleotree/package.py index 9a4f31c872..f14ea30f0c 100644 --- a/var/spack/repos/builtin/packages/r-paleotree/package.py +++ b/var/spack/repos/builtin/packages/r-paleotree/package.py @@ -13,12 +13,16 @@ class RPaleotree(RPackage): extinct (i.e. fossil) lineages""" homepage = "https://github.com/dwbapst/paleotree" - url = "https://cran.r-project.org/src/contrib/paleotree_3.1.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/paleotree" + url = "https://cloud.r-project.org/src/contrib/paleotree_3.1.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/paleotree" + version('3.3.0', sha256='f8f6b0228dd5290b251cad3a8626689442b5aa793d8f072c8c2c7813a063df90') version('3.1.3', sha256='4c1cc8a5e171cbbbd88f78914f86d5e6d144ae573816fbeeff2ab54a814ec614') depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-ape@4.1:', type=('build', 'run')) depends_on('r-phangorn@2.0.0:', type=('build', 'run')) depends_on('r-phytools@0.6-00:', type=('build', 'run')) + depends_on('r-jsonlite', when='@3.3.0:', type=('build', 'run')) + depends_on('r-png', when='@3.3.0:', type=('build', 'run')) + depends_on('r-rcurl', when='@3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pamr/package.py b/var/spack/repos/builtin/packages/r-pamr/package.py index c56459b865..f4697f4c17 100644 --- a/var/spack/repos/builtin/packages/r-pamr/package.py +++ b/var/spack/repos/builtin/packages/r-pamr/package.py @@ -9,8 +9,13 @@ from spack import * class RPamr(RPackage): """Some functions for sample classification in microarrays.""" - homepage = "https://cran.r-project.org/package=pamr" - url = "https://cran.rstudio.com/src/contrib/pamr_1.55.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pamr" + homepage = "https://cloud.r-project.org/package=pamr" + url = "https://cloud.r-project.org/src/contrib/pamr_1.55.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pamr" + version('1.56.1', sha256='d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779') version('1.55', '108932d006a4de3a178b6f57f5d1a006') + + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) + depends_on('r-survival', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pan/package.py b/var/spack/repos/builtin/packages/r-pan/package.py index 21c6155ba5..176104e3df 100644 --- a/var/spack/repos/builtin/packages/r-pan/package.py +++ b/var/spack/repos/builtin/packages/r-pan/package.py @@ -9,8 +9,9 @@ from spack import * class RPan(RPackage): """Multiple imputation for multivariate panel or clustered data.""" - homepage = "https://cran.r-project.org/package=pan" - url = "https://cran.r-project.org/src/contrib/pan_1.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pan" + homepage = "https://cloud.r-project.org/package=pan" + url = "https://cloud.r-project.org/src/contrib/pan_1.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pan" + version('1.6', sha256='adc0df816ae38bc188bce0aef3aeb71d19c0fc26e063107eeee71a81a49463b6') version('1.4', 'cdead963110561fc42dc544a60ac44ed') diff --git a/var/spack/repos/builtin/packages/r-parallelmap/package.py b/var/spack/repos/builtin/packages/r-parallelmap/package.py index b5911996c8..cc43793728 100644 --- a/var/spack/repos/builtin/packages/r-parallelmap/package.py +++ b/var/spack/repos/builtin/packages/r-parallelmap/package.py @@ -15,10 +15,12 @@ class RParallelmap(RPackage): this operation.""" homepage = "https://github.com/berndbischl/parallelMap" - url = "https://cran.r-project.org/src/contrib/parallelMap_1.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/parallelMap" + url = "https://cloud.r-project.org/src/contrib/parallelMap_1.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/parallelMap" + version('1.4', sha256='fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b') version('1.3', 'dd62866b395847b0bd5b13bed98c0081') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-bbmisc@1.8:', type=('build', 'run')) - depends_on('r-checkmate@1.5.1:', type=('build', 'run')) + depends_on('r-checkmate@1.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-paramhelpers/package.py b/var/spack/repos/builtin/packages/r-paramhelpers/package.py index 5898de58fe..2aa307b30d 100644 --- a/var/spack/repos/builtin/packages/r-paramhelpers/package.py +++ b/var/spack/repos/builtin/packages/r-paramhelpers/package.py @@ -14,10 +14,14 @@ class RParamhelpers(RPackage): function evaluations is also provided.""" homepage = "https://github.com/berndbischl/ParamHelpers" - url = "https://cran.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ParamHelpers" + url = "https://cloud.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ParamHelpers" + version('1.12', sha256='b54db9e6608ba530345c380c757a60cb2b78ab08992a890b1a41914ce7abcc14') + version('1.11', sha256='1614f4c0842cf822befc01228ab7263417f3423dd6a1dc24347b14f8491637a0') version('1.10', '36e9060488ebd484d62cd991a4693332') depends_on('r-bbmisc@1.10:', type=('build', 'run')) - depends_on('r-checkmate@1.8.1:', type=('build', 'run')) + depends_on('r-checkmate@1.8.2:', type=('build', 'run')) + depends_on('r-backports', when='@1.11:', type=('build', 'run')) + depends_on('r-fastmatch', when='@1.11:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-party/package.py b/var/spack/repos/builtin/packages/r-party/package.py index 73fc0c8233..db876b5faf 100644 --- a/var/spack/repos/builtin/packages/r-party/package.py +++ b/var/spack/repos/builtin/packages/r-party/package.py @@ -9,16 +9,18 @@ from spack import * class RParty(RPackage): """A computational toolbox for recursive partitioning.""" - homepage = "https://cran.r-project.org/web/packages/party/index.html" - url = "https://cran.r-project.org/src/contrib/party_1.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/party" + homepage = "https://cloud.r-project.org/package=party" + url = "https://cloud.r-project.org/src/contrib/party_1.1-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/party" + version('1.3-3', sha256='9f72eea02d43a4cee105790ae7185b0478deb6011ab049cc9d31a0df3abf7ce9') + version('1.3-2', sha256='9f350fa21114151c49bccc3d5f8536dbc5a608cfd88f60461c9805a4c630510b') version('1.1-2', '40a00336cf8418042d2ab616675c8ddf') - depends_on('r@2.14.0:') - + depends_on('r@2.14.0:', when='@:1.2-2', type=('build', 'run')) + depends_on('r@3.0.0:', when='@1.2-3:', type=('build', 'run')) depends_on('r-mvtnorm@1.0-2:', type=('build', 'run')) - depends_on('r-modeltools@0.1-21:', type=('build', 'run')) + depends_on('r-modeltools@0.2-21:', type=('build', 'run')) depends_on('r-strucchange', type=('build', 'run')) depends_on('r-survival@2.37-7:', type=('build', 'run')) depends_on('r-coin@1.1-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py index d01292d307..1e914397a0 100644 --- a/var/spack/repos/builtin/packages/r-partykit/package.py +++ b/var/spack/repos/builtin/packages/r-partykit/package.py @@ -18,10 +18,17 @@ class RPartykit(RPackage): provided based on the new infrastructure.""" homepage = "http://partykit.r-forge.r-project.org/partykit" - url = "https://cran.r-project.org/src/contrib/partykit_1.1-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/partykit" + url = "https://cloud.r-project.org/src/contrib/partykit_1.1-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/partykit" + version('1.2-5', sha256='f48e30790f93fa5d03e68e8ce71ce33d009d107d46d45d85da2016b38b27629c') + version('1.2-3', sha256='56749b246e283f94ac2ad2cdcfc0a477e05cd44b5e8f6e462c26f4dff818da35') version('1.1-1', '8fcb31d73ec1b8cd3bcd9789639a9277') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) - depends_on('r-formula', type=('build', 'run')) + depends_on('r-formula@1.2-1:', type=('build', 'run')) + depends_on('r-libcoin@1.0-0:', when='@1.2-0:', type=('build', 'run')) + depends_on('r-mvtnorm', when='@1.2-0:', type=('build', 'run')) + depends_on('r-inum@1.0-0:', when='@1.2-0:', type=('build', 'run')) + depends_on('r-rpart@4.1-11:', when='@1.2-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbapply/package.py b/var/spack/repos/builtin/packages/r-pbapply/package.py index 0a230ab759..cc481c277a 100644 --- a/var/spack/repos/builtin/packages/r-pbapply/package.py +++ b/var/spack/repos/builtin/packages/r-pbapply/package.py @@ -10,14 +10,16 @@ class RPbapply(RPackage): """A lightweight package that adds progress bar to vectorized R apply functions.""" - homepage = "https://cran.r-project.org/web/packages/pbapply/index.html" - url = "https://cran.r-project.org/src/contrib/pbapply_1.3-3.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/pbapply" + homepage = "https://cloud.r-project.org/package=pbapply" + url = "https://cloud.r-project.org/src/contrib/pbapply_1.3-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pbapply" + version('1.4-1', sha256='b3633349181db944e1dfc4422b4728a6562e454117a232cbb51633906cd27cad') + version('1.3-4', sha256='cdfdaf9b8aecbe48daac858aecaf65a766b74a363d1eb7cd6ebf27c0549f6552') version('1.3-3', '570db6795179a1439c174be881c77d18') version('1.3-2', 'd72a777bfe4a28ba4e1585e31680f82e') version('1.3-1', '13d64dead441426aa96a3bf3fde29daf') version('1.3-0', 'a3f93cd05054657a01893a3817fa1f08') version('1.2-2', '23e2bfe531c704b79308b0b5fbe1ace8') - depends_on('r@3.4.0:3.4.9') + depends_on('r@3.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index e0a8ef25ba..48625786c1 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -17,10 +17,14 @@ class RPbdzmq(RPackage): functions compatible with 'rzmq' are also provided.""" homepage = "http://r-pbd.org/" - url = "https://cran.r-project.org/src/contrib/pbdZMQ_0.2-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pbdZMQ" + url = "https://cloud.r-project.org/src/contrib/pbdZMQ_0.2-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pbdZMQ" + version('0.3-3', sha256='ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca') + version('0.3-2', sha256='ece2a2881c662f77126e4801ba4e01c991331842b0d636ce5a2b591b9de3fc37') version('0.2-4', 'e5afb70199aa54d737ee7a0e26bde060') - depends_on('r-r6', type=('build', 'run')) - depends_on('zeromq') + depends_on('r@3.0.0:', when='@:0.2-5', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.2-6:', type=('build', 'run')) + depends_on('r-r6', when='@:0.2-6', type=('build', 'run')) + depends_on('zeromq@4.0.4:') diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py index 42cca11729..a696abf87a 100644 --- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py +++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py @@ -14,14 +14,15 @@ class RPbkrtest(RPackage): models.""" homepage = "http://people.math.aau.dk/~sorenh/software/pbkrtest/" - url = "https://cran.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pbkrtest" + url = "https://cloud.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pbkrtest" + version('0.4-7', sha256='5cbb03ad2b2468720a5a610a0ebda48ac08119a34fca77810a85f554225c23ea') version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9') version('0.4-4', '5e54b1b1b35413dd1d24ef15735ec645') - depends_on('r@3.2.3:') - + depends_on('r@3.0.2:', when='@:0.4-5', type=('build', 'run')) + depends_on('r@3.2.3:', when='@0.4-6:', type=('build', 'run')) depends_on('r-lme4@1.1.10:', type=('build', 'run')) depends_on('r-matrix@1.2.3:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pcapp/package.py b/var/spack/repos/builtin/packages/r-pcapp/package.py index 4e49bd47aa..bcc1b7a472 100644 --- a/var/spack/repos/builtin/packages/r-pcapp/package.py +++ b/var/spack/repos/builtin/packages/r-pcapp/package.py @@ -7,16 +7,18 @@ from spack import * class RPcapp(RPackage): - """Provides functions for robust PCA by projection pursuit.""" + """Provides functions for robust PCA by projection pursuit.""" - homepage = "https://cran.r-project.org/web/packages/pcaPP/index.html" - url = "https://cran.r-project.org/src/contrib/pcaPP_1.9-72.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/pcaPP" + homepage = "https://cloud.r-project.org/package=pcaPP" + url = "https://cloud.r-project.org/src/contrib/pcaPP_1.9-72.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pcaPP" - version('1.9-72', '87c08f8ecab69311bba395c026bbc91c') - version('1.9-70', '3fcc809ec1cdc910f10e9ebf372888e8') - version('1.9-61', '1bd5bc3aff968b168493e8c523d726ea') - version('1.9-60', '23dd468abb9fedc11e40166446df1017') - version('1.9-50', 'be44f173404fd6e86ba0a5515711bfa3') + version('1.9-73', sha256='ca4566b0babfbe83ef9418283b08a12b3420dc362f93c6562f265df7926b53fc') + version('1.9-72.1', sha256='a9e39ee15a650930c07672092f9f0c431807869b68b5471037eb7290a4d65bd5') + version('1.9-72', '87c08f8ecab69311bba395c026bbc91c') + version('1.9-70', '3fcc809ec1cdc910f10e9ebf372888e8') + version('1.9-61', '1bd5bc3aff968b168493e8c523d726ea') + version('1.9-60', '23dd468abb9fedc11e40166446df1017') + version('1.9-50', 'be44f173404fd6e86ba0a5515711bfa3') - depends_on('r-mvtnorm', type=('build', 'run')) + depends_on('r-mvtnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-permute/package.py b/var/spack/repos/builtin/packages/r-permute/package.py index 4798b844ef..a386df053b 100644 --- a/var/spack/repos/builtin/packages/r-permute/package.py +++ b/var/spack/repos/builtin/packages/r-permute/package.py @@ -16,9 +16,10 @@ class RPermute(RPackage): (and later) by Cajo ter Braak.""" homepage = "https://github.com/gavinsimpson/permute" - url = "https://cran.r-project.org/src/contrib/permute_0.9-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/permute" + url = "https://cloud.r-project.org/src/contrib/permute_0.9-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/permute" + version('0.9-5', sha256='d2885384a07497e8df273689d6713fc7c57a7c161f6935f3572015e16ab94865') version('0.9-4', '569fc2442d72a1e3b7e2d456019674c9') - depends_on('r@2.14:') + depends_on('r@2.14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phangorn/package.py b/var/spack/repos/builtin/packages/r-phangorn/package.py index b147d5c9f1..3b0c34fb7e 100644 --- a/var/spack/repos/builtin/packages/r-phangorn/package.py +++ b/var/spack/repos/builtin/packages/r-phangorn/package.py @@ -12,12 +12,15 @@ class RPhangorn(RPackage): and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.""" - homepage = "https://cran.r-project.org/package=phangorn" - url = "https://cran.r-project.org/src/contrib/phangorn_2.3.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/phangorn" + homepage = "https://cloud.r-project.org/package=phangorn" + url = "https://cloud.r-project.org/src/contrib/phangorn_2.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/phangorn" + version('2.5.5', sha256='c58dc1ace26cb4358619a15da3ea4765dbdde1557acccc5103c85589a7571346') + version('2.5.3', sha256='a306585a0aabe7360a2adaf9116ae2993fb5ceff641b198f2e01e4329d3768af') version('2.3.1', '85e7309900d061432508ab6f7e3e627e') + depends_on('r@3.2.0:', type=('build', 'run')) depends_on('r-ape@5.0:', type=('build', 'run')) depends_on('r-quadprog', type=('build', 'run')) depends_on('r-igraph@1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-phytools/package.py b/var/spack/repos/builtin/packages/r-phytools/package.py index 385e76ff36..718e54cb4b 100644 --- a/var/spack/repos/builtin/packages/r-phytools/package.py +++ b/var/spack/repos/builtin/packages/r-phytools/package.py @@ -10,9 +10,10 @@ class RPhytools(RPackage): """Phylogenetic Tools for Comparative Biology (and Other Things)""" homepage = "http://github.com/liamrevell/phytools" - url = "https://cran.r-project.org/src/contrib/phytools_0.6-60.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/phytools/" + url = "https://cloud.r-project.org/src/contrib/phytools_0.6-60.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/phytools/" + version('0.6-99', sha256='2ef532cba77c5f73803bd34582bef05709705311a0b50e42316e69944567390f') version('0.6-60', sha256='55cad759510d247ebbf03a53a46caddadd3bf87584ccf7fcd6dd06d44516b377') depends_on('r@3.2.0:', type=('build', 'run')) @@ -30,3 +31,4 @@ class RPhytools(RPackage): depends_on('r-phangorn@2.3.1:', type=('build', 'run')) depends_on('r-plotrix', type=('build', 'run')) depends_on('r-scatterplot3d', type=('build', 'run')) + depends_on('r-gtools', when='@0.6-99:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-picante/package.py b/var/spack/repos/builtin/packages/r-picante/package.py index e9e20b030f..6cfa91cfc2 100644 --- a/var/spack/repos/builtin/packages/r-picante/package.py +++ b/var/spack/repos/builtin/packages/r-picante/package.py @@ -9,10 +9,12 @@ from spack import * class RPicante(RPackage): """R tools for integrating phylogenies and ecology""" - homepage = "https://cran.r-project.org/package=picante" - url = "https://cran.r-project.org/src/contrib/picante_1.6-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/picante" + homepage = "https://cloud.r-project.org/package=picante" + url = "https://cloud.r-project.org/src/contrib/picante_1.6-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/picante" + version('1.8', sha256='81a6308dbb53c9cdab30c1f9ac727abee76314351823b3a2142c21ed8e1498ad') + version('1.7', sha256='75e4d73080db67e776562a1d58685438461cbde39af46900c7838da56aef0a62') version('1.6-2', 'e3eba6ef254068d2cfa9e96760bcd7a3') version('1.6-1', '73d86b90eceda582654e995d47236d6e') diff --git a/var/spack/repos/builtin/packages/r-pillar/package.py b/var/spack/repos/builtin/packages/r-pillar/package.py index d23c6eb662..213a2658db 100644 --- a/var/spack/repos/builtin/packages/r-pillar/package.py +++ b/var/spack/repos/builtin/packages/r-pillar/package.py @@ -10,10 +10,12 @@ class RPillar(RPackage): """Provides a 'pillar' generic designed for formatting columns of data using the full range of colours provided by modern terminals.""" - homepage = "https://cran.r-project.org/package=pillar" - url = "https://cran.r-project.org/src/contrib/pillar_1.3.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pillar" + homepage = "https://cloud.r-project.org/package=pillar" + url = "https://cloud.r-project.org/src/contrib/pillar_1.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pillar" + version('1.4.2', sha256='bababb76b6db06dc32ccd947dbad6c164a1749ff5b558c6783ad03570f010825') + version('1.4.1', sha256='f571ca7a3ef0927747510b972da31a26da24b9da68990fe1bbc9d4ae58028c55') version('1.3.1', sha256='b338b55f956dd7134f379d39bb94dfb25e13cf27999d6a6e6dc9f292755acbf6') version('1.3.0', sha256='aed845ae4888be9a7340eed57536e3fe6cb46e89d905897fb9b0635797cfcae0') version('1.2.3', sha256='c81d1b5c6b55d789a6717dc3c7be1200eb0efbcfc5013db00d553d9cafd6f0e7') @@ -25,7 +27,8 @@ class RPillar(RPackage): version('1.0.0', sha256='7478d0765212c5f0333b8866231a6fe350393b7fa49840e6fed3516ac64540dc') depends_on('r-cli', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) + depends_on('r-crayon@1.3.4:', type=('build', 'run')) depends_on('r-fansi', type=('build', 'run')) - depends_on('r-rlang', type=('build', 'run')) - depends_on('r-utf8', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', type=('build', 'run')) + depends_on('r-utf8@1.1.0:', type=('build', 'run')) + depends_on('r-vctrs', when='@1.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pkgbuild/package.py b/var/spack/repos/builtin/packages/r-pkgbuild/package.py index 723180c333..2e4dedfa1b 100644 --- a/var/spack/repos/builtin/packages/r-pkgbuild/package.py +++ b/var/spack/repos/builtin/packages/r-pkgbuild/package.py @@ -9,18 +9,20 @@ from spack import * class RPkgbuild(RPackage): """pkgbuild: Find Tools Needed to Build R Packages""" - homepage = "https://cran.r-project.org/package=pkgbuild" - url = "https://cran.r-project.org/src/contrib/pkgbuild_1.0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pkgbuild/" + homepage = "https://cloud.r-project.org/package=pkgbuild" + url = "https://cloud.r-project.org/src/contrib/pkgbuild_1.0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgbuild/" + version('1.0.4', sha256='2934efa5ff9ccfe1636d360aedec36713f3bb3128a493241dbb728d842ea3b5f') version('1.0.3', sha256='c93aceb499886e42bcd61eb7fb59e47a76c9ba5ab5349a426736d46c8ce21f4d') depends_on('r@3.1:', type=('build', 'run')) - depends_on('r-callr', type=('build', 'run')) + depends_on('r-callr@2.0.0:', when='@:1.0.3', type=('build', 'run')) + depends_on('r-callr@3.2.0:', when='@1.0.4:', type=('build', 'run')) depends_on('r-cli', type=('build', 'run')) depends_on('r-crayon', type=('build', 'run')) depends_on('r-desc', type=('build', 'run')) depends_on('r-prettyunits', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) depends_on('r-rprojroot', type=('build', 'run')) - depends_on('r-withr', type=('build', 'run')) + depends_on('r-withr@2.1.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pkgconfig/package.py b/var/spack/repos/builtin/packages/r-pkgconfig/package.py index 1f589b5b61..947d6f4ee5 100644 --- a/var/spack/repos/builtin/packages/r-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/r-pkgconfig/package.py @@ -11,9 +11,9 @@ class RPkgconfig(RPackage): given package only apply to that package, other packages are unaffected.""" - homepage = "https://cran.rstudio.com/web/packages/pkgconfig/index.html" - url = "https://cran.rstudio.com/src/contrib/pkgconfig_2.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pkgconfig" + homepage = "https://cloud.r-project.org/package=pkgconfig" + url = "https://cloud.r-project.org/src/contrib/pkgconfig_2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgconfig" version('2.0.2', sha256='25997754d1adbe7a251e3bf9879bb52dced27dd8b84767d558f0f644ca8d69ca') version('2.0.1', 'a20fd9588e37995995fa62dc4828002e') diff --git a/var/spack/repos/builtin/packages/r-pkgload/package.py b/var/spack/repos/builtin/packages/r-pkgload/package.py index e1a579adaf..fa6d0aa635 100644 --- a/var/spack/repos/builtin/packages/r-pkgload/package.py +++ b/var/spack/repos/builtin/packages/r-pkgload/package.py @@ -9,9 +9,9 @@ from spack import * class RPkgload(RPackage): """pkgload: Simulate Package Installation and Attach""" - homepage = "https://cran.r-project.org/package=pkgload" - url = "https://cran.r-project.org/src/contrib/pkgload_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pkgload/" + homepage = "https://cloud.r-project.org/package=pkgload" + url = "https://cloud.r-project.org/src/contrib/pkgload_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgload/" version('1.0.2', sha256='3186564e690fb05eabe76e1ac0bfd4312562c3ac8794b29f8850399515dcf27c') diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index 29628b68e7..b89ec59b80 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -16,8 +16,8 @@ class RPkgmaker(RPackage): changes in the interface(s) are more than likely to happen.""" homepage = "https://renozao.github.io/pkgmaker" - url = "https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pkgmaker" + url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker" version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a') version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4') @@ -32,11 +32,3 @@ class RPkgmaker(RPackage): depends_on('r-xtable', type=('build', 'run')) depends_on('r-withr', type=('build', 'run')) depends_on('r-bibtex@0.4:', type=('build', 'run')) - depends_on('r-devtools@0.8:', type=('build', 'run')) - depends_on('r-roxygen2', type=('build', 'run')) - depends_on('r-runit', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-rmarkdown', type=('build', 'run')) - depends_on('r-yaml', type=('build', 'run')) - depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plogr/package.py b/var/spack/repos/builtin/packages/r-plogr/package.py index b85fdaf2b0..c35e0900e4 100644 --- a/var/spack/repos/builtin/packages/r-plogr/package.py +++ b/var/spack/repos/builtin/packages/r-plogr/package.py @@ -11,9 +11,9 @@ class RPlogr(RPackage): 'LinkingTo: plogr' to 'DESCRIPTION', and '#include <plogr.h>' in your C++ modules to use it.""" - homepage = "https://cran.r-project.org/package=plogr" - url = "https://cran.r-project.org/src/contrib/plogr_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/plogr" + homepage = "https://cloud.r-project.org/package=plogr" + url = "https://cloud.r-project.org/src/contrib/plogr_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plogr" version('0.2.0', sha256='0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29') version('0.1-1', '5ee46ed21b5c571d02900219098517c0') diff --git a/var/spack/repos/builtin/packages/r-plot3d/package.py b/var/spack/repos/builtin/packages/r-plot3d/package.py index b856601463..8e338d123b 100644 --- a/var/spack/repos/builtin/packages/r-plot3d/package.py +++ b/var/spack/repos/builtin/packages/r-plot3d/package.py @@ -11,10 +11,11 @@ class RPlot3d(RPackage): slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.""" - homepage = "https://CRAN.R-project.org/package=plot3D" - url = "https://cran.r-project.org/src/contrib/plot3D_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/plot3D" + homepage = "https://cloud.r-project.org/package=plot3D" + url = "https://cloud.r-project.org/src/contrib/plot3D_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plot3D" version('1.1.1', '5135aa1f3cf6106f2ded3f393a24e75d') + depends_on('r@2.15:', type=('build', 'run')) depends_on('r-misc3d', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plotly/package.py b/var/spack/repos/builtin/packages/r-plotly/package.py index 7b7cc8999d..29d1ea37a5 100644 --- a/var/spack/repos/builtin/packages/r-plotly/package.py +++ b/var/spack/repos/builtin/packages/r-plotly/package.py @@ -10,25 +10,38 @@ class RPlotly(RPackage): """Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R.""" - homepage = "https://cran.r-project.org/web/packages/plotly/index.html" - url = "https://cran.r-project.org/src/contrib/plotly_4.7.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/plotly" + homepage = "https://cloud.r-project.org/package=plotly" + url = "https://cloud.r-project.org/src/contrib/plotly_4.7.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plotly" + version('4.9.0', sha256='f761148338231f210fd7fe2f8325ffe9cfdaaaeddd7b933b65c44ebb4f85e2cf') + version('4.8.0', sha256='78f90282c831bbbb675ed4811fb506a98dd05e37251fabd42ebc263c80bae8a6') version('4.7.1', '4799c8b429291d4c52fb904380806548') version('4.7.0', '5bd52d515c01af7ff291c30a6cf23bec') version('4.6.0', '27ff3de288bacfaad6e6694752ea2929') version('4.5.6', 'e6e00177fa64dc6b1a199facfd73f585') version('4.5.2', '7eb11b24a9faa9a572657fd89ed72fa5') - depends_on('r@3.4.0:3.4.9') - depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-htmltools@0.3.6:', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) depends_on('r-dplyr', type=('build', 'run')) - depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r-htmlwidgets@1.3:', type=('build', 'run')) depends_on('r-data-table', type=('build', 'run')) depends_on('r-hexbin', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) - depends_on('r-crosstalk', type=('build', 'run')) + depends_on('r-crosstalk', when='@4.6.0:', type=('build', 'run')) + depends_on('r-scales', type=('build', 'run')) + depends_on('r-jsonlite@1.6:', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-viridislite', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run')) + depends_on('r-lazyeval@0.2.0:', type=('build', 'run')) + depends_on('r-rcolorbrewer', when='@4.6.0:', type=('build', 'run')) + depends_on('r-data-table', when='@4.7.0:', type=('build', 'run')) + depends_on('r-rlang', when='@4.8.0:', type=('build', 'run')) + depends_on('r-promises', when='@4.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py index 6ef2607342..a03e77b93a 100644 --- a/var/spack/repos/builtin/packages/r-plotrix/package.py +++ b/var/spack/repos/builtin/packages/r-plotrix/package.py @@ -9,9 +9,13 @@ from spack import * class RPlotrix(RPackage): """Lots of plots, various labeling, axis and color scaling functions.""" - homepage = "https://cran.r-project.org/package=plotrix" - url = "https://cran.r-project.org/src/contrib/plotrix_3.6-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/plotrix" + homepage = "https://cloud.r-project.org/package=plotrix" + url = "https://cloud.r-project.org/src/contrib/plotrix_3.6-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plotrix" + version('3.7-6', sha256='83d5f7574592953288b4fe39c4c0dd7670d097598ad7f6bddbb0687a32954e46') + version('3.7-5', sha256='b22f3f9d93961d23ad46e41597d1e45d2665ced04dcad8c40f6806a67cded14c') version('3.6-4', 'efe9b9b093d8903228a9b56c46d943fa') version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef') + + depends_on('r@3.5.0:', when='@3.7-6:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pls/package.py b/var/spack/repos/builtin/packages/r-pls/package.py index 706448e19d..d310c5d5fb 100644 --- a/var/spack/repos/builtin/packages/r-pls/package.py +++ b/var/spack/repos/builtin/packages/r-pls/package.py @@ -11,10 +11,12 @@ class RPls(RPackage): Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).""" - homepage = "https://cran.r-project.org/package=pls" - url = "https://cran.r-project.org/src/contrib/pls_2.6-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pls" + homepage = "https://cloud.r-project.org/package=pls" + url = "https://cloud.r-project.org/src/contrib/pls_2.6-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pls" + version('2.7-1', sha256='f8fd817fc2aa046970c49a9a481489a3a2aef8b6f09293fb1f0218f00bfd834b') + version('2.7-0', sha256='5ddc1249a14d69a7a39cc4ae81595ac8c0fbb1e46c911af67907baddeac35875') version('2.6-0', '04e02e8e46d983c5ed53c1f952b329df') - depends_on('r@2.10:') + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py index 077c331b50..c5fc1bf68d 100644 --- a/var/spack/repos/builtin/packages/r-plyr/package.py +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -16,9 +16,10 @@ class RPlyr(RPackage): Dickinson'.""" homepage = "http://had.co.nz/plyr" - url = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/plyr" + url = "https://cloud.r-project.org/src/contrib/plyr_1.8.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/plyr" version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pmcmr/package.py b/var/spack/repos/builtin/packages/r-pmcmr/package.py index 25936e929b..3097e0861f 100644 --- a/var/spack/repos/builtin/packages/r-pmcmr/package.py +++ b/var/spack/repos/builtin/packages/r-pmcmr/package.py @@ -21,8 +21,11 @@ class RPmcmr(RPackage): balanced incomplete block design (BIBD) is also given in this package.""" - homepage = "https://cran.r-project.org/package=PMCMR" - url = "https://cran.rstudio.com/src/contrib/PMCMR_4.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/PMCMR" + homepage = "https://cloud.r-project.org/package=PMCMR" + url = "https://cloud.r-project.org/src/contrib/PMCMR_4.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/PMCMR" + version('4.3', sha256='328a2880dd614dc412e8dca21d29ed9d5eea29ccbe0eff98c8068100856c7b25') version('4.1', 'b9c0c4e4cb4f73ae36f45a47abae986a') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py index 80689773af..a9bdc3318b 100644 --- a/var/spack/repos/builtin/packages/r-png/package.py +++ b/var/spack/repos/builtin/packages/r-png/package.py @@ -12,9 +12,10 @@ class RPng(RPackage): and in-memory raw vectors.""" homepage = "http://www.rforge.net/png/" - url = "https://cran.r-project.org/src/contrib/png_0.1-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/png" + url = "https://cloud.r-project.org/src/contrib/png_0.1-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/png" version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f') + depends_on('r@2.9.0:', type=('build', 'run')) depends_on('libpng') diff --git a/var/spack/repos/builtin/packages/r-polynom/package.py b/var/spack/repos/builtin/packages/r-polynom/package.py new file mode 100644 index 0000000000..4244a2a4ea --- /dev/null +++ b/var/spack/repos/builtin/packages/r-polynom/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RPolynom(RPackage): + """A collection of functions to implement a class for univariate polynomial + manipulations.""" + + homepage = "https://cloud.r-project.org/package=polynom" + url = "https://cloud.r-project.org/src/contrib/polynom_1.4-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/polynom" + + version('1.4-0', sha256='c5b788b26f7118a18d5d8e7ba93a0abf3efa6603fa48603c70ed63c038d3d4dd') diff --git a/var/spack/repos/builtin/packages/r-popgenome/package.py b/var/spack/repos/builtin/packages/r-popgenome/package.py index de573b59f5..70ca45e3b4 100644 --- a/var/spack/repos/builtin/packages/r-popgenome/package.py +++ b/var/spack/repos/builtin/packages/r-popgenome/package.py @@ -12,9 +12,10 @@ class RPopgenome(RPackage): genomes.""" homepage = "https://popgenome.weebly.com" - url = "https://cran.r-project.org/src/contrib/PopGenome_2.6.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/PopGenome" + url = "https://cloud.r-project.org/src/contrib/PopGenome_2.6.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/PopGenome" + version('2.7.1', sha256='a84903b151528fa026ccaba42ada22cd89babbc1824afd40269b7204e488a5fa') version('2.6.1', sha256='7a2922ed505fa801117a153e479d246bcf4854b91c6ab0241acc620a9d779b1c') depends_on('r@2.14.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-popvar/package.py b/var/spack/repos/builtin/packages/r-popvar/package.py index c5398eb1bf..15e1c03645 100644 --- a/var/spack/repos/builtin/packages/r-popvar/package.py +++ b/var/spack/repos/builtin/packages/r-popvar/package.py @@ -10,9 +10,9 @@ class RPopvar(RPackage): """PopVar: Genomic Breeding Tools: Genetic Variance Prediction andCross- Validation""" - homepage = "https://cran.r-project.org/package=PopVar" - url = "https://cran.r-project.org/src/contrib/PopVar_1.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/PopVar" + homepage = "https://cloud.r-project.org/package=PopVar" + url = "https://cloud.r-project.org/src/contrib/PopVar_1.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/PopVar" version('1.2.1', sha256='5e3df79634ab63708a431e4b8e6794675972ac6c58d2bc615726aa0f142f5f25') diff --git a/var/spack/repos/builtin/packages/r-powerlaw/package.py b/var/spack/repos/builtin/packages/r-powerlaw/package.py index f406a2f56a..0ee38127a0 100644 --- a/var/spack/repos/builtin/packages/r-powerlaw/package.py +++ b/var/spack/repos/builtin/packages/r-powerlaw/package.py @@ -13,9 +13,12 @@ class RPowerlaw(RPackage): is used to estimate the lower cut-off for the scaling region.""" homepage = "https://github.com/csgillespie/poweRlaw" - url = "https://cran.rstudio.com/src/contrib/poweRlaw_0.70.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/poweRlaw" + url = "https://cloud.r-project.org/src/contrib/poweRlaw_0.70.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/poweRlaw" + version('0.70.2', sha256='240f1454389b1a00ad483fb63e5b53243cc9367f21a3e7253ab2c293673459ab') version('0.70.1', '4117cb95c37f72441f320ea12f553065') + depends_on('r@3.1.0:', when='@:0.70.1', type=('build', 'run')) + depends_on('r@3.4.0:', when='@0.70.2:', type=('build', 'run')) depends_on('r-vgam', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-prabclus/package.py b/var/spack/repos/builtin/packages/r-prabclus/package.py index 124049d0ca..fd12aaddee 100644 --- a/var/spack/repos/builtin/packages/r-prabclus/package.py +++ b/var/spack/repos/builtin/packages/r-prabclus/package.py @@ -11,11 +11,13 @@ class RPrabclus(RPackage): Multilocus Genetic Data""" homepage = "http://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cran.r-project.org/src/contrib/prabclus_2.2-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/prabclus" + url = "https://cloud.r-project.org/src/contrib/prabclus_2.2-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/prabclus" + version('2.3-1', sha256='ef3294767d43bc3f72478fdaf0d1f13c8de18881bf9040c9f1add68af808b3c0') + version('2.2-7.1', sha256='2c5bf3bbb0d225e04c53bb0e11e9c2a6809f0e46d95b8f6dc14b9dd6a2452975') version('2.2-6', '7f835dcc113243e1db74aad28ce93d11') - depends_on('r@2.1.0:') - # depends_on('r-mass', type=('build', 'run')) + depends_on('r@2.1.0:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) depends_on('r-mclust', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py index be0785716b..830b9cfc00 100644 --- a/var/spack/repos/builtin/packages/r-praise/package.py +++ b/var/spack/repos/builtin/packages/r-praise/package.py @@ -11,7 +11,7 @@ class RPraise(RPackage): something good, or they just need it to feel better.""" homepage = "https://github.com/gaborcsardi/praise" - url = "https://cran.r-project.org/src/contrib/praise_1.0.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/praise" + url = "https://cloud.r-project.org/src/contrib/praise_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/praise" version('1.0.0', '9318724cec0454884b5f762bee2da6a1') diff --git a/var/spack/repos/builtin/packages/r-prettyunits/package.py b/var/spack/repos/builtin/packages/r-prettyunits/package.py index 3a3a3bf029..00d903db5c 100644 --- a/var/spack/repos/builtin/packages/r-prettyunits/package.py +++ b/var/spack/repos/builtin/packages/r-prettyunits/package.py @@ -11,9 +11,9 @@ class RPrettyunits(RPackage): 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB.""" - homepage = "https://cran.r-project.org/package=prettyunits" - url = "https://cran.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/prettyunits" + homepage = "https://cloud.r-project.org/package=prettyunits" + url = "https://cloud.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/prettyunits" version('1.0.2', '0a091a297e8b37df54e7fcf28697ee50') diff --git a/var/spack/repos/builtin/packages/r-processx/package.py b/var/spack/repos/builtin/packages/r-processx/package.py index 86a2a3e73c..d6661875b4 100644 --- a/var/spack/repos/builtin/packages/r-processx/package.py +++ b/var/spack/repos/builtin/packages/r-processx/package.py @@ -10,17 +10,19 @@ class RProcessx(RPackage): """Tools to run system processes in the background""" homepage = "https://github.com/r-lib/processx" - url = "https://cran.r-project.org/src/contrib/processx_3.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/processx/processx_3.1.0.tar.gz" + url = "https://cloud.r-project.org/src/contrib/processx_3.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/processx" + version('3.4.1', sha256='f1abddb48fa78f2b176552e2ec5d808d4d87d79ce72e9b3d25c9a7d715bbd1bc') + version('3.3.1', sha256='6123dbdf9f3bb6e5e8678980fb4587dcefb56d2190adf2ef494d7cd199720bae') version('3.2.0', sha256='c4ba602fcbdc032ae9d94701b3e6b83a2dab1b53d0b4f9937b07a84eae22fddf') version('3.1.0', sha256='11ac120ab4e4aa0e99c9b2eda87d07bc683bab735f1761e95e5ddacd311b5972') version('3.0.3', sha256='53781dba3c538605a02e28b3b577e7de79e2064bfc502025f7ec0e5945e302bf') version('2.0.0.1', sha256='8f61b2952d0f2d13c74465bfba174ce11eee559475c2f7b9be6bcb9e2e1d827b') version('2.0.0', sha256='8325b56a60a276909228756281523cda9256bc754c5f3ca03b41c5c17cc398ad') - depends_on('r-assertthat', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) - depends_on('r-ps', type=('build', 'run')) + depends_on('r-assertthat', when='@:3.2.9', type=('build', 'run')) + depends_on('r-crayon', when='@:3.2.9', type=('build', 'run')) + depends_on('r-ps@1.2.0:', when='@3.2.0:', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) - depends_on('r-utils', type=('build', 'run')) + depends_on('r-debugme', when='@:3.0.9', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-prodlim/package.py b/var/spack/repos/builtin/packages/r-prodlim/package.py index 157fa3b832..e945333a1c 100644 --- a/var/spack/repos/builtin/packages/r-prodlim/package.py +++ b/var/spack/repos/builtin/packages/r-prodlim/package.py @@ -11,14 +11,15 @@ class RProdlim(RPackage): user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.""" - homepage = "https://cran.r-project.org/package=prodlim" - url = "https://cran.r-project.org/src/contrib/prodlim_1.5.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/prodlim" + homepage = "https://cloud.r-project.org/package=prodlim" + url = "https://cloud.r-project.org/src/contrib/prodlim_1.5.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/prodlim" + version('2018.04.18', sha256='4b22b54fdf712439309be0ff74f63cde9080464667b00e19823372ac0fc254ab') + version('1.6.1', sha256='3f2665257118a3db8682731a500b1ae4d669af344672dc2037f987bee3cca154') version('1.5.9', 'e0843053c9270e41b657a733d6675dc9') - depends_on('r@2.9.0:') - + depends_on('r@2.9.0:', type=('build', 'run')) depends_on('r-rcpp@0.11.5:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-kernsmooth', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-progress/package.py b/var/spack/repos/builtin/packages/r-progress/package.py index 44955975ae..1d74872e34 100644 --- a/var/spack/repos/builtin/packages/r-progress/package.py +++ b/var/spack/repos/builtin/packages/r-progress/package.py @@ -13,10 +13,15 @@ class RProgress(RPackage): The package also provides a 'C++' 'API', that works with or without 'Rcpp'.""" - homepage = "https://cran.r-project.org/package=progress" - url = "https://cran.r-project.org/src/contrib/progress_1.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/progress" + homepage = "https://cloud.r-project.org/package=progress" + url = "https://cloud.r-project.org/src/contrib/progress_1.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/progress" + version('1.2.2', sha256='b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35') + version('1.2.1', sha256='7401e86ff76bef4d26508b74ee8bd169a0377b2738d9ec79ebff0b7fd5c55326') version('1.1.2', 'b3698672896125137e0077bc97132428') + depends_on('r-r6', type=('build', 'run')) depends_on('r-prettyunits', type=('build', 'run')) + depends_on('r-hms', when='@1.2.0:', type=('build', 'run')) + depends_on('r-crayon', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-promises/package.py b/var/spack/repos/builtin/packages/r-promises/package.py new file mode 100644 index 0000000000..6b0f6bf679 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-promises/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RPromises(RPackage): + """Provides fundamental abstractions for doing asynchronous programming in + R using promises. Asynchronous programming is useful for allowing a single + R process to orchestrate multiple tasks in the background while also + attending to something else. Semantics are similar to 'JavaScript' + promises, but with a syntax that is idiomatic R.""" + + homepage = "https://rstudio.github.io/promises" + url = "https://cloud.r-project.org/src/contrib/promises_1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/promises" + + version('1.0.1', sha256='c2dbc7734adf009377a41e570dfe0d82afb91335c9d0ca1ef464b9bdcca65558') + + depends_on('r-r6', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-later', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py index 2b8aa7211a..d2f5012ccb 100644 --- a/var/spack/repos/builtin/packages/r-proto/package.py +++ b/var/spack/repos/builtin/packages/r-proto/package.py @@ -11,8 +11,8 @@ class RProto(RPackage): prototype-based, rather than class-based object oriented ideas.""" homepage = "http://r-proto.googlecode.com/" - url = "https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/proto" + url = "https://cloud.r-project.org/src/contrib/proto_0.3-10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/proto" version('1.0.0', sha256='9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1') version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212') diff --git a/var/spack/repos/builtin/packages/r-proxy/package.py b/var/spack/repos/builtin/packages/r-proxy/package.py index 99ffc64571..94c954f821 100644 --- a/var/spack/repos/builtin/packages/r-proxy/package.py +++ b/var/spack/repos/builtin/packages/r-proxy/package.py @@ -11,7 +11,12 @@ class RProxy(RPackage): auto- and cross-proximities, along with implementations of the most popular ones.""" - homepage = "https://cran.r-project.org/package=proxy" - url = "https://cran.rstudio.com/src/contrib/proxy_0.4-19.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/proxy" + homepage = "https://cloud.r-project.org/package=proxy" + url = "https://cloud.r-project.org/src/contrib/proxy_0.4-19.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/proxy" + + version('0.4-23', sha256='9dd4eb0978f40e4fcb55c8a8a26266d32eff9c63ac9dfe70cf1f664ca9c3669d') version('0.4-19', '279a01a1cc12ed50208c98196d78a5d7') + + depends_on('r@3.3.2:', when='@:0.4-20', type=('build', 'run')) + depends_on('r@3.4.0:', when='@0.4-21:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py index d0d504a248..a3ba60d71e 100644 --- a/var/spack/repos/builtin/packages/r-pryr/package.py +++ b/var/spack/repos/builtin/packages/r-pryr/package.py @@ -12,10 +12,14 @@ class RPryr(RPackage): at a deeper level.""" homepage = "https://github.com/hadley/pryr" - url = "https://cran.r-project.org/src/contrib/pryr_0.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pryr" + url = "https://cloud.r-project.org/src/contrib/pryr_0.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/pryr" + version('0.1.4', sha256='d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b') + version('0.1.3', sha256='6acd88341dde4fe247a5cafd3949b281dc6742b7d60f68b57c1feb84b96739ac') version('0.1.2', '66b597a762aa15a3b7037779522983b6') + depends_on('r@3.1.0:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-codetools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ps/package.py b/var/spack/repos/builtin/packages/r-ps/package.py index dc10f7b1a0..6c75998ed5 100644 --- a/var/spack/repos/builtin/packages/r-ps/package.py +++ b/var/spack/repos/builtin/packages/r-ps/package.py @@ -10,8 +10,12 @@ class RPs(RPackage): """Manipulate processes on Windows, Linux and MacOS""" homepage = "https://github.com/r-lib/ps" - url = "https://cran.r-project.org/src/contrib/ps_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ps/ps_1.0.0.tar.gz" + url = "https://cloud.r-project.org/src/contrib/ps_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ps" + version('1.3.0', sha256='289193d0ccd2db0b6fe8702e8c5711e935219b17f90f01a6e9684982413e98d1') + version('1.2.1', sha256='bd7207164e6557a9e4213c4b00dc5dc23d7705ab290569765998640b16a3beff') version('1.1.0', sha256='5d5240d5bf1d48c721b3fdf47cfc9dbf878e388ea1f057b764db05bffdc4a9fe') version('1.0.0', sha256='9bdaf64aaa44ae11866868402eb75bf56c2e3022100476d9b9dcd16ca784ffd8') + + depends_on('r@3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-psych/package.py b/var/spack/repos/builtin/packages/r-psych/package.py index b5fc1085ca..e98d427f3d 100644 --- a/var/spack/repos/builtin/packages/r-psych/package.py +++ b/var/spack/repos/builtin/packages/r-psych/package.py @@ -25,11 +25,14 @@ class RPsych(RPackage): page.""" homepage = "http://personality-project.org/r/psych" - url = "https://cran.r-project.org/src/contrib/psych_1.7.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/psych" + url = "https://cloud.r-project.org/src/contrib/psych_1.7.8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/psych" + version('1.8.12', sha256='6e175e049bc1ee5b79a9e51ccafb22b962b4e6c839ce5c9cfa1ad83967037743') + version('1.8.10', sha256='e8901ddab14729bfccbd82a8824fbb6523c10c2cd8fb7199b1ca56a7ffcb6e58') version('1.7.8', 'db37f2f85ff5470ee40bbc0a58ebe22b') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-mnormt', type=('build', 'run')) depends_on('r-foreign', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ptw/package.py b/var/spack/repos/builtin/packages/r-ptw/package.py index b0d8b89d50..a571c31e30 100644 --- a/var/spack/repos/builtin/packages/r-ptw/package.py +++ b/var/spack/repos/builtin/packages/r-ptw/package.py @@ -18,10 +18,11 @@ class RPtw(RPackage): error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported.""" - homepage = "https://cran.r-project.org/package=ptw" - url = "https://cran.rstudio.com/src/contrib/ptw_1.9-12.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ptw" + homepage = "https://cloud.r-project.org/package=ptw" + url = "https://cloud.r-project.org/src/contrib/ptw_1.9-12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ptw" + version('1.9-13', sha256='7855e74a167db3d3eba9df9d9c3daa25d7cf487cbcfe8b095f16d96eba862f46') version('1.9-12', 'ddff887752d789ea72db3ee235ae7c67') depends_on('r-nloptr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-purrr/package.py b/var/spack/repos/builtin/packages/r-purrr/package.py index 67ab921aec..5e80aec44e 100644 --- a/var/spack/repos/builtin/packages/r-purrr/package.py +++ b/var/spack/repos/builtin/packages/r-purrr/package.py @@ -10,11 +10,14 @@ class RPurrr(RPackage): """A complete and consistent functional programming toolkit for R.""" homepage = "http://purrr.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/purrr_0.2.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/purrr" + url = "https://cloud.r-project.org/src/contrib/purrr_0.2.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/purrr" + version('0.3.2', sha256='27c74dd9e4f6f14bf442473df22bcafc068822f7f138f0870326532f143a9a31') + version('0.3.1', sha256='c2a3c9901192efd8a04976676f84885a005db88deb1432e4750900c7b3b7883b') version('0.2.4', 'd9a11e6c14771beb3ebe8f4771a552f3') - depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-rlang', type=('build', 'run')) - depends_on('r-tibble', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-magrittr@1.5:', type=('build', 'run')) + depends_on('r-rlang@0.3.1:', type=('build', 'run')) + depends_on('r-tibble', when='@:0.2.9', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-qtl/package.py b/var/spack/repos/builtin/packages/r-qtl/package.py index fcacfb58af..010b95665c 100644 --- a/var/spack/repos/builtin/packages/r-qtl/package.py +++ b/var/spack/repos/builtin/packages/r-qtl/package.py @@ -10,8 +10,8 @@ class RQtl(RPackage): """qtl: Tools for Analyzing QTL Experiments""" homepage = "http://rqtl.org" - url = "https://cran.r-project.org/src/contrib/qtl_1.44-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/qtl" + url = "https://cloud.r-project.org/src/contrib/qtl_1.44-9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/qtl" version('1.44-9', sha256='315063f0c3fbb95cd2169eb4109ade0339e8f3c28670b38c3167214b9bdf950e') diff --git a/var/spack/repos/builtin/packages/r-quadprog/package.py b/var/spack/repos/builtin/packages/r-quadprog/package.py index 4991cf03b7..d9ff67e804 100644 --- a/var/spack/repos/builtin/packages/r-quadprog/package.py +++ b/var/spack/repos/builtin/packages/r-quadprog/package.py @@ -10,8 +10,12 @@ class RQuadprog(RPackage): """This package contains routines and documentation for solving quadratic programming problems.""" - homepage = "https://cran.r-project.org/web/packages/quadprog/index.html" - url = "https://cran.r-project.org/src/contrib/quadprog_1.5-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/quadprog" + homepage = "https://cloud.r-project.org/package=quadprog" + url = "https://cloud.r-project.org/src/contrib/quadprog_1.5-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/quadprog" + version('1.5-7', sha256='1af41e57df6f2d08ee8b72a1a5ada137beadb36c7ec9ab9bdb7c05226e8ae76d') + version('1.5-6', sha256='1443e5ffdf884b13dd454e4f6aa260fce6ec47e6845d85b62238c206ce57dcba') version('1.5-5', '8442f37afd8d0b19b12e77d63e6515ad') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py index 972fe3e71d..9fb04ff133 100644 --- a/var/spack/repos/builtin/packages/r-quantmod/package.py +++ b/var/spack/repos/builtin/packages/r-quantmod/package.py @@ -11,13 +11,16 @@ class RQuantmod(RPackage): strategies.""" homepage = "http://www.quantmod.com/" - url = "https://cran.r-project.org/src/contrib/quantmod_0.4-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/quantmod" + url = "https://cloud.r-project.org/src/contrib/quantmod_0.4-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/quantmod" + version('0.4-15', sha256='7ef2e798d4d8e4d2af0a5b2b9fecebec30568087afbd24bfd923cdeb8b53df53') + version('0.4-14', sha256='d95b1acf73328d675bbad18a93fa3c40faf58959e0401458ad21cf6b9f9254b3') version('0.4-10', 'e4119c673567801eee16dcbbd0265de8') version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631') - depends_on('r-xts', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.4-11:', type=('build', 'run')) + depends_on('r-xts@0.9-0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) - depends_on('r-ttr', type=('build', 'run')) + depends_on('r-ttr@0.2:', type=('build', 'run')) depends_on('r-curl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py index deaffa31f3..65b538146e 100644 --- a/var/spack/repos/builtin/packages/r-quantreg/package.py +++ b/var/spack/repos/builtin/packages/r-quantreg/package.py @@ -14,13 +14,17 @@ class RQuantreg(RPackage): selection methods based on expected shortfall risk are also included.""" - homepage = "https://cran.r-project.org/package=quantreg" - url = "https://cran.r-project.org/src/contrib/quantreg_5.29.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/quantreg" + homepage = "https://cloud.r-project.org/package=quantreg" + url = "https://cloud.r-project.org/src/contrib/quantreg_5.29.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/quantreg" + version('5.51', sha256='df1330d245f66ee6d924b209bd4c15d44ff8cce52667959ec0d299975428bdb1') + version('5.42.1', sha256='4cc2b0883c52694e58fcfde83e30e4a54be9f4d9cbcf6138f6498cc8e0b3ccab') + version('5.40', sha256='86e310a235009ab85635dfb8803c175f80a35892e237db2525c4ef37a98936eb') version('5.29', '643ca728200d13f8c2e62365204e9907') version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f') + depends_on('r@2.6:', type=('build', 'run')) depends_on('r-sparsem', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) depends_on('r-matrixmodels', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-methodss3/package.py b/var/spack/repos/builtin/packages/r-r-methodss3/package.py index f52de95e12..e2887c572d 100644 --- a/var/spack/repos/builtin/packages/r-methodss3/package.py +++ b/var/spack/repos/builtin/packages/r-r-methodss3/package.py @@ -6,7 +6,7 @@ from spack import * -class RMethodss3(RPackage): +class RRMethodss3(RPackage): """Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for @@ -17,8 +17,10 @@ class RMethodss3(RPackage): a cross-platform package implemented in pure R that generates standard S3 methods.""" - homepage = "https://cran.r-project.org/package=R.methodsS3" - url = "https://cran.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/R.methodsS3" + homepage = "https://cloud.r-project.org/package=R.methodsS3" + url = "https://cloud.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/R.methodsS3" version('1.7.1', 'c88e815837f268affd4f2a39c737d969') + + depends_on('r@2.13.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-oo/package.py b/var/spack/repos/builtin/packages/r-r-oo/package.py index cef0f76cd8..8dc62a1b16 100644 --- a/var/spack/repos/builtin/packages/r-oo/package.py +++ b/var/spack/repos/builtin/packages/r-r-oo/package.py @@ -6,7 +6,7 @@ from spack import * -class ROo(RPackage): +class RROo(RPackage): """Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of @@ -16,9 +16,11 @@ class ROo(RPackage): standard S3 classes without any tricks.""" homepage = "https://github.com/HenrikBengtsson/R.oo" - url = "https://cran.rstudio.com/src/contrib/R.oo_1.21.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/R.oo" + url = "https://cloud.r-project.org/src/contrib/R.oo_1.21.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/R.oo" + version('1.22.0', sha256='c0862e4608fb2b8f91ec4494d46c2f3ba7bc44999f9aa3d7b9625d3792e7dd4c') version('1.21.0', 'f0062095c763faaeba30558303f68bc3') - depends_on('r-methodss3', type=('build', 'run')) + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r-utils/package.py b/var/spack/repos/builtin/packages/r-r-utils/package.py new file mode 100644 index 0000000000..9318bdc1d9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-r-utils/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRUtils(RPackage): + """Utility functions useful when programming and + developing R packages.""" + + homepage = "https://github.com/HenrikBengtsson/R.utils" + url = "https://cloud.r-project.org/src/contrib/R.utils_2.5.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/R.utils" + + version('2.9.0', sha256='b2aacc5a55d3ea86c41ac576d2583e446af145f4cb1103ad7b6f95b09ab09ff0') + version('2.5.0', 'a728ef3ceb35cafc4c39ea577cecc38b') + + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-r-oo@1.22.0:', type=('build', 'run')) + depends_on('r-r-methodss3@1.7.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py index 2e8209fd5e..983cabee2d 100644 --- a/var/spack/repos/builtin/packages/r-r6/package.py +++ b/var/spack/repos/builtin/packages/r-r6/package.py @@ -15,11 +15,12 @@ class RR6(RPackage): classes are defined in different packages.""" homepage = "https://github.com/wch/R6/" - url = "https://cran.rstudio.com/src/contrib/R6_2.2.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/R6" + url = "https://cloud.r-project.org/src/contrib/R6_2.2.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/R6" + version('2.4.0', sha256='70be110174fbf5f5304049b186a6f9c05b77bfaec6d8caf980fcef5da6e0abce') version('2.2.2', '635b58c65bff624a1fab69c6b1989801') version('2.2.0', '659d83b2d3f7a308a48332b4cfbdab49') version('2.1.2', 'b6afb9430e48707be87638675390e457') - depends_on('r@3.0:') + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomfields/package.py b/var/spack/repos/builtin/packages/r-randomfields/package.py index b8a6232842..815eba3557 100644 --- a/var/spack/repos/builtin/packages/r-randomfields/package.py +++ b/var/spack/repos/builtin/packages/r-randomfields/package.py @@ -11,12 +11,14 @@ class RRandomfields(RPackage): are provided, as well as methods for the simulation of extreme value random fields.""" - homepage = "https://cran.r-project.org/web/packages/RandomFields" - url = "https://cran.r-project.org/src/contrib/RandomFields_3.1.50.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RandomFields" + homepage = "https://cloud.r-project.org/package=RandomFields" + url = "https://cloud.r-project.org/src/contrib/RandomFields_3.1.50.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFields" + version('3.3.6', sha256='51b7bfb4e5bd7fd0ce1207c77f428508a6cd3dfc9de01545a8724dfd9c050213') + version('3.3.4', sha256='a340d4f3ba7950d62acdfa19b9724c82e439d7b1a9f73340124038b7c90c73d4') version('3.1.50', 'fd91aea76365427c0ba3b25fb3af43a6') - depends_on('r@3.3:', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) - depends_on('r-randomfieldsutils@0.3.25:', type=('build', 'run')) + depends_on('r-randomfieldsutils@0.5.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py index cbd0199257..fa51ba6c9a 100644 --- a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py +++ b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py @@ -12,10 +12,12 @@ class RRandomfieldsutils(RPackage): checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.""" - homepage = "https://cran.r-project.org/web/packages/RandomFieldsUtils" - url = "https://cran.r-project.org/src/contrib/RandomFieldsUtils_0.3.25.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RandomFieldsUtils" + homepage = "https://cloud.r-project.org/package=RandomFieldsUtils" + url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.3.25.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFieldsUtils" + version('0.5.3', sha256='ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d') + version('0.5.1', sha256='a95aab4e2025c4247503ff513570a65aa3c8e63cb7ce2979c9317a2798dfaca2') version('0.3.25', '026c15a23296c9726012135891f016d5') - depends_on('r@3.3:', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py index b2e9987393..b24defd121 100644 --- a/var/spack/repos/builtin/packages/r-randomforest/package.py +++ b/var/spack/repos/builtin/packages/r-randomforest/package.py @@ -11,7 +11,11 @@ class RRandomforest(RPackage): inputs.""" homepage = "https://www.stat.berkeley.edu/~breiman/RandomForests/" - url = "https://cran.r-project.org/src/contrib/randomForest_4.6-12.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/randomForest" + url = "https://cloud.r-project.org/src/contrib/randomForest_4.6-12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/randomForest" + version('4.6-14', sha256='f4b88920419eb0a89d0bc5744af0416d92d112988702dc726882394128a8754d') version('4.6-12', '071c03af974198e861f1475c5bab9e7a') + + depends_on('r@2.5.0:', when='@:4.6-12', type=('build', 'run')) + depends_on('r@3.2.2:', when='@4.6-14:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-randomglm/package.py b/var/spack/repos/builtin/packages/r-randomglm/package.py index 47e513968d..817d6467b4 100644 --- a/var/spack/repos/builtin/packages/r-randomglm/package.py +++ b/var/spack/repos/builtin/packages/r-randomglm/package.py @@ -10,8 +10,8 @@ class RRandomglm(RPackage): """randomGLM: Random General Linear Model Prediction""" homepage = "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/" - url = "https://cran.r-project.org/src/contrib/randomGLM_1.02-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/randomGLM" + url = "https://cloud.r-project.org/src/contrib/randomGLM_1.02-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/randomGLM" version('1.02-1', sha256='3bf7c1dbdacc68125f8ae3014b9bc546dd3328d04ad015d154781bdf3f1a230c') diff --git a/var/spack/repos/builtin/packages/r-ranger/package.py b/var/spack/repos/builtin/packages/r-ranger/package.py index 0a95a55635..a8cf0f0d0a 100644 --- a/var/spack/repos/builtin/packages/r-ranger/package.py +++ b/var/spack/repos/builtin/packages/r-ranger/package.py @@ -10,17 +10,19 @@ class RRanger(RPackage): """A fast implementation of Random Forests, particularly suited for high dimensional data.""" - homepage = "https://cran.r-project.org/web/packages/ranger/index.html" - url = "https://cran.r-project.org/src/contrib/ranger_0.8.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/ranger" + homepage = "https://cloud.r-project.org/package=ranger" + url = "https://cloud.r-project.org/src/contrib/ranger_0.8.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ranger" + version('0.11.2', sha256='13ac8a9433fdd92f62f66de44abc52477dcbb436b2045c1947951a266bffbeeb') + version('0.11.1', sha256='999fb114602e27601ff0fe8ab461c39d667c6f5e8434e7feb3d21c7caf0dcffb') version('0.8.0', '1501380f418e784a6159bc1fb06fd32c') version('0.7.0', 'c7fbcbab7c195bc8e65b1ceb3baeb87f') version('0.6.0', '047ad26289c9b528b7476aa4811b4111') version('0.5.0', 'd45001c8ff58d3078de7353971219927') version('0.4.0', 'd404d8a9142372e3c77482b6b7dc469b') - depends_on('r@3.4.0:3.4.9') + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.2:', type=('build', 'run')) depends_on('r-rcppeigen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rann/package.py b/var/spack/repos/builtin/packages/r-rann/package.py new file mode 100644 index 0000000000..bbe014ee45 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rann/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRann(RPackage): + """Finds the k nearest neighbours for every point in a given dataset in O(N + log N) time using Arya and Mount's ANN library (v1.1.3). There is support + for approximate as well as exact searches, fixed radius searches and 'bd' + as well as 'kd' trees. The distance is computed using the L2 (Euclidean) + metric. Please see package 'RANN.L1' for the same functionality using the + L1 (Manhattan, taxicab) metric.""" + + homepage = "https://github.com/jefferis/RANN" + url = "https://cloud.r-project.org/src/contrib/RANN_2.6.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RANN" + + version('2.6.1', sha256='b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182') diff --git a/var/spack/repos/builtin/packages/r-rappdirs/package.py b/var/spack/repos/builtin/packages/r-rappdirs/package.py index 49e24bf0d5..5366f07494 100644 --- a/var/spack/repos/builtin/packages/r-rappdirs/package.py +++ b/var/spack/repos/builtin/packages/r-rappdirs/package.py @@ -11,9 +11,9 @@ class RRappdirs(RPackage): you should use to save data, caches and logs. A port of Python's 'Appdirs' to R.""" - homepage = "https://cran.r-project.org/package=rappdirs" - url = "https://cran.rstudio.com/src/contrib/rappdirs_0.3.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rappdirs" + homepage = "https://cloud.r-project.org/package=rappdirs" + url = "https://cloud.r-project.org/src/contrib/rappdirs_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rappdirs" version('0.3.1', 'fbbdceda2aa49374e61c7d387bf9ea21') diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py index e0cc4a9555..912f9c17e0 100644 --- a/var/spack/repos/builtin/packages/r-raster/package.py +++ b/var/spack/repos/builtin/packages/r-raster/package.py @@ -11,11 +11,14 @@ class RRaster(RPackage): spatial data. The package implements basic and high-level functions. Processing of very large files is supported.""" - homepage = "http://cran.r-project.org/package=raster" - url = "https://cran.r-project.org/src/contrib/raster_2.5-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/raster" + homepage = "https://cloud.r-project.org/package=raster" + url = "https://cloud.r-project.org/src/contrib/raster_2.5-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/raster" + version('2.9-23', sha256='90aaec9e3b1e3e6015d9993ea7491e008f2f71990f8abb8610f979c4e28b38af') + version('2.9-22', sha256='8107d95f1aa85cea801c8101c6aa391becfef4b5b915d9bc7a323531fee26128') version('2.5-8', '2a7db931c74d50516e82d04687c0a577') - depends_on('r-sp', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-sp@1.2-0:', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py index 332de772ba..b0e8e510f7 100644 --- a/var/spack/repos/builtin/packages/r-rbokeh/package.py +++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py @@ -12,12 +12,12 @@ class RRbokeh(RPackage): Analytics.""" homepage = "https://hafen.github.io/rbokeh" - url = "https://cran.r-project.org/src/contrib/rbokeh_0.5.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rbokeh" + url = "https://cloud.r-project.org/src/contrib/rbokeh_0.5.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rbokeh" version('0.5.0', '4e14778c3fbd9286460ca28c68f57d10') - depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r-htmlwidgets@0.5:', type=('build', 'run')) depends_on('r-maps', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcmdcheck/package.py b/var/spack/repos/builtin/packages/r-rcmdcheck/package.py new file mode 100644 index 0000000000..c64a59bc97 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcmdcheck/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRcmdcheck(RPackage): + """Run 'R CMD check' from 'R' and capture the results of the individual + checks. Supports running checks in the background, timeouts, pretty + printing and comparing check results.""" + + homepage = "https://github.com/r-Lib/rcmdcheck#readme" + url = "https://cloud.r-project.org/src/contrib/rcmdcheck_1.3.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rcmdcheck" + + version('1.3.3', sha256='1ab679eb1976d74cd3be5bcad0af7fcc673dbdfd4406bbce32591c8fddfb93b4') + + depends_on('r-callr@3.1.1.9000:', type=('build', 'run')) + depends_on('r-cli@1.1.0:', type=('build', 'run')) + depends_on('r-crayon', type=('build', 'run')) + depends_on('r-desc@1.2.0:', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-pkgbuild', type=('build', 'run')) + depends_on('r-prettyunits', type=('build', 'run')) + depends_on('r-r6', type=('build', 'run')) + depends_on('r-rprojroot', type=('build', 'run')) + depends_on('r-sessioninfo@1.1.1:', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run')) + depends_on('r-xopen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py index 287e846c7c..b2cb38aa1f 100644 --- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -11,7 +11,9 @@ class RRcolorbrewer(RPackage): Brewer as described at http://colorbrewer2.org""" homepage = "http://colorbrewer2.org" - url = "https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RColorBrewer" + url = "https://cloud.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RColorBrewer" version('1.1-2', '66054d83eade4dff8a43ad4732691182') + + depends_on('r@2.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 3ee436d104..e2abba3b83 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -18,9 +18,10 @@ class RRcpp(RPackage): last two.""" homepage = "http://dirk.eddelbuettel.com/code/rcpp.html" - url = "https://cran.rstudio.com/src/contrib/Rcpp_0.12.13.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/Rcpp" + url = "https://cloud.r-project.org/src/contrib/Rcpp_0.12.13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Rcpp" + version('1.0.2', sha256='ad9338d6fc89dd116a3e2c5ecef1956e4be63b6c6aa1b21b2e5f249d65a5129c') version('1.0.0', sha256='b7378bf0dda17ef72aa3f2a318a9cb5667bef50b601dc1096431e17426e18bc2') version('0.12.19', sha256='63aeb6d4b58cd2899ded26f38a77d461397d5b0dc5936f187d3ca6cd958ab582') version('0.12.18', sha256='fcecd01e53cfcbcf58dec19842b7235a917b8d98988e4003cc090478c5bbd300') diff --git a/var/spack/repos/builtin/packages/r-rcppannoy/package.py b/var/spack/repos/builtin/packages/r-rcppannoy/package.py new file mode 100644 index 0000000000..64ee9a72aa --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcppannoy/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRcppannoy(RPackage): + """'Annoy' is a small C++ library for Approximate Nearest Neighbors written + for efficient memory usage as well an ability to load from / save to disk. + This package provides an R interface by relying on the 'Rcpp' package, + exposing the same interface as the original Python wrapper to 'Annoy'. See + <https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released + under Version 2.0 of the Apache License. Also included is a small Windows + port of 'mmap' which is released under the MIT license.""" + + homepage = "https://cloud.r-project.org/package=RcppAnnoy" + url = "https://cloud.r-project.org/src/contrib/RcppAnnoy_0.0.12.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppAnnoy" + + version('0.0.12', sha256='8f736cbbb4a32c80cb08ba4e81df633846d725f27867e983af2012966eac0eac') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-rcpp@0.11.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py index 51ef1b3daf..55f412a45c 100644 --- a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py +++ b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py @@ -10,10 +10,13 @@ class RRcpparmadillo(RPackage): """'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library.""" - homepage = "https://cran.r-project.org/package=RcppArmadillo" - url = "https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.100.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RcppArmadillo" + homepage = "https://cloud.r-project.org/package=RcppArmadillo" + url = "https://cloud.r-project.org/src/contrib/RcppArmadillo_0.8.100.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppArmadillo" + version('0.9.600.4.0', sha256='2057b7aa965a4c821dd734276d8e6a01cd59a1b52536b65cb815fa7e8c114f1e') + version('0.9.400.3.0', sha256='56936d501fe8e6f8796ae1a6badb9294d7dad98a0b557c3b3ce6bd4ecaad13b0') version('0.8.100.1.0', 'a79c0ee967f502702414bc3c80c88f56') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@3.3.0:', when='@0.8.500.0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppblaze/package.py b/var/spack/repos/builtin/packages/r-rcppblaze/package.py index d2161ceaa2..e9af43aded 100644 --- a/var/spack/repos/builtin/packages/r-rcppblaze/package.py +++ b/var/spack/repos/builtin/packages/r-rcppblaze/package.py @@ -35,12 +35,12 @@ class RRcppblaze(RPackage): the most compilers and system.""" homepage = "https://github.com/Chingchuan-chen/RcppBlaze" - url = "https://cran.rstudio.com/src/contrib/RcppBlaze_0.2.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/RcppBlaze" + url = "https://cloud.r-project.org/src/contrib/RcppBlaze_0.2.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppBlaze" version('0.2.2', '22ecae73cf1bebce06ed6387d49f2c77') + depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-matrix@1.1-0:', type=('build', 'run')) depends_on('r-bh@1.54.0-2:', type=('build', 'run')) - depends_on('r@3.0.2:') diff --git a/var/spack/repos/builtin/packages/r-rcppcctz/package.py b/var/spack/repos/builtin/packages/r-rcppcctz/package.py index ad2b03965b..d4f48d3a5c 100644 --- a/var/spack/repos/builtin/packages/r-rcppcctz/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcctz/package.py @@ -14,9 +14,11 @@ class RRcppcctz(RPackage): <https://github.com/google/cctz> for more details.""" homepage = "https://github.com/eddelbuettel/rcppcctz" - url = "https://cran.r-project.org/src/contrib/RcppCCTZ_0.2.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RcppCCTZ" + url = "https://cloud.r-project.org/src/contrib/RcppCCTZ_0.2.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppCCTZ" + version('0.2.6', sha256='0e9a76055d29da24cd4c4069c78c1f44998f3461be60c7a6c3e7a35059fb79ae') + version('0.2.4', sha256='98b6867d38abe03957fe803e88b6cc2d122b85a68ef07fa86f7e1009d6c00819') version('0.2.3', '7635014a1cc696a3f00a7619fb5d7008') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py index 1344d5931f..dc517e9060 100644 --- a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py +++ b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py @@ -10,11 +10,11 @@ class RRcppcnpy(RPackage): """Rcpp bindings for NumPy files.""" homepage = "https://github.com/eddelbuettel/rcppcnpy" - url = "https://cran.r-project.org/src/contrib/RcppCNPy_0.2.9.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/RcppCNPy" + url = "https://cloud.r-project.org/src/contrib/RcppCNPy_0.2.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppCNPy" + version('0.2.10', sha256='77d6fbc86520a08da40d44c0b82767099f8f719ca95870d91efff1a9cab1ab9c') version('0.2.9', '7f63354d15928b6716830c2975b3baf0') depends_on('r@3.1.0:', type=('build', 'run')) - depends_on('cnpy') depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py index 1f07972974..221a998383 100644 --- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -22,12 +22,15 @@ class RRcppeigen(RPackage): GNU GPL version 2 or later, as is the rest of 'Rcpp'.""" homepage = "http://eigen.tuxfamily.org/" - url = "https://cran.r-project.org/src/contrib/RcppEigen_0.3.2.9.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen" + url = "https://cloud.r-project.org/src/contrib/RcppEigen_0.3.2.9.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppEigen" + version('0.3.3.5.0', sha256='e5c6af17770c5f57b7cf2fba04ad1a519901b446e8138bfff221952458207f05') + version('0.3.3.4.0', sha256='11020c567b299b1eac95e8a4d57abf0315931286907823dc7b66c44d0dd6dad4') version('0.3.3.3.1', '1a5ae17828813e40e6b3e7400e408a2b') version('0.3.2.9.0', '14a7786882a5d9862d53c4b2217df318') version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@2.15.1:', type=('build', 'run')) + depends_on('r-matrix@1.1-0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcppparallel/package.py b/var/spack/repos/builtin/packages/r-rcppparallel/package.py new file mode 100644 index 0000000000..ad723a0de5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcppparallel/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRcppparallel(RPackage): + """High level functions for parallel programming with 'Rcpp'. For example, + the 'parallelFor()' function can be used to convert the work of a standard + serial "for" loop into a parallel one and the 'parallelReduce()' function + can be used for accumulating aggregate or other values.""" + + homepage = "http://rcppcore.github.io/RcppParallel" + url = "https://cloud.r-project.org/src/contrib/RcppParallel_4.4.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppParallel" + + version('4.4.3', sha256='7a04929ecab97e46c0b09fe5cdbac9d7bfa17ad7d111f1a9787a9997f45fa0fa') + + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rcppprogress/package.py b/var/spack/repos/builtin/packages/r-rcppprogress/package.py index 5ef2b4ea1f..4680b00964 100644 --- a/var/spack/repos/builtin/packages/r-rcppprogress/package.py +++ b/var/spack/repos/builtin/packages/r-rcppprogress/package.py @@ -11,14 +11,15 @@ class RRcppprogress(RPackage): computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.""" - homepage = "https://cran.r-project.org/web/packages/RcppProgress/index.html" - url = "https://cran.r-project.org/src/contrib/RcppProgress_0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RcppProgress" + homepage = "https://cloud.r-project.org/package=RcppProgress" + url = "https://cloud.r-project.org/src/contrib/RcppProgress_0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RcppProgress" + version('0.4.1', sha256='11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a') + version('0.4', sha256='706e14360dbc5976db05c2ac6692c3279c0f8c95e72bf9d4becd9e1348025e3e') version('0.3', '3cd527af84bc6fcb3c77422e0ff09dba') version('0.2.1', 'c9cd69759ff457acfee0b52353f9af1b') version('0.2', '9522c962ecddd4895b5636e7a499bda5') version('0.1', '34afefe0580ca42b6353533fe758d5bf') - depends_on('r@3.4.0:3.4.9') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.9.4:', when='@:0.4', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rcurl/package.py b/var/spack/repos/builtin/packages/r-rcurl/package.py index 2c88de66fe..0af3d5275e 100644 --- a/var/spack/repos/builtin/packages/r-rcurl/package.py +++ b/var/spack/repos/builtin/packages/r-rcurl/package.py @@ -18,11 +18,14 @@ class RRcurl(RPackage): SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.""" - homepage = "https://cran.rstudio.com/web/packages/RCurl/index.html" - url = "https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl" + homepage = "https://cloud.r-project.org/package=RCurl" + url = "https://cloud.r-project.org/src/contrib/RCurl_1.95-4.8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RCurl" + version('1.95-4.12', sha256='393779efafdf40823dac942a1e028905d65c34f3d41cfd21bcd225e411385ff4') version('1.95-4.8', '9c8aaff986eb2792c89dd3ae54d21580') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-bitops', type=('build', 'run')) depends_on('curl') + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rda/package.py b/var/spack/repos/builtin/packages/r-rda/package.py index 3dc929a13a..4cdbe65ac0 100644 --- a/var/spack/repos/builtin/packages/r-rda/package.py +++ b/var/spack/repos/builtin/packages/r-rda/package.py @@ -10,8 +10,12 @@ class RRda(RPackage): """Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.""" - homepage = "https://cran.r-project.org/web/packages/rda/index.html" - url = "https://cran.r-project.org/src/contrib/rda_1.0.2-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rda" + homepage = "https://cloud.r-project.org/package=rda" + url = "https://cloud.r-project.org/src/contrib/rda_1.0.2-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rda" + version('1.0.2-2.1', sha256='6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8') + version('1.0.2-2', sha256='52ee41249b860af81dc692eee38cd4f8f26d3fbe34cb274f4e118de0013b58bc') version('1.0.2-1', '78060c5e054a63a2df4ae4002d7247bc') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rdpack/package.py b/var/spack/repos/builtin/packages/r-rdpack/package.py new file mode 100644 index 0000000000..2febe78186 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rdpack/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRdpack(RPackage): + """Functions for manipulation of R documentation objects, including + functions reprompt() and ereprompt() for updating 'Rd' documentation for + functions, methods and classes; 'Rd' macros for citations and import of + references from 'bibtex' files for use in 'Rd' files and 'roxygen2' + comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and + the results of its evaluation or creating graphics on the fly; and many + functions for manipulation of references and Rd files.""" + + homepage = "https://github.com/GeoBosh/Rdpack" + url = "https://cloud.r-project.org/src/contrib/Rdpack_0.11-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Rdpack" + + version('0.11-0', sha256='8fb449c80fbe931cdce51f728fb03a1978009ccce66fd6b9edacdc6ff4118d85') + + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-bibtex@0.4.0:', type=('build', 'run')) + depends_on('r-gbrd', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-readr/package.py b/var/spack/repos/builtin/packages/r-readr/package.py index 1b6753916b..586d0d9528 100644 --- a/var/spack/repos/builtin/packages/r-readr/package.py +++ b/var/spack/repos/builtin/packages/r-readr/package.py @@ -12,14 +12,20 @@ class RReadr(RPackage): flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.""" - homepage = "https://cran.rstudio.com/web/packages/readr/index.html" - url = "https://cran.rstudio.com/src/contrib/readr_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/readr/" + homepage = "https://cloud.r-project.org/package=readr" + url = "https://cloud.r-project.org/src/contrib/readr_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/readr" + version('1.3.1', sha256='33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3') version('1.1.1', 'cffb6669664f6a0f6fe172542e64cb47') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@3.0.2:', when='@:1.2.1', type=('build', 'run')) + depends_on('r@3.1:', when='@1.3.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.0.5:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) - depends_on('r-hms', type=('build', 'run')) + depends_on('r-hms@0.4.1:', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) depends_on('r-bh', type=('build', 'run')) + depends_on('r-clipr', when='@1.2.0:', type=('build', 'run')) + depends_on('r-crayon', when='@1.3.1:', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-readxl/package.py b/var/spack/repos/builtin/packages/r-readxl/package.py index f01cc790ff..599534113d 100644 --- a/var/spack/repos/builtin/packages/r-readxl/package.py +++ b/var/spack/repos/builtin/packages/r-readxl/package.py @@ -14,12 +14,15 @@ class RReadxl(RPackage): without external dependencies.""" homepage = "http://readxl.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/readxl_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/readxl/readxl_1.0.0.tar.gz" + url = "https://cloud.r-project.org/src/contrib/readxl_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/readxl" + version('1.3.1', sha256='24b441713e2f46a3e7c6813230ad6ea4d4ddf7e0816ad76614f33094fbaaaa96') + version('1.3.0', sha256='8379d1026dcfc662d073eb1c69ed1d90aa6439d6cb3c6fc1b5d1db4f51b3fadc') version('1.1.0', sha256='b63d21fc6510acb373e96deaec45e966a523ec75cbec75a089529297ed443116') version('1.0.0', '030c47ae1af5dd4168087160c29131e4') - depends_on('r-tibble', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-tibble@1.3.1:', type=('build', 'run')) + depends_on('r-rcpp@0.12.18:', type=('build', 'run')) depends_on('r-cellranger', type=('build', 'run')) + depends_on('r-progress', when='@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-recipes/package.py b/var/spack/repos/builtin/packages/r-recipes/package.py new file mode 100644 index 0000000000..12c00f6613 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-recipes/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRecipes(RPackage): + """An extensible framework to create and preprocess design matrices. + Recipes consist of one or more data manipulation and analysis "steps". + Statistical parameters for the steps can be estimated from an initial data + set and then applied to other data sets. The resulting design matrices can + then be used as inputs into statistical or machine learning models.""" + + homepage = "https://github.com/tidymodels/recipes" + url = "https://cloud.r-project.org/src/contrib/recipes_0.1.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/recipes" + + version('0.1.6', sha256='51e0db72de171d58d13ad8ffcf1dea402ab8f82100d161722041b6fd014cbfd9') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-generics', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run')) + depends_on('r-gower', type=('build', 'run')) + depends_on('r-ipred', type=('build', 'run')) + depends_on('r-lubridate', type=('build', 'run')) + depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-purrr@0.2.3:', type=('build', 'run')) + depends_on('r-rlang@0.4.0:', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run')) + depends_on('r-tidyr', type=('build', 'run')) + depends_on('r-tidyselect@0.2.5:', type=('build', 'run')) + depends_on('r-timedate', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py index 4c6acb2624..457908f4df 100644 --- a/var/spack/repos/builtin/packages/r-registry/package.py +++ b/var/spack/repos/builtin/packages/r-registry/package.py @@ -9,8 +9,12 @@ from spack import * class RRegistry(RPackage): """Provides a generic infrastructure for creating and using registries.""" - homepage = "https://cran.r-project.org/web/packages/registry/index.html" - url = "https://cran.r-project.org/src/contrib/registry_0.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/registry" + homepage = "https://cloud.r-project.org/package=registry" + url = "https://cloud.r-project.org/src/contrib/registry_0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/registry" + version('0.5-1', sha256='dfea36edb0a703ec57e111016789b47a1ba21d9c8ff30672555c81327a3372cc') + version('0.5', sha256='5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb') version('0.3', '85345b334ec81eb3da6edcbb27c5f421') + + depends_on('r@2.6.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rematch/package.py b/var/spack/repos/builtin/packages/r-rematch/package.py index 00f5d75da5..2887630876 100644 --- a/var/spack/repos/builtin/packages/r-rematch/package.py +++ b/var/spack/repos/builtin/packages/r-rematch/package.py @@ -11,10 +11,8 @@ class RRematch(RPackage): captured groups from the match of a regular expression to a character vector.""" - homepage = "https://cran.r-project.org/package=rematch" - url = "https://cran.r-project.org/src/contrib/rematch_1.0.1.tar.gz" + homepage = "https://cloud.r-project.org/package=rematch" + url = "https://cloud.r-project.org/src/contrib/rematch_1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rematch" version('1.0.1', '5271666295e232931f21499522489dd3') - - depends_on('r-covr', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-remotes/package.py b/var/spack/repos/builtin/packages/r-remotes/package.py new file mode 100644 index 0000000000..9c4a790dcb --- /dev/null +++ b/var/spack/repos/builtin/packages/r-remotes/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRemotes(RPackage): + """Download and install R packages stored in 'GitHub', 'BitBucket', or + plain 'subversion' or 'git' repositories. This package provides the + 'install_*' functions in 'devtools'. Indeed most of the code was copied + over from 'devtools'.""" + + homepage = "https://github.com/r-lib/remotes#readme" + url = "https://cloud.r-project.org/src/contrib/remotes_2.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/remotes" + + version('2.1.0', sha256='8944c8f6fc9f0cd0ca04d6cf1221b716eee08facef9f4b4c4d91d0346d6d68a7') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reordercluster/package.py b/var/spack/repos/builtin/packages/r-reordercluster/package.py index d1ed897d0e..5d63690aa8 100644 --- a/var/spack/repos/builtin/packages/r-reordercluster/package.py +++ b/var/spack/repos/builtin/packages/r-reordercluster/package.py @@ -11,10 +11,12 @@ class RReordercluster(RPackage): that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together.""" - homepage = "https://cran.r-project.org/package=ReorderCluster" - url = "https://cran.rstudio.com/src/contrib/ReorderCluster_1.0.tar.gz" + homepage = "https://cloud.r-project.org/package=ReorderCluster" + url = "https://cloud.r-project.org/src/contrib/ReorderCluster_1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ReorderCluster" version('1.0', '67ba34acb15dda75389a822bd2fdd31a') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-gplots', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py index eed19834ad..de4930c4c8 100644 --- a/var/spack/repos/builtin/packages/r-reportingtools/package.py +++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py @@ -41,7 +41,7 @@ class RReportingtools(RPackage): depends_on('r-gseabase', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) - depends_on('r-utils', type=('build', 'run')) + depends_on('r-r-utils', type=('build', 'run')) depends_on('r-deseq2', type=('build', 'run')) depends_on('r-ggplot2', type=('build', 'run')) depends_on('r-ggbio', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py index ca7f3a37e6..90da8713f6 100644 --- a/var/spack/repos/builtin/packages/r-repr/package.py +++ b/var/spack/repos/builtin/packages/r-repr/package.py @@ -12,7 +12,15 @@ class RRepr(RPackage): mime types.""" homepage = "https://github.com/IRkernel/repr" - url = "https://cran.r-project.org/src/contrib/repr_0.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/repr" + url = "https://cloud.r-project.org/src/contrib/repr_0.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/repr" + version('1.0.1', sha256='ecde22c17fd800e1ff5c2b2962689119aa486fba40fbc6f2c50e8d4cc61bc44b') + version('1.0.0', sha256='98b2eb1058c1cb2caa8f98708b63726f5564b45de03d38b95ff6b963a8261f49') version('0.9', 'db5ff74893063b492f684e42283070bd') + + depends_on('r@3.0.1:', type=('build', 'run')) + depends_on('r-htmltools', when='@0.13:', type=('build', 'run')) + depends_on('r-base64enc', when='@0.13:', type=('build', 'run')) + depends_on('r-jsonlite', when='@0.19.1:', type=('build', 'run')) + depends_on('r-pillar@1.4.0:', when='@1.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reprex/package.py b/var/spack/repos/builtin/packages/r-reprex/package.py index c0c0393f73..7a0f506389 100644 --- a/var/spack/repos/builtin/packages/r-reprex/package.py +++ b/var/spack/repos/builtin/packages/r-reprex/package.py @@ -16,13 +16,21 @@ class RReprex(RPackage): formats, such as copy/paste from an R session.""" homepage = "https://github.com/jennybc/reprex" - url = "https://cran.r-project.org/src/contrib/reprex_0.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/reprex" + url = "https://cloud.r-project.org/src/contrib/reprex_0.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/reprex" + version('0.3.0', sha256='203c2ae6343f6ff887e7a5a3f5d20bae465f6e8d9745c982479f5385f4effb6c') + version('0.2.1', sha256='5d234ddfbcadc5a5194a58eb88973c51581e7e2e231f146974af8f42747b45f3') version('0.1.1', 'fcd89995d7b35a2ddd4269973937bde3') - depends_on('r-callr', type=('build', 'run')) - depends_on('r-clipr', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) + depends_on('r@3.0.2:', when='@:0.1.2', type=('build', 'run')) + depends_on('r@3.1:', when='@0.2.0:', type=('build', 'run')) + depends_on('r-callr@2.0.0:', type=('build', 'run')) + depends_on('r-clipr@0.4.0:', type=('build', 'run')) + depends_on('r-knitr', when='@:0.1.9', type=('build', 'run')) depends_on('r-rmarkdown', type=('build', 'run')) depends_on('r-whisker', type=('build', 'run')) + depends_on('r-rlang', when='@0.2.0:', type=('build', 'run')) + depends_on('r-withr', when='@0.2.0:', type=('build', 'run')) + depends_on('r-fs', when='@0.2.1:', type=('build', 'run')) + depends_on('pandoc@1.12.3:') diff --git a/var/spack/repos/builtin/packages/r-reshape/package.py b/var/spack/repos/builtin/packages/r-reshape/package.py index 7e38c9fdc1..ed783c9def 100644 --- a/var/spack/repos/builtin/packages/r-reshape/package.py +++ b/var/spack/repos/builtin/packages/r-reshape/package.py @@ -10,10 +10,12 @@ class RReshape(RPackage): """Flexibly restructure and aggregate data using just two functions: melt and cast.""" - homepage = "https://cran.r-project.org/package=reshape" - url = "https://cran.r-project.org/src/contrib/reshape_0.8.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/reshape" + homepage = "https://cloud.r-project.org/package=reshape" + url = "https://cloud.r-project.org/src/contrib/reshape_0.8.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/reshape" + version('0.8.8', sha256='4d5597fde8511e8fe4e4d1fd7adfc7ab37ff41ac68c76a746f7487d7b106d168') version('0.8.7', '0b0eececc5eb74dea9d59a985bce6211') + depends_on('r@2.6.1:', type=('build', 'run')) depends_on('r-plyr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py index cd2a9d59b3..0a04e1b4ed 100644 --- a/var/spack/repos/builtin/packages/r-reshape2/package.py +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -11,12 +11,14 @@ class RReshape2(RPackage): and dcast (or acast).""" homepage = "https://github.com/hadley/reshape" - url = "https://cran.r-project.org/src/contrib/reshape2_1.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/reshape2" + url = "https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/reshape2" + version('1.4.3', sha256='8aff94c935e75032344b52407593392ddd4e16a88bb206984340c816d42c710e') version('1.4.2', 'c851a0312191b8c5bab956445df7cf5f') version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00') - depends_on('r-plyr', type=('build', 'run')) + depends_on('r@3.1:', when='@1.4.3:', type=('build', 'run')) + depends_on('r-plyr@1.8.1:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-reticulate/package.py b/var/spack/repos/builtin/packages/r-reticulate/package.py new file mode 100644 index 0000000000..f1dc039491 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-reticulate/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RReticulate(RPackage): + """Interface to 'Python' modules, classes, and functions. When calling into + 'Python', R data types are automatically converted to their equivalent + 'Python' types. When values are returned from 'Python' to R they are + converted back to R types. Compatible with all versions of 'Python' >= + 2.7.""" + + homepage = "https://github.com/rstudio/reticulate" + url = "https://cloud.r-project.org/src/contrib/reticulate_1.13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/reticulate" + + version('1.13', sha256='adbe41d556b667c4419d563680f8608a56b0f792b8bc427b3bf4c584ff819de3') + + depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-rcpp@0.12.7:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('python@2.7.0:') diff --git a/var/spack/repos/builtin/packages/r-rex/package.py b/var/spack/repos/builtin/packages/r-rex/package.py index 968f4a0959..54d124d84a 100644 --- a/var/spack/repos/builtin/packages/r-rex/package.py +++ b/var/spack/repos/builtin/packages/r-rex/package.py @@ -9,9 +9,9 @@ from spack import * class RRex(RPackage): """A friendly interface for the construction of regular expressions.""" - homepage = "https://cran.r-project.org/package=rex" - url = "https://cran.r-project.org/src/contrib/rex_1.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rex" + homepage = "https://cloud.r-project.org/package=rex" + url = "https://cloud.r-project.org/src/contrib/rex_1.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rex" version('1.1.2', '8820b4d4fe3718f275847b6f2cf83689') diff --git a/var/spack/repos/builtin/packages/r-rgdal/package.py b/var/spack/repos/builtin/packages/r-rgdal/package.py index 1146e0ff58..39c95f3cb5 100644 --- a/var/spack/repos/builtin/packages/r-rgdal/package.py +++ b/var/spack/repos/builtin/packages/r-rgdal/package.py @@ -17,13 +17,16 @@ class RRgdal(RPackage): Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.""" - homepage = "https://cran.r-project.org/package=rgdal" - url = "https://cran.rstudio.com/src/contrib/rgdal_1.3-9.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rgdal" + homepage = "https://cloud.r-project.org/package=rgdal" + url = "https://cloud.r-project.org/src/contrib/rgdal_1.3-9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rgdal" + version('1.4-4', sha256='2532e76e0af27d145f799d70006a5dbecb2d3be698e3d0bbf580f4c41a34c5d7') version('1.3-9', sha256='3e44f88d09894be4c0abd8874d00b40a4a5f4542b75250d098ffbb3ba41e2654') version('1.2-16', 'de83bf08519a53de68a7632ecb7f2dc9') - depends_on('r-sp', type=('build', 'run')) - depends_on('gdal') - depends_on('proj@:5') + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-sp@1.1-0:', type=('build', 'run')) + depends_on('gdal@1.11.4:') + depends_on('proj@4.8.0:5', when='@:1.3-9') + depends_on('proj@4.8.0:', when='@1.4-2:') diff --git a/var/spack/repos/builtin/packages/r-rgenoud/package.py b/var/spack/repos/builtin/packages/r-rgenoud/package.py index 7b836f82fb..f5cc12720d 100644 --- a/var/spack/repos/builtin/packages/r-rgenoud/package.py +++ b/var/spack/repos/builtin/packages/r-rgenoud/package.py @@ -10,7 +10,11 @@ class RRgenoud(RPackage): """A genetic algorithm plus derivative optimizer.""" homepage = "http://sekhon.berkeley.edu/rgenoud/" - url = "https://cran.r-project.org/src/contrib/rgenoud_5.8-1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rgenoud" + url = "https://cloud.r-project.org/src/contrib/rgenoud_5.8-1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rgenoud" + version('5.8-3.0', sha256='9beb11b5edab3ab3aa6001daa39668b240a8e0328be9d55db4e23ff88ce3235d') + version('5.8-2.0', sha256='106c4f6a6df5159578e929a0141b3cfbaa88141a70703ff59a1fc48a27e2d239') version('5.8-1.0', '85801093d2f1e6789683b46ab4a7d70f') + + depends_on('r@2.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgeos/package.py b/var/spack/repos/builtin/packages/r-rgeos/package.py index fb889dda96..fd982f9996 100644 --- a/var/spack/repos/builtin/packages/r-rgeos/package.py +++ b/var/spack/repos/builtin/packages/r-rgeos/package.py @@ -13,11 +13,13 @@ class RRgeos(RPackage): must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.""" - homepage = "https://cran.r-project.org/package=rgeos" - url = "https://cran.rstudio.com/src/contrib/rgeos_0.3-26.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rgeos" + homepage = "https://cloud.r-project.org/package=rgeos" + url = "https://cloud.r-project.org/src/contrib/rgeos_0.3-26.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rgeos" + version('0.5-1', sha256='8408973e7fe5648e39aa53f3d4bfe800638021a146a4e06f86496c0132e05488') version('0.3-26', '7d10a28011b49f68c5817b6fbca132df') - depends_on('r-sp', type=('build', 'run')) - depends_on('geos') + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-sp@1.1-0:', type=('build', 'run')) + depends_on('geos@3.2.0:') diff --git a/var/spack/repos/builtin/packages/r-rgexf/package.py b/var/spack/repos/builtin/packages/r-rgexf/package.py new file mode 100644 index 0000000000..3a98d90035 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rgexf/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRgexf(RPackage): + """Create, read and write GEXF (Graph Exchange XML Format) graph files + (used in Gephi and others). Using the XML package, it allows the user to + easily build/read graph files including attributes, GEXF viz attributes + (such as color, size, and position), network dynamics (for both edges and + nodes) and edge weighting. Users can build/handle graphs element-by-element + or massively through data-frames, visualize the graph on a web browser + through "sigmajs" (a javascript library) and interact with the igraph + package.""" + + homepage = "http://bitbucket.org/gvegayon/rgexf" + url = "https://cloud.r-project.org/src/contrib/rgexf_0.15.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rgexf" + + version('0.15.3', sha256='2e8a7978d1fb977318e6310ba65b70a9c8890185c819a7951ac23425c6dc8147') + + depends_on('r-xml', type=('build', 'run')) + depends_on('r-rook', type=('build', 'run')) + depends_on('r-igraph', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rgl/package.py b/var/spack/repos/builtin/packages/r-rgl/package.py index 372833f8ab..2195923a6e 100644 --- a/var/spack/repos/builtin/packages/r-rgl/package.py +++ b/var/spack/repos/builtin/packages/r-rgl/package.py @@ -15,27 +15,30 @@ class RRgl(RPackage): including PNG, Postscript, SVG, PGF.""" homepage = "https://r-forge.r-project.org/projects/rgl" - url = "https://cran.r-project.org/src/contrib/rgl_0.99.16.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rgl" + url = "https://cloud.r-project.org/src/contrib/rgl_0.99.16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rgl" + version('0.100.26', sha256='e1889c2723ad458b39fdf9366fdaf590d7657d3762748f8534a8491ef754e740') + version('0.100.24', sha256='1233a7bdc5a2b908fc64d5f56e92a0e123e8f7c0b9bac93dfd005608b78fa35a') version('0.99.16', sha256='692a545ed2ff0f5e15289338736f0e3c092667574c43ac358d8004901d7a1a61') version('0.98.1', 'bd69e1d33f1590feb4b6dc080b133e5b') - depends_on('r@3.2:3.9') - depends_on('zlib', type=('link')) - depends_on('libpng', type=('link')) - depends_on('libx11') - depends_on('freetype', type=('link')) - depends_on('gl') - depends_on('glu') + depends_on('r@3.2:', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-knitr', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-jsonlite@0.9.20:', type=('build', 'run')) depends_on('r-shiny', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-crosstalk', type=('build', 'run'), when='@0.99.16:') - depends_on('r-manipulatewidget', type=('build', 'run'), when='@0.99.16:') + depends_on('r-crosstalk', when='@0.99.16:', type=('build', 'run')) + depends_on('r-manipulatewidget@0.9.0:', when='@0.99.16:', type=('build', 'run')) + depends_on('zlib', type='link') + depends_on('libpng@1.2.9:', type='link') + depends_on('libx11') + depends_on('freetype', type='link') + depends_on('gl') + depends_on('glu') + depends_on('pandoc@1.14:', type='build') def configure_args(self): args = ['--x-includes=%s' % self.spec['libx11'].prefix.include, diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py index 5450d5dd8e..1c615f7e77 100644 --- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py +++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py @@ -12,11 +12,14 @@ class RRgooglemaps(RPackage): background image to overlay plots within R. This requires proper coordinate scaling.""" - homepage = "https://cran.r-project.org/package=RgoogleMaps" - url = "https://cran.r-project.org/src/contrib/RgoogleMaps_1.2.0.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RgoogleMaps" + homepage = "https://cloud.r-project.org/package=RgoogleMaps" + url = "https://cloud.r-project.org/src/contrib/RgoogleMaps_1.2.0.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RgoogleMaps" + version('1.4.3', sha256='44cb62bcd23e5b4807e91c5825352eb8d38aaaeb3b38a8271ca9f21c1e1d4b19') + version('1.4.2', sha256='b479996fcb72f067644a7ea7f00325e44e76efd202e84aaab022753c4a6d5584') version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-png', type=('build', 'run')) - depends_on('r-rjsonio', type=('build', 'run')) + depends_on('r-rjsonio', when='@1.2.0.5:1.2.0.7', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rhmmer/package.py b/var/spack/repos/builtin/packages/r-rhmmer/package.py index 4fe328f739..23854fb2b1 100644 --- a/var/spack/repos/builtin/packages/r-rhmmer/package.py +++ b/var/spack/repos/builtin/packages/r-rhmmer/package.py @@ -9,9 +9,9 @@ from spack import * class RRhmmer(RPackage): """rhmmer: Utilities Parsing 'HMMER' Results""" - homepage = "https://cran.r-project.org/package=rhmmer" - url = "https://cran.r-project.org/src/contrib/rhmmer_0.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rhmmer/" + homepage = "https://cloud.r-project.org/package=rhmmer" + url = "https://cloud.r-project.org/src/contrib/rhmmer_0.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rhmmer/" version('0.1.0', sha256='5022cefc9ba335160c1ad8d1b614610ae0ad48287c9fdbaf8f8966149358e520') @@ -21,5 +21,3 @@ class RRhmmer(RPackage): depends_on('r-dplyr', type=('build', 'run')) depends_on('r-tidyr', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) - depends_on('r-covr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py index 7ed751394e..5681e87113 100644 --- a/var/spack/repos/builtin/packages/r-rinside/package.py +++ b/var/spack/repos/builtin/packages/r-rinside/package.py @@ -23,11 +23,12 @@ class RRinside(RPackage): available at the 'RInside' website as well.""" homepage = "http://dirk.eddelbuettel.com/code/rinside.html" - url = "https://cran.r-project.org/src/contrib/RInside_0.2.15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RInside" + url = "https://cloud.r-project.org/src/contrib/RInside_0.2.15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RInside" version('0.2.15', '3b8c13dc53c6958c1f82c0a25dd6c211') version('0.2.14', 'fc72761e22b1f597433eb53d6eb122ff') version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rio/package.py b/var/spack/repos/builtin/packages/r-rio/package.py new file mode 100644 index 0000000000..5b4934f429 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rio/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRio(RPackage): + """Streamlined data import and export by making assumptions that the user + is probably willing to make: 'import()' and 'export()' determine the data + structure from the file extension, reasonable defaults are used for data + import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is + natively supported (including from SSL/HTTPS), compressed files can be read + directly without explicit decompression, and fast import packages are used + where appropriate. An additional convenience function, 'convert()', + provides a simple method for converting between file types.""" + + homepage = "https://github.com/leeper/rio" + url = "https://cloud.r-project.org/src/contrib/rio_0.5.16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rio" + + version('0.5.16', sha256='d3eb8d5a11e0a3d26169bb9d08f834a51a6516a349854250629072d59c29d465') + + depends_on('r@2.15.0:', type=('build', 'run')) + depends_on('r-foreign', type=('build', 'run')) + depends_on('r-haven@1.1.0:', type=('build', 'run')) + depends_on('r-curl@0.6:', type=('build', 'run')) + depends_on('r-data-table@1.9.8:', type=('build', 'run')) + depends_on('r-readxl@0.1.1:', type=('build', 'run')) + depends_on('r-openxlsx', type=('build', 'run')) + depends_on('r-tibble', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rjags/package.py b/var/spack/repos/builtin/packages/r-rjags/package.py index dc66dd0c39..0b86c0e8e6 100644 --- a/var/spack/repos/builtin/packages/r-rjags/package.py +++ b/var/spack/repos/builtin/packages/r-rjags/package.py @@ -11,15 +11,16 @@ class RRjags(RPackage): """Interface to the JAGS MCMC library. Usage: $ spack load r-rjags """ - homepage = "https://cran.r-project.org/web/packages/rjags/index.html" - url = "https://cran.r-project.org/src/contrib/rjags_4-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rjags/" + homepage = "https://cloud.r-project.org/package=rjags" + url = "https://cloud.r-project.org/src/contrib/rjags_4-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rjags/" version('4-8', sha256='1529827ab11493fb5f05552e239d700ae2f818995d86d3c9e4c92523f594b59f') version('4-6', 'c26b7cc8e8ddcdb55e14cba28df39f4c') - depends_on('jags', type=('link')) - depends_on('r-coda', type=('build', 'run')) + depends_on('r@2.14.0:', type=('build', 'run')) + depends_on('r-coda@0.13:', type=('build', 'run')) + depends_on('jags@4.0.0:4.999.999', type=('link')) def configure_args(self): args = ['--with-jags-lib=%s' % self.spec['jags'].prefix.lib, diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py index 8148ed2d74..cc6bb3cdfb 100644 --- a/var/spack/repos/builtin/packages/r-rjava/package.py +++ b/var/spack/repos/builtin/packages/r-rjava/package.py @@ -11,10 +11,12 @@ class RRjava(RPackage): Allows creation of objects, calling methods and accessing fields.""" homepage = "http://www.rforge.net/rJava/" - url = "https://cran.r-project.org/src/contrib/rJava_0.9-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rJava" + url = "https://cloud.r-project.org/src/contrib/rJava_0.9-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rJava" version('0.9-11', sha256='c28ae131456a98f4d3498aa8f6eac9d4df48727008dacff1aa561fc883972c69') version('0.9-8', '51ae0d690ceed056ebe7c4be71fc6c7a') - depends_on('java') + depends_on('r@2.5:', type=('build', 'run')) + depends_on('java@1.2:') + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py index b6c928ad06..9c2c7a1409 100644 --- a/var/spack/repos/builtin/packages/r-rjson/package.py +++ b/var/spack/repos/builtin/packages/r-rjson/package.py @@ -9,8 +9,12 @@ from spack import * class RRjson(RPackage): """Converts R object into JSON objects and vice-versa.""" - homepage = "https://cran.r-project.org/package=rjson" - url = "https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rjson" + homepage = "https://cloud.r-project.org/package=rjson" + url = "https://cloud.r-project.org/src/contrib/rjson_0.2.15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rjson" + version('0.2.20', sha256='3a287c1e5ee7c333ed8385913c0a307daf99335fbdf803e9dcca6e3d5adb3f6c') + version('0.2.19', sha256='5c2672461986f2b715416cab92ed262abe9875f31299bc8a1a072ef7c6dd49bc') version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9') + + depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py index 2f68f67596..b981fa80fe 100644 --- a/var/spack/repos/builtin/packages/r-rjsonio/package.py +++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py @@ -23,8 +23,10 @@ class RRjsonio(RPackage): aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.""" - homepage = "https://cran.r-project.org/package=RJSONIO" - url = "https://cran.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RJSONIO" + homepage = "https://cloud.r-project.org/package=RJSONIO" + url = "https://cloud.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RJSONIO" + version('1.3-1.2', sha256='550e18f7c04186376d67747b8258f529d205bfc929da9194fe45ec384e092d7e') + version('1.3-1.1', sha256='c72493b441758cd1e3e9d91296b9ea31068e71104649f46ad84c854a02c09693') version('1.3-0', '72c395622ba8d1435ec43849fd32c830') diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py index 2fada49290..f7a5344ba4 100644 --- a/var/spack/repos/builtin/packages/r-rlang/package.py +++ b/var/spack/repos/builtin/packages/r-rlang/package.py @@ -10,10 +10,12 @@ class RRlang(RPackage): """A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.""" - homepage = "https://cran.r-project.org/package=rlang" - url = "https://cran.r-project.org/src/contrib/rlang_0.2.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rlang" + homepage = "https://cloud.r-project.org/package=rlang" + url = "https://cloud.r-project.org/src/contrib/rlang_0.2.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rlang" + version('0.4.0', sha256='9748a4a217548bbe5631c18fd88c94811950446f798ff21fb327703aebaa150d') + version('0.3.4', sha256='4e467f7b0dcbde91b60c292137d2c69cecaa713a6e4c9b7157ef6fd5453b7ade') version('0.3.1', sha256='30427b2be2288e88acd30c4ea348ee06043a649fd73623a63148b1ad96317151') version('0.3.0.1', sha256='29451db0a3cabd75761d32df47a5d43ccadbde07ecb693ffdd73f122a0b9f348') version('0.3.0', sha256='9ab10ea3e19b2d60a289602ebbefa83509f430db1c8161e523896c374241b893') @@ -21,3 +23,6 @@ class RRlang(RPackage): version('0.1.4', 'daed5104d557c0cbfb4a654ec8ffb579') version('0.1.2', '170f8cf7b61898040643515a1746a53a') version('0.1.1', '38a51a0b8f8487eb52b4f3d986313682') + + depends_on('r@3.1.0:', when='@:0.3.4', type=('build', 'run')) + depends_on('r@3.2.0:', when='@0.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py index 30c61e6770..aec117f37a 100644 --- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py +++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py @@ -11,20 +11,25 @@ class RRmarkdown(RPackage): """Convert R Markdown documents into a variety of formats.""" homepage = "http://rmarkdown.rstudio.com/" - url = "https://cran.r-project.org/src/contrib/rmarkdown_1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rmarkdown" + url = "https://cloud.r-project.org/src/contrib/rmarkdown_1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rmarkdown" + version('1.14', sha256='f636b1048c5be56e06aa0b2b4342ad5c8192734f1e9b27468fef62be672edc61') + version('1.13', sha256='96fb6b08d27bbb8054145e0a55721f905341941d4f6691480a2a234e2d5a63ef') version('1.7', '477c50840581ba7947b3d905c67a511b') version('1.0', '264aa6a59e9680109e38df8270e14c58') - depends_on('r-knitr@1.14:', type=('build', 'run')) - depends_on('r-yaml@2.1.5:', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) + depends_on('r-knitr@1.22:', type=('build', 'run')) + depends_on('r-yaml@2.1.19:', type=('build', 'run')) depends_on('r-htmltools@0.3.5:', type=('build', 'run')) - depends_on('r-evaluate@0.8:', type=('build', 'run')) + depends_on('r-evaluate@0.13:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) - depends_on('r-rprojroot', type=('build', 'run')) - depends_on('r-mime', type=('build', 'run')) - depends_on('r-stringr@1.2.0:', type=('build', 'run')) - depends_on('r-catools', type=('build', 'run')) - depends_on('r@3.0:') + depends_on('r-rprojroot', when='@1.3:1.7', type=('build', 'run')) + depends_on('r-mime', when='@1.8:', type=('build', 'run')) + depends_on('r-stringr@1.2.0:', when='@1.6:', type=('build', 'run')) + depends_on('r-catools', when='@:1.7', type=('build', 'run')) + depends_on('r-tinytex@0.11:', when='@1.10:', type=('build', 'run')) + depends_on('r-xfun', when='@1.13:', type=('build', 'run')) + depends_on('pandoc@1.12.3:') diff --git a/var/spack/repos/builtin/packages/r-rminer/package.py b/var/spack/repos/builtin/packages/r-rminer/package.py index 08b8ea7aa3..92b99dd9f7 100644 --- a/var/spack/repos/builtin/packages/r-rminer/package.py +++ b/var/spack/repos/builtin/packages/r-rminer/package.py @@ -12,8 +12,8 @@ class RRminer(RPackage): and coherent set of functions.""" homepage = "http://www3.dsi.uminho.pt/pcortez/rminer.html" - url = "https://cran.r-project.org/src/contrib/rminer_1.4.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rminer" + url = "https://cloud.r-project.org/src/contrib/rminer_1.4.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rminer" version('1.4.2', '7d5d90f4ae030cf647d67aa962412c05') diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py index 54d9238265..840a4f3f20 100644 --- a/var/spack/repos/builtin/packages/r-rmpfr/package.py +++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py @@ -14,10 +14,16 @@ class RRmpfr(RPackage): is based on the GMP (GNU Multiple Precision) Library.""" homepage = "http://rmpfr.r-forge.r-project.org" - url = "https://cran.r-project.org/src/contrib/Rmpfr_0.6-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Rmpfr" + url = "https://cloud.r-project.org/src/contrib/Rmpfr_0.6-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Rmpfr" + version('0.7-2', sha256='ec1da6ec5292ea6ac95495c6a299591d367e520ae324719817fb884c865603ff') + version('0.7-1', sha256='9b3021617a22b0710b0f1acc279290762317ff123fd9e8fd03f1449f4bbfe204') version('0.6-1', '55d4ec257bd2a9233bafee9e444d0265') + depends_on('r@3.0.1:', when='@:0.6-1', type=('build', 'run')) + depends_on('r@3.1.0:', when='@0.7-0', type=('build', 'run')) + depends_on('r@3.3.0:', when='@0.7-1:', type=('build', 'run')) depends_on('r-gmp@0.5-8:', type=('build', 'run')) depends_on('mpfr@3.0.0:') + depends_on('gmp@4.2.3:') diff --git a/var/spack/repos/builtin/packages/r-rmpi/package.py b/var/spack/repos/builtin/packages/r-rmpi/package.py index 614e7be67e..fe43add7b8 100644 --- a/var/spack/repos/builtin/packages/r-rmpi/package.py +++ b/var/spack/repos/builtin/packages/r-rmpi/package.py @@ -11,12 +11,15 @@ class RRmpi(RPackage): manager and worker environment.""" homepage = "http://www.stats.uwo.ca/faculty/yu/Rmpi" - url = "https://cran.r-project.org/src/contrib/Rmpi_0.6-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Rmpi" + url = "https://cloud.r-project.org/src/contrib/Rmpi_0.6-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Rmpi" + version('0.6-9', sha256='b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6') + version('0.6-8', sha256='9b453ce3bd7284eda33493a0e47bf16db6719e3c48ac5f69deac6746f5438d96') version('0.6-6', 'a6fa2ff5e1cd513334b4e9e9e7a2286f') + + depends_on('r@2.15.1:', type=('build', 'run')) depends_on('mpi') - depends_on('r@2.15.1:') # The following MPI types are not supported conflicts('^intel-mpi') diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py index 4e73352019..6739bdb104 100644 --- a/var/spack/repos/builtin/packages/r-rmysql/package.py +++ b/var/spack/repos/builtin/packages/r-rmysql/package.py @@ -10,11 +10,13 @@ class RRmysql(RPackage): """Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.""" homepage = "https://github.com/rstats-db/rmysql" - url = "https://cran.r-project.org/src/contrib/RMySQL_0.10.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RMySQL" + url = "https://cloud.r-project.org/src/contrib/RMySQL_0.10.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RMySQL" version('0.10.17', sha256='754df4fce159078c1682ef34fc96aa5ae30981dc91f4f2bada8d1018537255f5') version('0.10.9', '3628200a1864ac3005cfd55cc7cde17a') depends_on('r-dbi@0.4:', type=('build', 'run')) - depends_on('mariadb@:5.5.56') + depends_on('mariadb@:5.5') + + depends_on('r@2.8.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index 4ab784813f..ea11d03f0f 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -14,12 +14,17 @@ class RRngtools(RPackage): the way current RNG settings can be changed.""" homepage = "https://renozao.github.io/rngtools" - url = "https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rngtools" + url = "https://cloud.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rngtools" + version('1.4', sha256='3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce') + version('1.3.1.1', sha256='99e1a8fde6b81128d0946746c1ef84ec5b6c2973ad843a080098baf73aa3364c') version('1.3.1', sha256='763fc493cb821a4d3e514c0dc876d602a692c528e1d67f295dde70c77009e224') version('1.2.4', '715967f8b3af2848a76593a7c718c1cd') - depends_on('r-pkgmaker', type=('build', 'run')) + depends_on('r@3.0.0:', when='@:1.3.1', type=('build', 'run')) + depends_on('r@3.6.0:', when='@1.3.1.1', type=('build', 'run')) + depends_on('r@3.2.0:', when='@1.4:', type=('build', 'run')) + depends_on('r-pkgmaker@0.20:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rnoaa/package.py b/var/spack/repos/builtin/packages/r-rnoaa/package.py index 0eabbc6585..7434fb58ba 100644 --- a/var/spack/repos/builtin/packages/r-rnoaa/package.py +++ b/var/spack/repos/builtin/packages/r-rnoaa/package.py @@ -10,8 +10,8 @@ class RRnoaa(RPackage): """rnoaa: 'NOAA' Weather Data from R""" homepage = "https://github.com/ropensci/rnoaa" - url = "https://cran.r-project.org/src/contrib/rnoaa_0.8.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rnoaa" + url = "https://cloud.r-project.org/src/contrib/rnoaa_0.8.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rnoaa" version('0.8.4', sha256='fb9ae771111dd5f638c1eff3290abad2ff9cc7e68a6678bf2414433ebed2dbbf') diff --git a/var/spack/repos/builtin/packages/r-robust/package.py b/var/spack/repos/builtin/packages/r-robust/package.py index 3e83224ead..b49de8879f 100644 --- a/var/spack/repos/builtin/packages/r-robust/package.py +++ b/var/spack/repos/builtin/packages/r-robust/package.py @@ -10,10 +10,11 @@ from spack import * class RRobust(RPackage): """robust: Port of the S+ Robust Library """ - homepage = "https://cran.r-project.org/package=robust" - url = "https://cran.r-project.org/src/contrib/robust_0.4-18.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/robust/" + homepage = "https://cloud.r-project.org/package=robust" + url = "https://cloud.r-project.org/src/contrib/robust_0.4-18.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/robust/" + version('0.4-18.1', sha256='de31901882873ef89748bb6863caf55734431df5b3eb3c6663ed17ee2e4a4077') version('0.4-18', sha256='e4196f01bb3b0d768759d4411d524238b627eb8dc213d84cb30014e75480f8ac') depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-robustbase/package.py b/var/spack/repos/builtin/packages/r-robustbase/package.py index f8b96ddcf0..6b8c510639 100644 --- a/var/spack/repos/builtin/packages/r-robustbase/package.py +++ b/var/spack/repos/builtin/packages/r-robustbase/package.py @@ -14,9 +14,13 @@ class RRobustbase(RPackage): by 'Maronna, Martin and Yohai'; Wiley 2006.""" homepage = "https://robustbase.r-forge.r-project.org" - url = "https://cran.r-project.org/src/contrib/robustbase_0.92-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/robustbase" + url = "https://cloud.r-project.org/src/contrib/robustbase_0.92-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/robustbase" + version('0.93-5', sha256='bde564dbd52f04ab32f9f2f9dd09b9578f3ccd2541cf5f8ff430da42a55e7f56') + version('0.93-4', sha256='ea9e03d484ef52ea805803477ffc48881e4c8c86ffda4eea56109f8b23f0a6e0') version('0.92-7', 'db3c8d12f9729b35bad17abf09e80b72') + depends_on('r@3.0.2:', when='@:0.93-1.1', type=('build', 'run')) + depends_on('r@3.1.0:', when='@0.93-2:', type=('build', 'run')) depends_on('r-deoptimr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rocr/package.py b/var/spack/repos/builtin/packages/r-rocr/package.py index 02d3b7e367..4952136ac5 100644 --- a/var/spack/repos/builtin/packages/r-rocr/package.py +++ b/var/spack/repos/builtin/packages/r-rocr/package.py @@ -23,9 +23,9 @@ class RRocr(RPackage): mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.""" - homepage = "https://cran.r-project.org/package=ROCR" - url = "https://cran.rstudio.com/src/contrib/ROCR_1.0-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/ROCR" + homepage = "https://cloud.r-project.org/package=ROCR" + url = "https://cloud.r-project.org/src/contrib/ROCR_1.0-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ROCR" version('1.0-7', '46cbd43ae87fc4e1eff2109529a4820e') depends_on('r-gplots', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py index 4eb0f0d017..a21269c1ef 100644 --- a/var/spack/repos/builtin/packages/r-rodbc/package.py +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -9,10 +9,13 @@ from spack import * class RRodbc(RPackage): """An ODBC database interface.""" - homepage = "https://cran.rstudio.com/web/packages/RODBC/" - url = "https://cran.rstudio.com/src/contrib/RODBC_1.3-13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RODBC/" + homepage = "https://cloud.r-project.org/package=RODBC" + url = "https://cloud.r-project.org/src/contrib/RODBC_1.3-13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RODBC/" + version('1.3-15', sha256='c43e5a2f0aa2f46607e664bfc0bb3caa230bbb779f4ff084e01727642da136e1') version('1.3-13', 'c52ef9139c2ed85adc53ad6effa7d68e') depends_on('unixodbc') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rook/package.py b/var/spack/repos/builtin/packages/r-rook/package.py new file mode 100644 index 0000000000..4d3b1dbda9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rook/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRook(RPackage): + """This package contains the Rook specification and convenience software + for building and running Rook applications. To get started, be sure and + read the 'Rook' help file first.""" + + homepage = "https://cloud.r-project.org/package=Rook" + url = "https://cloud.r-project.org/src/contrib/Rook_1.1-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Rook" + + version('1.1-1', sha256='00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903') + + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('r-brew', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py index f85b27187c..3958ab1298 100644 --- a/var/spack/repos/builtin/packages/r-roxygen2/package.py +++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py @@ -11,12 +11,14 @@ class RRoxygen2(RPackage): 'NAMESPACE' files.""" homepage = "https://github.com/klutometis/roxygen" - url = "https://cran.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/roxygen2" + url = "https://cloud.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/roxygen2" version('6.1.1', sha256='ed46b7e062e0dfd8de671c7a5f6d120fb2b720982e918dbeb01e6985694c0273') version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7') + depends_on('r@3.0.2:', when='@:6.0.1', type=('build', 'run')) + depends_on('r@3.1:', when='@6.1.0:', type=('build', 'run')) depends_on('r-brew', type=('build', 'run')) depends_on('r-commonmark', type=('build', 'run')) depends_on('r-desc@1.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rpart-plot/package.py b/var/spack/repos/builtin/packages/r-rpart-plot/package.py index 59a74efa90..4671e1078a 100644 --- a/var/spack/repos/builtin/packages/r-rpart-plot/package.py +++ b/var/spack/repos/builtin/packages/r-rpart-plot/package.py @@ -10,10 +10,14 @@ class RRpartPlot(RPackage): """Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.""" - homepage = "https://cran.r-project.org/package=rpart.plot" - url = "https://cran.r-project.org/src/contrib/rpart.plot_2.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rpart.plot" + homepage = "https://cloud.r-project.org/package=rpart.plot" + url = "https://cloud.r-project.org/src/contrib/rpart.plot_2.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rpart.plot" + version('3.0.7', sha256='04e7fcadfa907507b74529c3ecfae4a0c782badf55e87d9c62dbd9a536ea9144') + version('3.0.6', sha256='1c584290c8f58ded5c3f0638790a0da63408eca3ecd5d5c4d8c46954de9f4b02') version('2.1.0', 'fb0f8edfe22c464683ee82aa429136f9') - depends_on('r-rpart@4.1-0:', type=('build', 'run')) + depends_on('r@3.2.0:', when='@2.1.2:3.0.6', type=('build', 'run')) + depends_on('r@3.4.0:', when='@3.0.7:', type=('build', 'run')) + depends_on('r-rpart@4.1-10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rpart/package.py b/var/spack/repos/builtin/packages/r-rpart/package.py index 1679317b6d..4c309ba4ab 100644 --- a/var/spack/repos/builtin/packages/r-rpart/package.py +++ b/var/spack/repos/builtin/packages/r-rpart/package.py @@ -10,11 +10,13 @@ class RRpart(RPackage): """Recursive partitioning for classification, regression and survival trees.""" - homepage = "https://cran.r-project.org/package=rpart" - url = "https://cran.r-project.org/src/contrib/rpart_4.1-10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rpart" + homepage = "https://cloud.r-project.org/package=rpart" + url = "https://cloud.r-project.org/src/contrib/rpart_4.1-10.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rpart" + version('4.1-15', sha256='2b8ebe0e9e11592debff893f93f5a44a6765abd0bd956b0eb1f70e9394cfae5c') + version('4.1-13', sha256='8e11a6552224e0fbe23a85aba95acd21a0889a3fe48277f3d345de3147c7494c') version('4.1-11', 'f77b37cddf7e9a7b5993a52a750b8817') version('4.1-10', '15873cded4feb3ef44d63580ba3ca46e') - depends_on('r@2.15.0:') + depends_on('r@2.15.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py index 3aa969bed4..a5c9e11974 100644 --- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py +++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py @@ -18,10 +18,12 @@ class RRpostgresql(RPackage): https://code.google.com/p/rpostgresql/.""" homepage = "https://code.google.com/p/rpostgresql/" - url = "https://cran.r-project.org/src/contrib/RPostgreSQL_0.4-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RPostgreSQL" + url = "https://cloud.r-project.org/src/contrib/RPostgreSQL_0.4-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RPostgreSQL" + version('0.6-2', sha256='080118647208bfa2621bcaac0d324891cc513e07618fa22e3c50ec2050e1b0d5') version('0.4-1', 'e7b22e212afbb2cbb88bab937f93e55a') - depends_on('r-dbi', type=('build', 'run')) + depends_on('r@2.9.0:', type=('build', 'run')) + depends_on('r-dbi@0.3:', type=('build', 'run')) depends_on('postgresql') diff --git a/var/spack/repos/builtin/packages/r-rprojroot/package.py b/var/spack/repos/builtin/packages/r-rprojroot/package.py index 56ddb40aa0..b1ec14200d 100644 --- a/var/spack/repos/builtin/packages/r-rprojroot/package.py +++ b/var/spack/repos/builtin/packages/r-rprojroot/package.py @@ -11,11 +11,12 @@ class RRprojroot(RPackage): The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.""" - homepage = "https://cran.r-project.org/package=rprojroot" - url = "https://cran.rstudio.com/src/contrib/rprojroot_1.2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rprojroot" + homepage = "https://cloud.r-project.org/package=rprojroot" + url = "https://cloud.r-project.org/src/contrib/rprojroot_1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rprojroot" + version('1.3-2', sha256='df5665834941d8b0e377a8810a04f98552201678300f168de5f58a587b73238b') version('1.2', 'c1a0574aaac2a43a72f804abbaea19c3') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-backports', type=('build', 'run')) - depends_on('r@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-rrblup/package.py b/var/spack/repos/builtin/packages/r-rrblup/package.py index 882711f392..b165e2a527 100644 --- a/var/spack/repos/builtin/packages/r-rrblup/package.py +++ b/var/spack/repos/builtin/packages/r-rrblup/package.py @@ -10,8 +10,8 @@ class RRrblup(RPackage): """rrBLUP: Ridge Regression and Other Kernels for Genomic Selection""" homepage = "http://potatobreeding.cals.wisc.edu/software" - url = "https://cran.r-project.org/src/contrib/rrBLUP_4.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rrBLUP" + url = "https://cloud.r-project.org/src/contrib/rrBLUP_4.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rrBLUP" version('4.6', sha256='28b475a1466fcdc1780caace75cf34155338fda496cebd5799315598a4bc84af') diff --git a/var/spack/repos/builtin/packages/r-rrcov/package.py b/var/spack/repos/builtin/packages/r-rrcov/package.py index 78a0b65d46..7b1d3bd74a 100644 --- a/var/spack/repos/builtin/packages/r-rrcov/package.py +++ b/var/spack/repos/builtin/packages/r-rrcov/package.py @@ -9,9 +9,9 @@ from spack import * class RRrcov(RPackage): """rrcov: Scalable Robust Estimators with High Breakdown Point""" - homepage = "https://cran.r-project.org/package=rrcov" - url = "https://cran.r-project.org/src/contrib/rrcov_1.4-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rrcov" + homepage = "https://cloud.r-project.org/package=rrcov" + url = "https://cloud.r-project.org/src/contrib/rrcov_1.4-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rrcov" version('1.4-7', sha256='cbd08ccce8b583a2f88946a3267c8fc494ee2b44ba749b9296a6e3d818f6f293') @@ -21,5 +21,3 @@ class RRrcov(RPackage): depends_on('r-lattice', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) depends_on('r-pcapp', type=('build', 'run')) - depends_on('r-mass', type=('build', 'run')) - depends_on('r-ellipse', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rrpp/package.py b/var/spack/repos/builtin/packages/r-rrpp/package.py index c20f200845..a2448a3636 100644 --- a/var/spack/repos/builtin/packages/r-rrpp/package.py +++ b/var/spack/repos/builtin/packages/r-rrpp/package.py @@ -23,7 +23,9 @@ class RRrpp(RPackage): other fields, as well.""" homepage = "https://github.com/mlcollyer/RRPP" - url = "https://cran.r-project.org/src/contrib/RRPP_0.3.0.tar.gz" + url = "https://cloud.r-project.org/src/contrib/RRPP_0.3.0.tar.gz" list_url = "https://cron.r-project.org/src/contrib/Archive/RRPP" + version('0.4.2', sha256='21a4ebb549d21f66ee9107adf762eee630e478bc740f232f384ba1a6b1cd3bf4') + version('0.4.1', sha256='d7cd3b089240d7f7e13f65f0259487669a378ffae062aee33d4dc6ab0f86f899') version('0.3.0', sha256='34fea6ce7a78e4f38398d3b99585bab11a8171bc8b9a4e461b6d984ed1373739') diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py index 4bde5a8680..1fdc932652 100644 --- a/var/spack/repos/builtin/packages/r-rsnns/package.py +++ b/var/spack/repos/builtin/packages/r-rsnns/package.py @@ -17,9 +17,12 @@ class RRsnns(RPackage): and learning algorithms integrate seamlessly into R.""" homepage = "http://sci2s.ugr.es/dicits/software/RSNNS" - url = "https://cran.r-project.org/src/contrib/RSNNS_0.4-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RSNNS" + url = "https://cloud.r-project.org/src/contrib/RSNNS_0.4-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RSNNS" + version('0.4-11', sha256='87943126e98ae47f366e3025d0f3dc2f5eb0aa2924508fd9ee9a0685d7cb477c') + version('0.4-10.1', sha256='38bb3d172390bd01219332ec834744274b87b01f94d23b29a9d818c2bca04071') version('0.4-7', 'ade7736611c456effb5f72e0ce0a1e6f') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-rcpp@0.8.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsolnp/package.py b/var/spack/repos/builtin/packages/r-rsolnp/package.py index 65ecf288ec..03c24b0b46 100644 --- a/var/spack/repos/builtin/packages/r-rsolnp/package.py +++ b/var/spack/repos/builtin/packages/r-rsolnp/package.py @@ -10,10 +10,11 @@ class RRsolnp(RPackage): """General Non-linear Optimization Using Augmented Lagrange Multiplier Method.""" - homepage = "https://cran.r-project.org/package=Rsolnp" - url = "https://cran.rstudio.com/src/contrib/Rsolnp_1.16.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/Rsolnp" + homepage = "https://cloud.r-project.org/package=Rsolnp" + url = "https://cloud.r-project.org/src/contrib/Rsolnp_1.16.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Rsolnp" version('1.16', '507e1e1a64f5f1d32b7e4e12ed19599f') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-truncnorm', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rspectra/package.py b/var/spack/repos/builtin/packages/r-rspectra/package.py new file mode 100644 index 0000000000..460a649c25 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rspectra/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRspectra(RPackage): + """R interface to the 'Spectra' library <https://spectralib.org/> for + large-scale eigenvalue and SVD problems. It is typically used to compute a + few eigenvalues/vectors of an n by n matrix, e.g., the k largest + eigenvalues, which is usually more efficient than eigen() if k << n. This + package provides the 'eigs()' function that does the similar job as in + 'Matlab', 'Octave', 'Python SciPy' and 'Julia'. It also provides the + 'svds()' function to calculate the largest k singular values and + corresponding singular vectors of a real matrix. The matrix to be computed + on can be dense, sparse, or in the form of an operator defined by the + user.""" + + homepage = "https://github.com/yixuan/RSpectra" + url = "https://cloud.r-project.org/src/contrib/RSpectra_0.15-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RSpectra" + + version('0.15-0', sha256='1ad5698201007044a0420cb10b7c48e94312a8a1d22b9d946d5de1c6743969a9') + + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-matrix@1.1-0:', type=('build', 'run')) + depends_on('r-rcpp@0.11.5:', type=('build', 'run')) + depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py index 9afd523511..d9e018304d 100644 --- a/var/spack/repos/builtin/packages/r-rsqlite/package.py +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -11,17 +11,20 @@ class RRsqlite(RPackage): interface compliant with the DBI package. The source for the SQLite engine (version 3.8.6) is included.""" - homepage = "https://cran.rstudio.com/web/packages/RSQLite/index.html" - url = "https://cran.r-project.org/src/contrib/RSQLite_2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RSQLite" + homepage = "https://cloud.r-project.org/package=RSQLite" + url = "https://cloud.r-project.org/src/contrib/RSQLite_2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RSQLite" + version('2.1.2', sha256='66dad425d22b09651c510bf84b7fc36375ce537782f02585cf1c6856ae82d9c6') + version('2.1.0', sha256='ad6081be2885be5921b1a44b1896e6a8568c8cff40789f43bfaac9f818767642') version('2.0', '63842410e78ccdfc52d4ee97992521d5') - depends_on('r-dbi', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-dbi@1.0.0:', type=('build', 'run')) depends_on('r-bit64', type=('build', 'run')) - depends_on('r-blob', type=('build', 'run')) + depends_on('r-blob@1.2.0:', type=('build', 'run')) depends_on('r-memoise', type=('build', 'run')) depends_on('r-pkgconfig', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.12.7:', type=('build', 'run')) depends_on('r-bh', type=('build', 'run')) - depends_on('r-plogr', type=('build', 'run')) + depends_on('r-plogr@0.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py index 9bebbc38a2..6e8bc94458 100644 --- a/var/spack/repos/builtin/packages/r-rstan/package.py +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -18,24 +18,26 @@ class RRstan(RPackage): the need to derive the partial derivatives.""" homepage = "http://mc-stan.org/" - url = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rstan" + url = "https://cloud.r-project.org/src/contrib/rstan_2.10.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rstan" + version('2.19.2', sha256='31e4ceb9c327cd62873225097ffa538c2ac4cb0547c52271e52e4c7652d508da') version('2.18.2', sha256='4d75dad95610d5a1d1c89a4ddbaf4326462e4ffe0ad28aed2129f2d9292e70ff') version('2.17.2', '60f4a0284c58f5efc1b1cbf488d7edda') version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a') - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-stanheaders', type=('build', 'run')) + depends_on('r@3.0.2:', when='@:2.17.3', type=('build', 'run')) + depends_on('r@3.4.0:', when='@2.18.1:', type=('build', 'run')) + depends_on('r-stanheaders@2.18.1:', type=('build', 'run')) + depends_on('r-ggplot2@2.0.0:', type=('build', 'run')) depends_on('r-inline', type=('build', 'run')) - depends_on('r-gridextra', type=('build', 'run')) - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-rcppeigen', type=('build', 'run')) - depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run'), when='@2.17.2:') - depends_on('r-bh', type=('build', 'run')) + depends_on('r-gridextra@2.0.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.0:', type=('build', 'run')) + depends_on('r-loo@2.0.0:', when='@2.18:', type=('build', 'run')) + depends_on('r-pkgbuild', when='@2.18:', type=('build', 'run')) + depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run')) + depends_on('r-bh@1.69.0:', type=('build', 'run')) + depends_on('gmake', type='build') + depends_on('pandoc', type='build') - depends_on('r-bh@1.66:', type=('build', 'run'), when='@2.18:') - depends_on('r-loo@2.0.0:', type=('build', 'run'), when='@2.18:') - depends_on('r-pkgbuild', type=('build', 'run'), when='@2.18:') - depends_on('r-stanheaders@2.18.0:', type=('build', 'run'), when='@2.18:') conflicts('%gcc@:4.9', when='@2.18:') diff --git a/var/spack/repos/builtin/packages/r-rstantools/package.py b/var/spack/repos/builtin/packages/r-rstantools/package.py index a50941c9d6..08f2e968bb 100644 --- a/var/spack/repos/builtin/packages/r-rstantools/package.py +++ b/var/spack/repos/builtin/packages/r-rstantools/package.py @@ -10,7 +10,9 @@ class RRstantools(RPackage): """rstantools: Tools for Developing R Packages Interfacing with 'Stan'""" homepage = "http://discourse.mc-stan.org/" - url = "https://cran.r-project.org/src/contrib/rstantools_1.5.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rstantools" + url = "https://cloud.r-project.org/src/contrib/rstantools_1.5.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rstantools" version('1.5.1', sha256='5cab16c132c12e84bd08e18cd6ef25ba39d67a04ce61015fc4490659c7cfb485') + + depends_on('pandoc', type='build') diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py index 13f4d0c10c..9a7779f063 100644 --- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py +++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py @@ -10,10 +10,12 @@ class RRstudioapi(RPackage): """Access the RStudio API (if available) and provide informative error messages when it's not.""" - homepage = "https://cran.r-project.org/web/packages/rstudioapi/index.html" - url = "https://cran.r-project.org/src/contrib/rstudioapi_0.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi" + homepage = "https://cloud.r-project.org/package=rstudioapi" + url = "https://cloud.r-project.org/src/contrib/rstudioapi_0.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rstudioapi" + version('0.10', sha256='80c5aa3063bcab649904cb92f0b164edffa2f6b0e6a8f7ea28ae317b80e1ab96') + version('0.9.0', sha256='5149a2830ae7134c396ce64764b263cf9f348d4399f53da3804f40d7d5bec13e') version('0.7', 'ee4ab567a7a9fdfac1a6fd01fe38de4a') version('0.6', 'fdb13bf46aab02421557e713fceab66b') version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') diff --git a/var/spack/repos/builtin/packages/r-rsvd/package.py b/var/spack/repos/builtin/packages/r-rsvd/package.py new file mode 100644 index 0000000000..554824aea5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rsvd/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RRsvd(RPackage): + """Low-rank matrix decompositions are fundamental tools and widely used for + data analysis, dimension reduction, and data compression. Classically, + highly accurate deterministic matrix algorithms are used for this task. + However, the emergence of large-scale data has severely challenged our + computational ability to analyze big data. The concept of randomness has + been demonstrated as an effective strategy to quickly produce approximate + answers to familiar problems such as the singular value decomposition + (SVD). The rsvd package provides several randomized matrix algorithms such + as the randomized singular value decomposition (rsvd), randomized principal + component analysis (rpca), randomized robust principal component analysis + (rrpca), randomized interpolative decomposition (rid), and the randomized + CUR decomposition (rcur). In addition several plot functions are provided. + The methods are discussed in detail by Erichson et al. (2016) + <arXiv:1608.02148>.""" + + homepage = "https://github.com/erichson/rSVD" + url = "https://cloud.r-project.org/src/contrib/rsvd_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rsvd" + + version('1.0.2', sha256='c8fe5c18bf7bcfe32604a897e3a7caae39b49e47e93edad9e4d07657fc392a3a') + + depends_on('r@3.2.2:', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rtsne/package.py b/var/spack/repos/builtin/packages/r-rtsne/package.py index 80909001a2..be053b293f 100644 --- a/var/spack/repos/builtin/packages/r-rtsne/package.py +++ b/var/spack/repos/builtin/packages/r-rtsne/package.py @@ -10,13 +10,13 @@ class RRtsne(RPackage): """An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation.""" - homepage = "https://CRAN.R-project.org/package=Rtsne" - url = "https://cran.r-project.org/src/contrib/Rtsne_0.13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Rtsne" + homepage = "https://cloud.r-project.org/package=Rtsne" + url = "https://cloud.r-project.org/src/contrib/Rtsne_0.13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Rtsne" + version('0.15', sha256='56376e4f0a382fad3d3d40e2cb0562224be5265b827622bcd235e8fc63df276c') version('0.13', 'ea1d2ef2bda16735bbf219ffda5b0661') version('0.11', '9a1eaa9b71d67cc27a55780e6e9df733') version('0.10', 'c587e1b76fdcea2629424f74c6e92340') - depends_on('r@3.4.0:3.4.9') - depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-runit/package.py b/var/spack/repos/builtin/packages/r-runit/package.py index 246c189cb2..03452d630e 100644 --- a/var/spack/repos/builtin/packages/r-runit/package.py +++ b/var/spack/repos/builtin/packages/r-runit/package.py @@ -9,11 +9,10 @@ from spack import * class RRunit(RPackage): """RUnit: R Unit Test Framework""" - homepage = "https://cran.r-project.org/package=RUnit" - url = "https://cran.r-project.org/src/contrib/RUnit_0.4.32.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/RUnit/" + homepage = "https://cloud.r-project.org/package=RUnit" + url = "https://cloud.r-project.org/src/contrib/RUnit_0.4.32.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/RUnit/" version('0.4.32', sha256='23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1') depends_on('r@2.5.0:', type=('build', 'run')) - depends_on('r-xml@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rvcheck/package.py b/var/spack/repos/builtin/packages/r-rvcheck/package.py index bd0fd37ed2..9adfd8d31d 100644 --- a/var/spack/repos/builtin/packages/r-rvcheck/package.py +++ b/var/spack/repos/builtin/packages/r-rvcheck/package.py @@ -10,8 +10,13 @@ class RRvcheck(RPackage): """Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').""" - homepage = "https://cran.r-project.org/package=rvcheck" - url = "https://cran.rstudio.com/src/contrib/rvcheck_0.0.9.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/rvcheck" + homepage = "https://cloud.r-project.org/package=rvcheck" + url = "https://cloud.r-project.org/src/contrib/rvcheck_0.0.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rvcheck" + version('0.1.3', sha256='0b59986c1ccc5b89f8aca8fa7cf62d0b875719addb40e08dbda1791cfd334fc4') version('0.0.9', '7e9821de754577f94fdcbf7b02a20edc') + + depends_on('r@3.3.0:', when='@:0.1.1', type=('build', 'run')) + depends_on('r@3.4.0:', when='@0.1.3:', type=('build', 'run')) + depends_on('r-rlang', when='@0.1.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rvest/package.py b/var/spack/repos/builtin/packages/r-rvest/package.py index 18353fe750..1872315f77 100644 --- a/var/spack/repos/builtin/packages/r-rvest/package.py +++ b/var/spack/repos/builtin/packages/r-rvest/package.py @@ -11,12 +11,17 @@ class RRvest(RPackage): download, then manipulate, HTML and XML.""" homepage = "https://github.com/hadley/rvest" - url = "https://cran.r-project.org/src/contrib/rvest_0.3.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rvest" + url = "https://cloud.r-project.org/src/contrib/rvest_0.3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rvest" + version('0.3.4', sha256='413e171b9e89b7dc4e8b41165027cf19eb97cd73e149c252237bbdf0d0a4254a') + version('0.3.3', sha256='b10a87fa2d733f7c0fc567242ef0ab10a1a77d58d51796996cc0fd81381a556f') version('0.3.2', '78c88740850e375fc5da50d37734d1b2') + depends_on('r@3.0.1:', when='@:0.3.2', type=('build', 'run')) + depends_on('r@3.1:', when='@0.3.3', type=('build', 'run')) + depends_on('r@3.2:', when='@0.3.4:', type=('build', 'run')) depends_on('r-xml2', type=('build', 'run')) - depends_on('r-httr', type=('build', 'run')) + depends_on('r-httr@0.5:', type=('build', 'run')) depends_on('r-selectr', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index fb6f0f5634..8b800c4b5f 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -11,9 +11,12 @@ class RRzmq(RPackage): """Interface to the ZeroMQ lightweight messaging kernel.""" homepage = "http://github.com/armstrtw/rzmq" - url = "https://cran.r-project.org/src/contrib/rzmq_0.7.7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/rzmq" + url = "https://cloud.r-project.org/src/contrib/rzmq_0.7.7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/rzmq" + version('0.9.6', sha256='80a3fc6eb6f7851224c4cd5e219ca4db0286551ad429359d4df853ccb9234316') + version('0.9.4', sha256='03fbda756d823c11fba359b94a6213c3440e61973331668eaac35779717f73ad') version('0.7.7', '8ba18fd1c222d1eb25bb622ccd2897e0') - depends_on('zeromq') + depends_on('r@3.1.0:', when='@0.9.0:', type=('build', 'run')) + depends_on('zeromq@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-samr/package.py b/var/spack/repos/builtin/packages/r-samr/package.py index 79ae1762c7..5ebc81a468 100644 --- a/var/spack/repos/builtin/packages/r-samr/package.py +++ b/var/spack/repos/builtin/packages/r-samr/package.py @@ -9,10 +9,15 @@ from spack import * class RSamr(RPackage): """Significance Analysis of Microarrays.""" - homepage = "https://cran.r-project.org/package=samr" - url = "https://cran.rstudio.com/src/contrib/samr_2.0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/samr" + homepage = "https://cloud.r-project.org/package=samr" + url = "https://cloud.r-project.org/src/contrib/samr_2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/samr" + version('3.0', sha256='25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506') version('2.0', 'e8f50b8b25069d03d42c2c61c72b0da0') depends_on('r-impute', type=('build', 'run')) depends_on('r-matrixstats', type=('build', 'run')) + depends_on('r-shiny', when='@3.0:', type=('build', 'run')) + depends_on('r-shinyfiles', when='@3.0:', type=('build', 'run')) + depends_on('r-openxlsx', when='@3.0:', type=('build', 'run')) + depends_on('r-gsa', when='@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py index 68feab8e3c..d303fe56cf 100644 --- a/var/spack/repos/builtin/packages/r-sandwich/package.py +++ b/var/spack/repos/builtin/packages/r-sandwich/package.py @@ -10,12 +10,13 @@ class RSandwich(RPackage): """Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.""" - homepage = "https://cran.r-project.org/package=sandwich" - url = "https://cran.r-project.org/src/contrib/sandwich_2.3-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sandwich" + homepage = "https://cloud.r-project.org/package=sandwich" + url = "https://cloud.r-project.org/src/contrib/sandwich_2.3-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sandwich" + version('2.5-1', sha256='dbef6f4d12b83e166f9a2508b7c732b04493641685d6758d29f3609e564166d6') + version('2.5-0', sha256='6cc144af20739eb23e5539010d3833d7c7fc53cbca2addb583ab933167c11399') version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5') - depends_on('r@2.0.0:') - + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py index fbc6d69d81..0ea8442689 100644 --- a/var/spack/repos/builtin/packages/r-scales/package.py +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -11,17 +11,20 @@ class RScales(RPackage): automatically determining breaks and labels for axes and legends.""" homepage = "https://github.com/hadley/scales" - url = "https://cran.r-project.org/src/contrib/scales_0.5.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/scales" + url = "https://cloud.r-project.org/src/contrib/scales_0.5.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/scales" + version('1.0.0', sha256='0c1f4a14edd336a404da34a3cc71a6a9d0ca2040ba19360c41a79f36e06ca30c') version('0.5.0', '435f6bd826c5cf8df703ffb8a6750fd1') version('0.4.1', '3fb2218866a7fe4c1f6e66790876f85a') version('0.4.0', '7b5602d9c55595901192248bca25c099') + depends_on('r@2.13:', when='@:0.5.0', type=('build', 'run')) + depends_on('r@3.1:', when='@1.0.0:', type=('build', 'run')) depends_on('r-rcolorbrewer', type=('build', 'run')) - depends_on('r-dichromat', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-munsell', type=('build', 'run')) + depends_on('r-dichromat', when='@:0.5.0', type=('build', 'run')) + depends_on('r-plyr', when='@:0.5.0', type=('build', 'run')) + depends_on('r-munsell@0.5:', type=('build', 'run')) depends_on('r-labeling', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-r6', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py index 2c53d96745..e4bb9abbc6 100644 --- a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py +++ b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py @@ -9,10 +9,11 @@ from spack import * class RScatterplot3d(RPackage): """scatterplot3d: 3D Scatter Plot""" - homepage = "https://CRAN.R-project.org/package=scatterplot3d" - url = "https://cran.r-project.org/src/contrib/scatterplot3d_0.3-40.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/scatterplot3d" + homepage = "https://cloud.r-project.org/package=scatterplot3d" + url = "https://cloud.r-project.org/src/contrib/scatterplot3d_0.3-40.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/scatterplot3d" + version('0.3-41', sha256='4c8326b70a3b2d37126ca806771d71e5e9fe1201cfbe5b0d5a0a83c3d2c75d94') version('0.3-40', '67b9ab6131d244d7fc1db39dcc911dfe') - depends_on('r@2.7.0:') + depends_on('r@2.7.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sctransform/package.py b/var/spack/repos/builtin/packages/r-sctransform/package.py new file mode 100644 index 0000000000..7dd0b4e703 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sctransform/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSctransform(RPackage): + """A normalization method for single-cell UMI count data using a variance + stabilizing transformation. The transformation is based on a negative + binomial regression model with regularized parameters. As part of the same + regression framework, this package also provides functions for batch + correction, and data correction. See Hafemeister and Satija 2019 + <doi:10.1101/576827> for more details.""" + + homepage = "https://github.com/ChristophH/sctransform" + url = "https://cloud.r-project.org/src/contrib/sctransform_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sctransform" + + version('0.2.0', sha256='d7f4c7958693823454f1426b23b0e1e9c207ad61a7a228602a1885a1318eb3e4') + + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-future', type=('build', 'run')) + depends_on('r-future-apply', type=('build', 'run')) + depends_on('r-ggplot2', type=('build', 'run')) + depends_on('r-reshape2', type=('build', 'run')) + depends_on('r-gridextra', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-rcppeigen', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sdmtools/package.py b/var/spack/repos/builtin/packages/r-sdmtools/package.py index 46acd8c8a6..e6dd23d74d 100644 --- a/var/spack/repos/builtin/packages/r-sdmtools/package.py +++ b/var/spack/repos/builtin/packages/r-sdmtools/package.py @@ -13,15 +13,15 @@ class RSdmtools(RPackage): This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises.""" - homepage = "https://cran.r-project.org/web/packages/SDMTools/index.html" - url = "https://cran.r-project.org/src/contrib/SDMTools_1.1-221.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/SDMTools" + homepage = "https://cloud.r-project.org/package=SDMTools" + url = "https://cloud.r-project.org/src/contrib/SDMTools_1.1-221.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/SDMTools" + version('1.1-221.1', sha256='3825856263bdb648ca018b27dc6ab8ceaef24691215c197f8d5cd17718b54fbb') version('1.1-221', '3604da1783d0c6081b62b29d35a32c3c') version('1.1-20', '27cc8de63cfdd86d4ba9983012121c58') version('1.1-13', '0d6a14d985988a81b9ff06c635675143') version('1.1-12', 'a13d75e4024d908a57ea462112d8a437') version('1.1-11', 'cb890ee06eb862f97141b73c7390a0a9') - depends_on('r@3.4.0:3.4.9') - depends_on('r-utils', type=('build', 'run')) + depends_on('r-r-utils', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-segmented/package.py b/var/spack/repos/builtin/packages/r-segmented/package.py index 45bc7df141..748d8811ef 100644 --- a/var/spack/repos/builtin/packages/r-segmented/package.py +++ b/var/spack/repos/builtin/packages/r-segmented/package.py @@ -11,9 +11,11 @@ class RSegmented(RPackage): one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.""" - homepage = "https://CRAN.R-project.org/package=segmented" - url = "https://cran.r-project.org/src/contrib/segmented_0.5-1.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/segmented" + homepage = "https://cloud.r-project.org/package=segmented" + url = "https://cloud.r-project.org/src/contrib/segmented_0.5-1.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/segmented" + version('1.0-0', sha256='eeadc89b4bb4744bbd1e4e6c3b6536ff96fc7ee09016228dfdc0a8ebdc74fac5') + version('0.5-4.0', sha256='7ff63a19915cbd1e190d3a4875892b4c7bd97890b0dc2909126348a19aec4071') version('0.5-2.2', '1511ec365aea289d5f0a574f6d10d2d6') version('0.5-1.4', 'f9d76ea9e22ef5f40aa126b697351cae') diff --git a/var/spack/repos/builtin/packages/r-selectr/package.py b/var/spack/repos/builtin/packages/r-selectr/package.py index 5b57993a85..628ee221f9 100644 --- a/var/spack/repos/builtin/packages/r-selectr/package.py +++ b/var/spack/repos/builtin/packages/r-selectr/package.py @@ -15,12 +15,13 @@ class RSelectr(RPackage): (<https://pythonhosted.org/cssselect/>).""" homepage = "https://sjp.co.nz/projects/selectr" - url = "https://cran.r-project.org/src/contrib/selectr_0.3-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/selectr" + url = "https://cloud.r-project.org/src/contrib/selectr_0.3-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/selectr" + version('0.4-1', sha256='8bd42f167629344e485e586f9b05fed342746132489079084d82133d7b3ee2ca') + version('0.4-0', sha256='40cd51bfe499954b300742c49f92167a68964b974268a7f47ca8864f32020ece') version('0.3-1', '7190fcdea1823ad7ef429cab6938e960') - depends_on('r-testthat', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-xml', type=('build', 'run')) - depends_on('r-xml2', type=('build', 'run')) + depends_on('r-r6', when='@0.4-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-seqinr/package.py b/var/spack/repos/builtin/packages/r-seqinr/package.py index a685f86a14..ab7685fc47 100644 --- a/var/spack/repos/builtin/packages/r-seqinr/package.py +++ b/var/spack/repos/builtin/packages/r-seqinr/package.py @@ -12,13 +12,13 @@ class RSeqinr(RPackage): data management under the ACNUC system.""" homepage = "http://seqinr.r-forge.r-project.org" - url = "https://cran.r-project.org/src/contrib/seqinr_3.3-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/seginr" + url = "https://cloud.r-project.org/src/contrib/seqinr_3.3-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/seqinr" version('3.4-5', 'd550525dcea754bbd5b83cb46b4124cc') version('3.3-6', '73023d627e72021b723245665e1ad055') - depends_on('r@2.10:') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-ade4', type=('build', 'run')) depends_on('r-segmented', type=('build', 'run')) depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/r-sessioninfo/package.py b/var/spack/repos/builtin/packages/r-sessioninfo/package.py new file mode 100644 index 0000000000..f8770c7f19 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sessioninfo/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSessioninfo(RPackage): + """Query and print information about the current R session. It is similar + to 'utils::sessionInfo()', but includes more information about packages, + and where they were installed from.""" + + homepage = "https://github.com/r-lib/sessioninfo#readme" + url = "https://cloud.r-project.org/src/contrib/sessioninfo_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sessioninfo" + + version('1.1.1', sha256='166b04678448a7decd50f24afabe5e2ad613e3c55b180ef6e8dd7a870a1dae48') + + depends_on('r-cli', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-seurat/package.py b/var/spack/repos/builtin/packages/r-seurat/package.py index abb49e0628..c3e5de9dce 100644 --- a/var/spack/repos/builtin/packages/r-seurat/package.py +++ b/var/spack/repos/builtin/packages/r-seurat/package.py @@ -11,44 +11,79 @@ class RSeurat(RPackage): single cell RNA-seq data.""" homepage = "http://satijalab.org/seurat/" - url = "https://cran.r-project.org/src/contrib/Seurat_2.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/Seurat" + url = "https://cloud.r-project.org/src/contrib/Seurat_2.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/Seurat" + version('3.1.0', sha256='d8d3fad2950a8f791376e3d20c72ea07c68bf8d82d800661cab5ce696db39d45') + version('3.0.2', sha256='16df5dec6b41d49320c5bf5ce30eb3b7dedeea69b054b55b77528f2f2b7bce04') + version('3.0.1', sha256='8c467bdbfdb9aff51bde6a897ff98a7389941f688639d8f1d36c71dde076a257') version('2.1.0', '46427837bb739883f9b7addd08fccee5') version('2.0.1', 'a77794891e93b9fa1ef41735fe8424ea') - depends_on('r@3.4.0:3.4.9') - depends_on('r-ggplot2', type=('build', 'run')) - depends_on('r-gplots', type=('build', 'run')) - depends_on('r-reshape2', type=('build', 'run')) + depends_on('r@3.2.0:', when='@:2.3.0', type=('build', 'run')) + depends_on('r@3.4.0:', when='@2.3.1:', type=('build', 'run')) + depends_on('r-ggplot2@3.0.0:', type=('build', 'run')) + depends_on('r-gplots', when='@:2.3.4', type=('build', 'run')) + depends_on('r-reshape2', when='@:2.3.4', type=('build', 'run')) depends_on('r-ape', type=('build', 'run')) - depends_on('r-tidyr', type=('build', 'run')) - depends_on('r-caret', type=('build', 'run')) - depends_on('r-gdata', type=('build', 'run')) - depends_on('r-glue', type=('build', 'run')) - depends_on('r-pkgconfig', type=('build', 'run')) - depends_on('r-plogr', type=('build', 'run')) - depends_on('r-gridextra', type=('build', 'run')) + depends_on('r-tidyr', when='@:2.3.4', type=('build', 'run')) + depends_on('r-caret', when='@:2.3.2', type=('build', 'run')) + depends_on('r-gdata', when='@:2.3.2', type=('build', 'run')) + depends_on('r-gridextra', when='@:2.3.0', type=('build', 'run')) depends_on('r-cowplot', type=('build', 'run')) depends_on('r-rocr', type=('build', 'run')) - depends_on('r-hmisc', type=('build', 'run')) - depends_on('r-nmf', type=('build', 'run')) + depends_on('r-hmisc', when='@:2.3.4', type=('build', 'run')) + depends_on('r-nmf', when='@:2.2.0', type=('build', 'run')) depends_on('r-irlba', type=('build', 'run')) depends_on('r-igraph', type=('build', 'run')) - depends_on('r-fpc', type=('build', 'run')) + depends_on('r-fpc', when='@:2.3.4', type=('build', 'run')) depends_on('r-rcppprogress', type=('build', 'run')) - depends_on('r-lars', type=('build', 'run')) - depends_on('r-dtw', type=('build', 'run')) - depends_on('r-mixtools', type=('build', 'run')) + depends_on('r-lars', when='@:2.3.4', type=('build', 'run')) + depends_on('r-dtw', when='@:2.3.4', type=('build', 'run')) + depends_on('r-mixtools', when='@:2.3.4', type=('build', 'run')) depends_on('r-ica', type=('build', 'run')) - depends_on('r-diffusionmap', type=('build', 'run')) + depends_on('r-diffusionmap', when='@:2.3.3', type=('build', 'run')) depends_on('r-tsne', type=('build', 'run')) depends_on('r-rtsne', type=('build', 'run')) - depends_on('r-ranger', type=('build', 'run')) + depends_on('r-ranger', when='@:2.3.2', type=('build', 'run')) depends_on('r-pbapply', type=('build', 'run')) - depends_on('r-ggjoy', type=('build', 'run')) + depends_on('r-ggjoy', when='@:2.1.0', type=('build', 'run')) depends_on('r-plotly', type=('build', 'run')) depends_on('r-sdmtools', type=('build', 'run')) - depends_on('r-tclust', type=('build', 'run')) - depends_on('r-fnn', type=('build', 'run')) - depends_on('r-vgam', type=('build', 'run')) + depends_on('r-tclust', when='@:2.3.2', type=('build', 'run')) + depends_on('r-fnn', when='@:2.3.2', type=('build', 'run')) + depends_on('r-vgam', when='@:2.3.2', type=('build', 'run')) + depends_on('r-matrix@1.2.14:', type=('build', 'run')) + depends_on('r-rcolorbrewer', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-rcpp@0.11.0:', type=('build', 'run')) + depends_on('r-rcppeigen', type=('build', 'run')) + depends_on('r-ggridges', when='@2.2.0:', type=('build', 'run')) + depends_on('r-e1071', when='@:2.0.1', type=('build', 'run')) + depends_on('r-compositions', when='@:2.0.1', type=('build', 'run')) + depends_on('r-nmof', when='@:2.0.1', type=('build', 'run')) + depends_on('r-metap', when='@2.2.1:', type=('build', 'run')) + depends_on('r-cluster', when='@2.3.0:', type=('build', 'run')) + depends_on('r-fitdistrplus', when='@2.3.0:', type=('build', 'run')) + depends_on('r-png', when='@2.3.0:', type=('build', 'run')) + depends_on('r-lmtest', when='@2.3.0:', type=('build', 'run')) + depends_on('r-rann', when='@2.3.0:', type=('build', 'run')) + depends_on('r-reticulate', when='@2.3.1:', type=('build', 'run')) + depends_on('r-stringr', when='@:2.3.2', type=('build', 'run')) + depends_on('r-dplyr', when='@:2.3.4', type=('build', 'run')) + depends_on('r-httr', when='@2.3.4:', type=('build', 'run')) + depends_on('r-dosnow', when='@2.3.0:2.3.4', type=('build', 'run')) + depends_on('r-foreach', when='@2.3.0:2.3.4', type=('build', 'run')) + depends_on('r-hdf5r', when='@2.3.2:2.3.4', type=('build', 'run')) + depends_on('r-future', when='@3.0.0:', type=('build', 'run')) + depends_on('r-future-apply', when='@3.0.0:', type=('build', 'run')) + depends_on('r-ggrepel', when='@3.0.0:', type=('build', 'run')) + depends_on('r-kernsmooth', when='@3.0.0:', type=('build', 'run')) + depends_on('r-rlang', when='@3.0.0:', type=('build', 'run')) + depends_on('r-rsvd', when='@3.0.0:', type=('build', 'run')) + depends_on('r-scales', when='@3.0.0:', type=('build', 'run')) + depends_on('r-sctransform@0.2.0:', when='@3.0.0:', type=('build', 'run')) + depends_on('r-leiden@0.3.1:', when='@3.1.0:', type=('build', 'run')) + depends_on('r-rcppannoy', when='@3.1.0:', type=('build', 'run')) + depends_on('r-uwot', when='@3.1.0:', type=('build', 'run')) + depends_on('java', when='@:2.3.0') diff --git a/var/spack/repos/builtin/packages/r-sf/package.py b/var/spack/repos/builtin/packages/r-sf/package.py index 711915fc6f..bd79b7a4fd 100644 --- a/var/spack/repos/builtin/packages/r-sf/package.py +++ b/var/spack/repos/builtin/packages/r-sf/package.py @@ -13,18 +13,20 @@ class RSf(RPackage): datum transformations.""" homepage = "https://github.com/r-spatial/sf/" - url = "https://cran.r-project.org/src/contrib/sf_0.5-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sf" + url = "https://cloud.r-project.org/src/contrib/sf_0.5-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sf" + version('0.7-7', sha256='d1780cb46a285b30c7cc41cae30af523fbc883733344e53f7291e2d045e150a4') + version('0.7-5', sha256='53ed0567f502216a116c4848f5a9262ca232810f82642df7b98e0541a2524868') version('0.5-5', '53ff32d0c9bf2844666c68ce7d75beb2') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-dbi@0.5:', type=('build', 'run')) - depends_on('r-units@0.4-6:', type=('build', 'run')) - depends_on('r-classint', type=('build', 'run')) + depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.18:', type=('build', 'run')) + depends_on('r-dbi@0.8:', type=('build', 'run')) + depends_on('r-units@0.6-0:', type=('build', 'run')) + depends_on('r-classint@0.2-1:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('gdal@2.0.0:') - depends_on('geos@3.3.0:') - # Since PROJ.4 and PROJ.6 have incompatible APIs, I'm assuming - # that since r-sf supports PROJ.4, it doesn't support PROJ.6 - depends_on('proj@4.8.0:5') + depends_on('gdal@2.0.1:') + depends_on('geos@3.4.0:') + depends_on('proj@4.8.0:5', when='@:0.7-3') + depends_on('proj@4.8.0:', when='@0.7-4:') diff --git a/var/spack/repos/builtin/packages/r-sfsmisc/package.py b/var/spack/repos/builtin/packages/r-sfsmisc/package.py index 8b9707d750..779d13959c 100644 --- a/var/spack/repos/builtin/packages/r-sfsmisc/package.py +++ b/var/spack/repos/builtin/packages/r-sfsmisc/package.py @@ -11,8 +11,13 @@ class RSfsmisc(RPackage): ETH Zurich, quite a few related to graphics; some were ported from S-plus.""" - homepage = "https://cran.r-project.org/web/packages/sfsmisc/index.html" - url = "https://cran.r-project.org/src/contrib/sfsmisc_1.1-0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sfsmisc" + homepage = "https://cloud.r-project.org/package=sfsmisc" + url = "https://cloud.r-project.org/src/contrib/sfsmisc_1.1-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sfsmisc" + version('1.1-4', sha256='44b6a9c859922e86b7182e54eb781d3264f3819f310343518ebc66f54f305c7d') + version('1.1-3', sha256='58eff7d4a9c79212321858efe98d2a6153630e263ff0218a31d5e104b8b545f8') version('1.1-0', '1ba4303076e2bbf018f7eecc7d04e178') + + depends_on('r@3.0.1:', when='@:1.1-1', type=('build', 'run')) + depends_on('r@3.2.0:', when='@1.1-2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shape/package.py b/var/spack/repos/builtin/packages/r-shape/package.py index f5cdc61858..67851868f1 100644 --- a/var/spack/repos/builtin/packages/r-shape/package.py +++ b/var/spack/repos/builtin/packages/r-shape/package.py @@ -10,9 +10,12 @@ class RShape(RPackage): """Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...""" - homepage = "https://cran.r-project.org/package=shape" - url = "https://cran.r-project.org/src/contrib/shape_1.4.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/shape" + homepage = "https://cloud.r-project.org/package=shape" + url = "https://cloud.r-project.org/src/contrib/shape_1.4.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/shape" + version('1.4.4', sha256='f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41') version('1.4.3', '2a807bf95e7decc71478f805221852da') version('1.4.2', '75557c43a385b9cc0c4dff361af6e06c') + + depends_on('r@2.0.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py index 4d6a9d83b1..3c1c3bcb47 100644 --- a/var/spack/repos/builtin/packages/r-shiny/package.py +++ b/var/spack/repos/builtin/packages/r-shiny/package.py @@ -13,17 +13,23 @@ class RShiny(RPackage): powerful applications with minimal effort.""" homepage = "http://shiny.rstudio.com/" - url = "https://cran.rstudio.com/src/contrib/shiny_1.0.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/shiny" + url = "https://cloud.r-project.org/src/contrib/shiny_1.0.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/shiny" + version('1.3.2', sha256='28b851ae6c196ca845f6e815c1379247595ac123a4faa10a16533d1a9ce0c24f') version('1.0.5', '419dd5d3ea0bd87a07f8f0b1ef14fc13') version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611') - depends_on('r-httpuv', type=('build', 'run')) - depends_on('r-mime', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-httpuv@1.5.0:', type=('build', 'run')) + depends_on('r-mime@0.3:', type=('build', 'run')) + depends_on('r-jsonlite@0.9.16:', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-htmltools', type=('build', 'run')) - depends_on('r-r6', type=('build', 'run')) + depends_on('r-htmltools@0.3.6:', type=('build', 'run')) + depends_on('r-r6@2.0:', type=('build', 'run')) depends_on('r-sourcetools', type=('build', 'run')) + depends_on('r-later@0.7.2:', when='@1.1.0:', type=('build', 'run')) + depends_on('r-promises@1.0.1:', when='@1.1.0:', type=('build', 'run')) + depends_on('r-crayon', when='@1.1.0:', type=('build', 'run')) + depends_on('r-rlang', when='@1.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shinydashboard/package.py b/var/spack/repos/builtin/packages/r-shinydashboard/package.py index 5c71ff533a..23733e9576 100644 --- a/var/spack/repos/builtin/packages/r-shinydashboard/package.py +++ b/var/spack/repos/builtin/packages/r-shinydashboard/package.py @@ -9,13 +9,15 @@ from spack import * class RShinydashboard(RPackage): """Create Dashboards with 'Shiny'""" - homepage = "https://cran.r-project.org/package=shinydashboard" - url = "https://cran.r-project.org/src/contrib/shinydashboard_0.7.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/shinydashboard" + homepage = "https://cloud.r-project.org/package=shinydashboard" + url = "https://cloud.r-project.org/src/contrib/shinydashboard_0.7.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/shinydashboard" + version('0.7.1', sha256='51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e') version('0.7.0', 'a572695884e3b45320b0ab5a7b364ffd') version('0.6.1', '0f6ad0448237e10d53d4d27ade1c6863') - depends_on('r@3.3.0:', type=('build', 'run')) + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-htmltools@0.2.6:', type=('build', 'run')) depends_on('r-shiny@1.0.0:', type=('build', 'run')) + depends_on('r-promises', when='@0.7.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-shinyfiles/package.py b/var/spack/repos/builtin/packages/r-shinyfiles/package.py new file mode 100644 index 0000000000..70b4864f40 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-shinyfiles/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RShinyfiles(RPackage): + """Provides functionality for client-side navigation of the server side + file system in shiny apps. In case the app is running locally this gives + the user direct access to the file system without the need to "download" + files to a temporary location. Both file and folder selection as well as + file saving is available.""" + + homepage = "https://github.com/thomasp85/shinyFiles" + url = "https://cloud.r-project.org/src/contrib/shinyFiles_0.7.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/shinyFiles" + + version('0.7.3', sha256='710c8a6191aaf336379bc748daff1160d0d2858e2aee0d98e2ad48e7121d5a05') + + depends_on('r-htmltools', type=('build', 'run')) + depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-shiny@1.1.0:', type=('build', 'run')) + depends_on('r-fs@1.2.6:', type=('build', 'run')) + depends_on('r-tibble@1.4.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sitmo/package.py b/var/spack/repos/builtin/packages/r-sitmo/package.py new file mode 100644 index 0000000000..eab70f5ac4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sitmo/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSitmo(RPackage): + """Provided within are two high quality and fast PPRNGs that may be used in + an 'OpenMP' parallel environment. In addition, there is a generator for one + dimensional low-discrepancy sequence. The objective of this library to + consolidate the distribution of the 'sitmo' (C++98 & C++11), 'threefry' and + 'vandercorput' (C++11-only) engines on CRAN by enabling others to link to + the header files inside of 'sitmo' instead of including a copy of each + engine within their individual package. Lastly, the package contains + example implementations using the 'sitmo' package and three accompanying + vignette that provide additional information.""" + + homepage = "https://github.com/coatless/sitmo" + url = "https://cloud.r-project.org/src/contrib/sitmo_2.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sitmo" + + version('2.0.1', sha256='0c90d357af334d5c99c8956739dc12623ddd87dda5efa59f4a43f7393c87ed2a') + + depends_on('r@3.2.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sm/package.py b/var/spack/repos/builtin/packages/r-sm/package.py index 89de1cb4e9..29a46acd05 100644 --- a/var/spack/repos/builtin/packages/r-sm/package.py +++ b/var/spack/repos/builtin/packages/r-sm/package.py @@ -12,9 +12,10 @@ class RSm(RPackage): Oxford University Press.""" homepage = "http://www.stats.gla.ac.uk/~adrian/sm" - url = "https://cran.r-project.org/src/contrib/sm_2.2-5.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sm" + url = "https://cloud.r-project.org/src/contrib/sm_2.2-5.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sm" + version('2.2-5.6', sha256='b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30') version('2.2-5.5', sha256='43e212a14c364b98b10018b56fe0a619ccffe4bde1294e6c45b3eafe7caf82e7') depends_on('r@3.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-smoof/package.py b/var/spack/repos/builtin/packages/r-smoof/package.py index 839d5a1ce2..60520006b8 100644 --- a/var/spack/repos/builtin/packages/r-smoof/package.py +++ b/var/spack/repos/builtin/packages/r-smoof/package.py @@ -14,8 +14,8 @@ class RSmoof(RPackage): functions.""" homepage = "http://github.com/jakobbossek/smoof" - url = "https://cran.r-project.org/src/contrib/smoof_1.5.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/smoof" + url = "https://cloud.r-project.org/src/contrib/smoof_1.5.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/smoof" version('1.5.1', 'c3e3b5dafed34608f933ae255cf49054') version('1.5', 'b371bde2724eade5a6d4d808fa3ad269') diff --git a/var/spack/repos/builtin/packages/r-sn/package.py b/var/spack/repos/builtin/packages/r-sn/package.py index 7b3fa2c3e9..61d84c1df2 100644 --- a/var/spack/repos/builtin/packages/r-sn/package.py +++ b/var/spack/repos/builtin/packages/r-sn/package.py @@ -12,16 +12,18 @@ class RSn(RPackage): related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.""" - homepage = "https://cran.r-project.org/web/packages/sn/index.html" - url = "https://cran.r-project.org/src/contrib/sn_1.5-0.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/sn" + homepage = "https://cloud.r-project.org/package=sn" + url = "https://cloud.r-project.org/src/contrib/sn_1.5-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sn" + version('1.5-4', sha256='46677ebc109263a68f62b5cf53ec59916cda490e5bc5bbb08276757a677f8674') + version('1.5-3', sha256='cc21b97ddd674c9b1296260f2a72ffb085cdcb877c8332f0bfa96ff028517183') version('1.5-0', 'a3349773be950199d7f4c17954be56d1') version('1.4-0', 'cfa604317ea54224b06abd1cec179375') version('1.3-0', '84d02ba2ab5ca6f3644626013e7ce36d') version('1.2-4', 'bf3a47b05016326e910fdb4cc4967e4d') version('1.2-3', '290ae511d974a6beb4c3c79c0106858f') - depends_on('r@3.4.0:3.4.9') - depends_on('r-mnormt', type=('build', 'run')) + depends_on('r@2.15.3:', type=('build', 'run')) + depends_on('r-mnormt@1.5-4:', type=('build', 'run')) depends_on('r-numderiv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snakecase/package.py b/var/spack/repos/builtin/packages/r-snakecase/package.py new file mode 100644 index 0000000000..fddcd2c56c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-snakecase/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSnakecase(RPackage): + """A consistent, flexible and easy to use tool to parse and convert strings + into cases like snake or camel among others.""" + + homepage = "https://github.com/Tazinho/snakecase" + url = "https://cloud.r-project.org/src/contrib/snakecase_0.11.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/snakecase" + + version('0.11.0', sha256='998420a58391ac85785e60bcdf6fd6927c82758ad2859a9a73a0e57299e8c1cf') + + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-stringr', type=('build', 'run')) + depends_on('r-stringi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snow/package.py b/var/spack/repos/builtin/packages/r-snow/package.py index ada2cfaefa..e7173b4c35 100644 --- a/var/spack/repos/builtin/packages/r-snow/package.py +++ b/var/spack/repos/builtin/packages/r-snow/package.py @@ -9,11 +9,11 @@ from spack import * class RSnow(RPackage): """Support for simple parallel computing in R.""" - homepage = "https://cran.r-project.org/web/packages/snow/index.html" - url = "https://cran.r-project.org/src/contrib/snow_0.4-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/snow" + homepage = "https://cloud.r-project.org/package=snow" + url = "https://cloud.r-project.org/src/contrib/snow_0.4-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/snow" + version('0.4-3', sha256='8512537daf334ea2b8074dbb80cf5e959a403a78d68bc1e97664e8a4f64576d8') version('0.4-2', 'afc7b0dfd4518aedb6fc81712fd2ac70') - depends_on('r-rmpi', type='run') depends_on('r@2.13.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-snowfall/package.py b/var/spack/repos/builtin/packages/r-snowfall/package.py index 880b8523d7..fbc86513af 100644 --- a/var/spack/repos/builtin/packages/r-snowfall/package.py +++ b/var/spack/repos/builtin/packages/r-snowfall/package.py @@ -13,9 +13,11 @@ class RSnowfall(RPackage): present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.""" - homepage = "https://cran.r-project.org/web/packages/snowfall/index.html" - url = "https://cran.r-project.org/src/contrib/snowfall_1.84-6.1.tar.gz" + homepage = "https://cloud.r-project.org/package=snowfall" + url = "https://cloud.r-project.org/src/contrib/snowfall_1.84-6.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/snowfall" version('1.84-6.1', '5ec38116aa9cac237d56f59ba5bd60e3') + depends_on('r@2.10:', type=('build', 'run')) depends_on('r-snow', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-som/package.py b/var/spack/repos/builtin/packages/r-som/package.py index a2de57deb0..f87b92c367 100644 --- a/var/spack/repos/builtin/packages/r-som/package.py +++ b/var/spack/repos/builtin/packages/r-som/package.py @@ -9,9 +9,9 @@ from spack import * class RSom(RPackage): """Self-Organizing Map (with application in gene clustering).""" - homepage = "https://cran.r-project.org/web/packages/som/index.html" - url = "https://cran.r-project.org/src/contrib/som_0.3-5.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/som" + homepage = "https://cloud.r-project.org/package=som" + url = "https://cloud.r-project.org/src/contrib/som_0.3-5.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/som" version('0.3-5.1', '802a5a80902579354ce3420faeeeb756') version('0.3-5', '72717499794c7aa945a768b742af8895') diff --git a/var/spack/repos/builtin/packages/r-sourcetools/package.py b/var/spack/repos/builtin/packages/r-sourcetools/package.py index 6a107c9d8e..2df62d25d8 100644 --- a/var/spack/repos/builtin/packages/r-sourcetools/package.py +++ b/var/spack/repos/builtin/packages/r-sourcetools/package.py @@ -9,11 +9,12 @@ from spack import * class RSourcetools(RPackage): """Tools for Reading, Tokenizing and Parsing R Code.""" - homepage = "https://cran.r-project.org/package=sourcetools" - url = "https://cran.r-project.org/src/contrib/sourcetools_0.1.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sourcetools" + homepage = "https://cloud.r-project.org/package=sourcetools" + url = "https://cloud.r-project.org/src/contrib/sourcetools_0.1.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sourcetools" + version('0.1.7', sha256='47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca') version('0.1.6', 'c78a816384b168d04af41bd7ff4d909d') version('0.1.5', 'b4d7902ffafd9802e8fbff5ce824bb28') - depends_on('r-testthat', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py index 373c373e87..2cdbaf6ffd 100644 --- a/var/spack/repos/builtin/packages/r-sp/package.py +++ b/var/spack/repos/builtin/packages/r-sp/package.py @@ -13,9 +13,12 @@ class RSp(RPackage): methods for retrieving coordinates, for subsetting, print, summary, etc.""" homepage = "https://github.com/edzer/sp/" - url = "https://cran.r-project.org/src/contrib/sp_1.2-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sp" + url = "https://cloud.r-project.org/src/contrib/sp_1.2-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sp" + version('1.3-1', sha256='57988b53ba8acc35f3912d62feba4b929a0f757c6b54080c623c5d805e0cb59f') + version('1.2-7', sha256='6d60e03e1abd30a7d4afe547d157ce3dd7a8c166fc5e407fd6d62ae99ff30460') version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1') + depends_on('r@3.0.0:', type=('build', 'run')) depends_on('r-lattice', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spacetime/package.py b/var/spack/repos/builtin/packages/r-spacetime/package.py index 88037ed699..e12bd4cc0b 100644 --- a/var/spack/repos/builtin/packages/r-spacetime/package.py +++ b/var/spack/repos/builtin/packages/r-spacetime/package.py @@ -10,8 +10,8 @@ class RSpacetime(RPackage): """spacetime: Classes and Methods for Spatio-Temporal Data""" homepage = "http://github.com/edzer/spacetime" - url = "https://cran.r-project.org/src/contrib/spacetime_1.2-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/spacetime" + url = "https://cloud.r-project.org/src/contrib/spacetime_1.2-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/spacetime" version('1.2-2', sha256='1e9d3f92e5c4614a69c82a58bf0b5c829b4ed262bf1250bef943ae286056ea2d') diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py index bd28089911..e5974e19af 100644 --- a/var/spack/repos/builtin/packages/r-sparsem/package.py +++ b/var/spack/repos/builtin/packages/r-sparsem/package.py @@ -12,8 +12,12 @@ class RSparsem(RPackage): subsetting and Kronecker products.""" homepage = "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html" - url = "https://cran.r-project.org/src/contrib/SparseM_1.74.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM" + url = "https://cloud.r-project.org/src/contrib/SparseM_1.74.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/SparseM" + version('1.77', sha256='a9329fef14ae4fc646df1f4f6e57efb0211811599d015f7bc04c04285495d45c') + version('1.76', sha256='c2c8e44376936a5fe6f09a37f3668016e66cbc687519cc952aa346a658a2b69b') version('1.74', 'a16c9b7db172dfd2b7b6508c48e81a5d') version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601') + + depends_on('r@2.15:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatial/package.py b/var/spack/repos/builtin/packages/r-spatial/package.py index 6129cf5865..6673560c04 100644 --- a/var/spack/repos/builtin/packages/r-spatial/package.py +++ b/var/spack/repos/builtin/packages/r-spatial/package.py @@ -9,9 +9,9 @@ from spack import * class RSpatial(RPackage): """spatial: Functions for Kriging and Point Pattern Analysis""" - homepage = "https://cran.r-project.org/package=spatial" - url = "https://cran.r-project.org/src/contrib/spatial_7.3-11.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/spatial" + homepage = "https://cloud.r-project.org/package=spatial" + url = "https://cloud.r-project.org/src/contrib/spatial_7.3-11.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/spatial" version('7.3-11', sha256='624448d2ac22e1798097d09fc5dc4605908a33f490b8ec971fc6ea318a445c11') diff --git a/var/spack/repos/builtin/packages/r-spatialreg/package.py b/var/spack/repos/builtin/packages/r-spatialreg/package.py index e99f955be8..bcbadc07a1 100644 --- a/var/spack/repos/builtin/packages/r-spatialreg/package.py +++ b/var/spack/repos/builtin/packages/r-spatialreg/package.py @@ -9,9 +9,9 @@ from spack import * class RSpatialreg(RPackage): """spatialreg: Spatial Regression Analysis""" - homepage = "https://cran.r-project.org/package=spatialreg" - url = "https://cran.r-project.org/src/contrib/spatialreg_1.1-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/spatialreg" + homepage = "https://cloud.r-project.org/package=spatialreg" + url = "https://cloud.r-project.org/src/contrib/spatialreg_1.1-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/spatialreg" version('1.1-3', sha256='7609cdfcdfe427d2643a0db6b5360be3f6d60ede8229436ab52092d1c9cf0480') @@ -26,3 +26,4 @@ class RSpatialreg(RPackage): depends_on('r-nlme', type=('build', 'run')) depends_on('r-spdata', type=('build', 'run')) depends_on('r-spdep', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spdata/package.py b/var/spack/repos/builtin/packages/r-spdata/package.py index 1a40030c36..0cfa061db6 100644 --- a/var/spack/repos/builtin/packages/r-spdata/package.py +++ b/var/spack/repos/builtin/packages/r-spdata/package.py @@ -10,8 +10,8 @@ class RSpdata(RPackage): """spData: Datasets for Spatial Analysis""" homepage = "https://github.com/Nowosad/spData" - url = "https://cran.r-project.org/src/contrib/spData_0.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/spData" + url = "https://cloud.r-project.org/src/contrib/spData_0.3.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/spData" version('0.3.0', sha256='de24ea659541a6c795cd26a1f6a213e15061af9c97a24cba1c24ce30c6c24c98') diff --git a/var/spack/repos/builtin/packages/r-spdep/package.py b/var/spack/repos/builtin/packages/r-spdep/package.py index 1ae0a16f0e..2c0f9bc47b 100644 --- a/var/spack/repos/builtin/packages/r-spdep/package.py +++ b/var/spack/repos/builtin/packages/r-spdep/package.py @@ -23,15 +23,24 @@ class RSpdep(RPackage): two stage least squares models.""" homepage = "https://r-forge.r-project.org/projects/spdep" - url = "https://cran.r-project.org/src/contrib/spdep_0.6-13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/spdep" + url = "https://cloud.r-project.org/src/contrib/spdep_0.6-13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/spdep" + version('1.1-2', sha256='ba0ca3a0ad6b9cc1dc46cadd9e79259949ad38c88f738e98e482d6c06640b31a') + version('1.0-2', sha256='6f9efa4347d5c13b49922b75481ac403431c3c76a65a109af29954aa7bb138b2') version('0.6-13', 'bfc68b3016b4894b152ecec4b86f85d1') - depends_on('r@3.0:') + depends_on('r@3.0.0:', when='@:0.7-7', type=('build', 'run')) + depends_on('r@3.3.0:', when='@0.7-8:', type=('build', 'run')) depends_on('r-sp@1.0:', type=('build', 'run')) depends_on('r-learnbayes', type=('build', 'run')) depends_on('r-deldir', type=('build', 'run')) depends_on('r-coda', type=('build', 'run')) depends_on('r-gmodels', type=('build', 'run')) depends_on('r-expm', type=('build', 'run')) + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-boot@1.3-1:', type=('build', 'run')) + depends_on('r-nlme', type=('build', 'run')) + depends_on('r-spdata@0.2.6.0:', when='@1.0-2:', type=('build', 'run')) + depends_on('r-sf', when='@1.0-2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-speedglm/package.py b/var/spack/repos/builtin/packages/r-speedglm/package.py index cd7e69ef2a..2371b3090e 100644 --- a/var/spack/repos/builtin/packages/r-speedglm/package.py +++ b/var/spack/repos/builtin/packages/r-speedglm/package.py @@ -10,9 +10,9 @@ class RSpeedglm(RPackage): """Fitting linear models and generalized linear models to large data sets by updating algorithms.""" - homepage = "https://cran.r-project.org/package=speedglm" - url = "https://cran.rstudio.com/src/contrib/speedglm_0.3-2.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/speedglm" + homepage = "https://cloud.r-project.org/package=speedglm" + url = "https://cloud.r-project.org/src/contrib/speedglm_0.3-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/speedglm" version('0.3-2', 'c4874d4c2a677d657a335186ebb63131') diff --git a/var/spack/repos/builtin/packages/r-splancs/package.py b/var/spack/repos/builtin/packages/r-splancs/package.py index 60cf5fa30e..4ef99ef42c 100644 --- a/var/spack/repos/builtin/packages/r-splancs/package.py +++ b/var/spack/repos/builtin/packages/r-splancs/package.py @@ -9,9 +9,9 @@ from spack import * class RSplancs(RPackage): """Spatial and Space-Time Point Pattern Analysis""" - homepage = "https://cran.r-project.org/web/packages/splancs/index.html" - url = "https://cran.r-project.org/src/contrib/splancs_2.01-40.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/splancs" + homepage = "https://cloud.r-project.org/package=splancs" + url = "https://cloud.r-project.org/src/contrib/splancs_2.01-40.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/splancs" version('2.01-40', 'dc08a5c9a1fd2098d78459152f4917ce') diff --git a/var/spack/repos/builtin/packages/r-splitstackshape/package.py b/var/spack/repos/builtin/packages/r-splitstackshape/package.py index 8ceb1fe1b9..a314d22134 100644 --- a/var/spack/repos/builtin/packages/r-splitstackshape/package.py +++ b/var/spack/repos/builtin/packages/r-splitstackshape/package.py @@ -19,10 +19,12 @@ class RSplitstackshape(RPackage): """ homepage = "http://github.com/mrdwab/splitstackshape" - url = "https://cran.r-project.org/src/contrib/splitstackshape_1.4.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/splitstackshape" + url = "https://cloud.r-project.org/src/contrib/splitstackshape_1.4.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/splitstackshape" + version('1.4.8', sha256='656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56') + version('1.4.6', sha256='b9888f9508babdb8e09f57674facaa8b158a06255ef1e61c8df813f58881860f') version('1.4.4', '54d2554fe92dfc4670a000b45baacc28') - depends_on('r-data-table@1.9.4:', type=('build', 'run')) depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-data-table@1.9.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sqldf/package.py b/var/spack/repos/builtin/packages/r-sqldf/package.py index dd9289fe0f..da7d95aa31 100644 --- a/var/spack/repos/builtin/packages/r-sqldf/package.py +++ b/var/spack/repos/builtin/packages/r-sqldf/package.py @@ -18,13 +18,14 @@ class RSqldf(RPackage): files are larger than R itself can handle. 'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' backends are supported.""" - homepage = "https://cran.r-project.org/package=sqldf" - url = "https://cran.r-project.org/src/contrib/sqldf_0.4-11.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/sqldf" + homepage = "https://cloud.r-project.org/package=sqldf" + url = "https://cloud.r-project.org/src/contrib/sqldf_0.4-11.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sqldf" version('0.4-11', '85def6fe2418569370c24e53522d2c2d') - depends_on('r-gsubfn', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-gsubfn@0.6:', type=('build', 'run')) depends_on('r-proto', type=('build', 'run')) depends_on('r-rsqlite', type=('build', 'run')) depends_on('r-dbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-squarem/package.py b/var/spack/repos/builtin/packages/r-squarem/package.py new file mode 100644 index 0000000000..a4f0e9de36 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-squarem/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSquarem(RPackage): + """Algorithms for accelerating the convergence of slow, monotone sequences + from smooth, contraction mapping such as the EM algorithm. It can be used + to accelerate any smooth, linearly convergent acceleration scheme. A + tutorial style introduction to this package is available in a vignette on + the CRAN download page or, when the package is loaded in an R session, with + vignette("SQUAREM").""" + + homepage = "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html" + url = "https://cloud.r-project.org/src/contrib/SQUAREM_2017.10-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/SQUAREM" + + version('2017.10-1', sha256='9b89905b436f1cf3faa9e3dabc585a76299e729e85ca659bfddb4b7cba11b283') + + depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-squash/package.py b/var/spack/repos/builtin/packages/r-squash/package.py index 580255de98..f38963c8d0 100644 --- a/var/spack/repos/builtin/packages/r-squash/package.py +++ b/var/spack/repos/builtin/packages/r-squash/package.py @@ -9,9 +9,9 @@ from spack import * class RSquash(RPackage): """Color-Based Plots for Multivariate Visualization""" - homepage = "https://cran.r-project.org/package=squash" - url = "https://cran.r-project.org/src/contrib/squash_1.0.8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/squash" + homepage = "https://cloud.r-project.org/package=squash" + url = "https://cloud.r-project.org/src/contrib/squash_1.0.8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/squash" version('1.0.8', '50d5743d306fa11cfa1a3c4daa75e508') version('1.0.7', '4ac381b17d4d7b77bdaa6f824fbb03ab') diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py index a1b2cb2e4c..2cac7d0963 100644 --- a/var/spack/repos/builtin/packages/r-stanheaders/package.py +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -24,9 +24,13 @@ class RStanheaders(RPackage): estimate, and analyze Stan models.""" homepage = "http://mc-stan.org/" - url = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders" + url = "https://cloud.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/StanHeaders" + version('2.18.1-10', sha256='8a9f7e22105428e97d14f44f75395c37cf8c809de148d279c620024452b3565a') version('2.18.1', sha256='ce0d609a7cd11725b1203bdeae92acc54da3a48b8266eb9dbdb9d95b14df9209') version('2.17.1', '11d8770277dd18e563852852633c6c25') version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57') + + depends_on('r@3.4.0:', when='@2.18.0:', type=('build', 'run')) + depends_on('pandoc', type='build') diff --git a/var/spack/repos/builtin/packages/r-statmod/package.py b/var/spack/repos/builtin/packages/r-statmod/package.py index b48e62a910..ceee29fceb 100644 --- a/var/spack/repos/builtin/packages/r-statmod/package.py +++ b/var/spack/repos/builtin/packages/r-statmod/package.py @@ -16,8 +16,11 @@ class RStatmod(RPackage): that implement secure convergence, dispersion modeling and Tweedie power-law families.""" - homepage = "https://cran.r-project.org/package=statmod" - url = "https://cran.rstudio.com/src/contrib/statmod_1.4.30.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/statmod" + homepage = "https://cloud.r-project.org/package=statmod" + url = "https://cloud.r-project.org/src/contrib/statmod_1.4.30.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/statmod" + version('1.4.32', sha256='2f67a1cfa66126e6345f8a40564a3077d08f1748f17cb8c8fb05c94ed0f57e20') version('1.4.30', '34e60132ce3df38208f9dc0db0479151') + + depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-statnet-common/package.py b/var/spack/repos/builtin/packages/r-statnet-common/package.py index b1b68e6522..7ad4104329 100644 --- a/var/spack/repos/builtin/packages/r-statnet-common/package.py +++ b/var/spack/repos/builtin/packages/r-statnet-common/package.py @@ -11,7 +11,12 @@ class RStatnetCommon(RPackage): Statnet Project. They may also be of use to others.""" homepage = "http://www.statnet.org" - url = "https://cran.r-project.org/src/contrib/statnet.common_3.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/statnet.common" + url = "https://cloud.r-project.org/src/contrib/statnet.common_3.3.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/statnet.common" + version('4.3.0', sha256='834a3359eac967df0420eee416ae4983e3b502a3de56bb24f494a7ca4104e959') + version('4.2.0', sha256='1176c3303436ebe858d02979cf0a0c33e4e2d1f3637516b4761d573ccd132461') version('3.3.0', '36bc11098dcd3652a4beb05c156ad6c8') + + depends_on('r@3.5:', when='@4.2.0:', type=('build', 'run')) + depends_on('r-coda', when='@4.1.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py index 5e10fff5f9..8c44256da8 100644 --- a/var/spack/repos/builtin/packages/r-stringi/package.py +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -18,12 +18,15 @@ class RStringi(RPackage): etc.""" homepage = "http://www.gagolewski.com/software/stringi/" - url = "https://cran.r-project.org/src/contrib/stringi_1.1.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/stringi" + url = "https://cloud.r-project.org/src/contrib/stringi_1.1.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/stringi" + version('1.4.3', sha256='13cecb396b700f81af38746e97b550a1d9fda377ca70c78f6cdfc770d33379ed') + version('1.3.1', sha256='32df663bb6e9527e1ac265eec2116d26f7b7e62ea5ae7cc5de217cbb8defc362') version('1.1.5', '0d5ec30ae368ab1b87a36fee3e228e7b') version('1.1.3', '3b89cee3b5ef7c031077cd7707718e07') version('1.1.2', '0ec2faa62643e1900734c0eaf5096648') version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9') - depends_on('icu4c') + depends_on('r@2.14:', type=('build', 'run')) + depends_on('icu4c@52:') diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py index 54a43fe9b7..aa6bee349d 100644 --- a/var/spack/repos/builtin/packages/r-stringr/package.py +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -13,13 +13,17 @@ class RStringr(RPackage): vectors in the same way, and the output from one function is easy to feed into the input of another.""" - homepage = "https://cran.r-project.org/web/packages/stringr/index.html" - url = "https://cran.r-project.org/src/contrib/stringr_1.1.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/stringr" + homepage = "https://cloud.r-project.org/package=stringr" + url = "https://cloud.r-project.org/src/contrib/stringr_1.1.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/stringr" + version('1.4.0', sha256='87604d2d3a9ad8fd68444ce0865b59e2ffbdb548a38d6634796bbd83eeb931dd') + version('1.3.1', sha256='7a8b8ea038e45978bd797419b16793f44f10c5355ad4c64b74d15276fef20343') version('1.2.0', '9054b1de91c578cc5cf454d656e9c697') version('1.1.0', '47973a33944c6d5db9524b1e835b8a5d') version('1.0.0', '5ca977c90351f78b1b888b379114a7b4') - depends_on('r-stringi', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-stringi@1.1.7:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) + depends_on('r-glue@1.2.0:', when='@1.3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-strucchange/package.py b/var/spack/repos/builtin/packages/r-strucchange/package.py index 4cf073e9e1..8e111a58d7 100644 --- a/var/spack/repos/builtin/packages/r-strucchange/package.py +++ b/var/spack/repos/builtin/packages/r-strucchange/package.py @@ -10,13 +10,12 @@ class RStrucchange(RPackage): """Testing, monitoring and dating structural changes in (linear) regression models.""" - homepage = "https://cran.r-project.org/package=strucchange" - url = "https://cran.r-project.org/src/contrib/strucchange_1.5-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/strucchange" + homepage = "https://cloud.r-project.org/package=strucchange" + url = "https://cloud.r-project.org/src/contrib/strucchange_1.5-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/strucchange" version('1.5-1', 'fc751fc011df9c8df82d577298cb8395') - depends_on('r@2.10.0:') - + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) depends_on('r-sandwich', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-subplex/package.py b/var/spack/repos/builtin/packages/r-subplex/package.py index cc9efbfb24..2ddbb19bf3 100644 --- a/var/spack/repos/builtin/packages/r-subplex/package.py +++ b/var/spack/repos/builtin/packages/r-subplex/package.py @@ -9,8 +9,12 @@ from spack import * class RSubplex(RPackage): """Unconstrained Optimization using the Subplex Algorithm""" - homepage = "https://cran.r-project.org/package=subplex" - url = "https://cran.r-project.org/src/contrib/subplex_1.4-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/subplex" + homepage = "https://cloud.r-project.org/package=subplex" + url = "https://cloud.r-project.org/src/contrib/subplex_1.4-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/subplex" + version('1.5-4', sha256='ff94cf6b1560f78c31712c05bc2bc1b703339e09c7fc777ee94abf15fa7a8b81') + version('1.5-2', sha256='6f8c3ccadf1ccd7f11f3eae28cec16eed3695f14e351b864d807dbaba6cd3ded') version('1.4-1', '2ed963dbbb1dbef47ebec7003f39a117') + + depends_on('r@2.5.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py index d0729c9996..a3f2249521 100644 --- a/var/spack/repos/builtin/packages/r-survey/package.py +++ b/var/spack/repos/builtin/packages/r-survey/package.py @@ -16,7 +16,19 @@ class RSurvey(RPackage): sampling without replacement. Principal components, factor analysis.""" homepage = "http://r-survey.r-forge.r-project.org/survey/" - url = "https://cran.r-project.org/src/contrib/survey_3.30-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/survey" + url = "https://cloud.r-project.org/src/contrib/survey_3.30-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/survey" + version('3.36', sha256='90f32e9d2b52eacf881e6717a4b5edfc5a3beb5da516f8372293549589d79475') + version('3.35-1', sha256='11e5ddde9c8c21dfaed0b1247036e068ad32782c76ff71f7937eb7585dd364db') version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0') + + depends_on('r@2.14.0:', when='@:3.31-5', type=('build', 'run')) + depends_on('r@2.16.0:', when='@3.32:3.34', type=('build', 'run')) + depends_on('r@3.1.0:', when='@3.35:', type=('build', 'run')) + depends_on('r-matrix', when='@3.31:', type=('build', 'run')) + depends_on('r-survival', when='@3.31:', type=('build', 'run')) + depends_on('r-lattice', when='@3.31:', type=('build', 'run')) + depends_on('r-minqa', when='@3.34:', type=('build', 'run')) + depends_on('r-numderiv', when='@3.34:', type=('build', 'run')) + depends_on('r-mitools@2.4:', when='@3.36:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py index fec334728b..34c23beca0 100644 --- a/var/spack/repos/builtin/packages/r-survival/package.py +++ b/var/spack/repos/builtin/packages/r-survival/package.py @@ -11,12 +11,15 @@ class RSurvival(RPackage): Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.""" - homepage = "https://cran.r-project.org/package=survival" - url = "https://cran.r-project.org/src/contrib/survival_2.41-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/survival" + homepage = "https://cloud.r-project.org/package=survival" + url = "https://cloud.r-project.org/src/contrib/survival_2.41-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/survival" + version('2.44-1.1', sha256='55b151e15fcd24ccb3acf60331c9a7ad82bc10f3841ab3be9bc2a37e9ee751b9') + version('2.44-1', sha256='82c44afa41fe4504295855f1da4a5940c3289dfd61bc664bf211bb67c051a909') version('2.41-3', '6edb8093d1177775685dc26f3ce78d73') version('2.40-1', 'a2474b656cd723791268e3114481b8a7') version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2') + depends_on('r@2.13.0:', type=('build', 'run')) depends_on('r-matrix', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-sys/package.py b/var/spack/repos/builtin/packages/r-sys/package.py new file mode 100644 index 0000000000..af8fb3ebbd --- /dev/null +++ b/var/spack/repos/builtin/packages/r-sys/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RSys(RPackage): + """Drop-in replacements for the base system2() function with fine control + and consistent behavior across platforms. Supports clean interruption, + timeout, background tasks, and streaming STDIN / STDOUT / STDERR over + binary or text connections. Arguments on Windows automatically get encoded + and quoted to work on different locales.""" + + homepage = "https://github.com/jeroen/sys#readme" + url = "https://cloud.r-project.org/src/contrib/sys_3.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/sys" + + version('3.2', sha256='2819498461fe2ce83d319d1a47844e86bcea6d01d10861818dba289e7099bbcc') diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py index a7ef6efd60..3637255bf1 100644 --- a/var/spack/repos/builtin/packages/r-tarifx/package.py +++ b/var/spack/repos/builtin/packages/r-tarifx/package.py @@ -9,10 +9,11 @@ from spack import * class RTarifx(RPackage): """A collection of various utility and convenience functions.""" - homepage = "https://cran.r-project.org/package=taRifx" - url = "https://cran.r-project.org/src/contrib/taRifx_1.0.6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/taRifx" + homepage = "https://cloud.r-project.org/package=taRifx" + url = "https://cloud.r-project.org/src/contrib/taRifx_1.0.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/taRifx" + version('1.0.6.1', sha256='d4c832b26d476a395ddf8349c42613270023c8bbf52a274d280be6284c11d7e2') version('1.0.6', '7e782e04bd69d929b29f91553382e6a2') depends_on('r-reshape2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-taxizedb/package.py b/var/spack/repos/builtin/packages/r-taxizedb/package.py index 384e90f63b..973d75262b 100644 --- a/var/spack/repos/builtin/packages/r-taxizedb/package.py +++ b/var/spack/repos/builtin/packages/r-taxizedb/package.py @@ -9,9 +9,9 @@ from spack import * class RTaxizedb(RPackage): """taxizedb: Tools for Working with 'Taxonomic' Databases""" - homepage = "https://cran.r-project.org/package=taxizedb" - url = "https://cran.r-project.org/src/contrib/taxizedb_0.1.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/taxizedb/" + homepage = "https://cloud.r-project.org/package=taxizedb" + url = "https://cloud.r-project.org/src/contrib/taxizedb_0.1.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/taxizedb/" version('0.1.4', sha256='5a40569a2b5abe56201f112a10220150353412df39b7e8d21ea8698f424cf295') @@ -24,5 +24,3 @@ class RTaxizedb(RPackage): depends_on('r-dbplyr@1.0.0:', type=('build', 'run')) depends_on('r-magrittr@1.5:', type=('build', 'run')) depends_on('r-hoardr@0.1.0:', type=('build', 'run')) - depends_on('r-roxygen2@6.0.1:', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tclust/package.py b/var/spack/repos/builtin/packages/r-tclust/package.py index b2a0f2d5c6..e053432981 100644 --- a/var/spack/repos/builtin/packages/r-tclust/package.py +++ b/var/spack/repos/builtin/packages/r-tclust/package.py @@ -9,18 +9,15 @@ from spack import * class RTclust(RPackage): """Provides functions for robust trimmed clustering.""" - homepage = "https://cran.r-project.org/web/packages/tclust/index.html" - url = "https://cran.r-project.org/src/contrib/tclust_1.3-1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/tclust" + homepage = "https://cloud.r-project.org/package=tclust" + url = "https://cloud.r-project.org/src/contrib/tclust_1.3-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tclust" + version('1.4-1', sha256='4b0be612c8ecd7b4eb19a44ab6ac8f5d40515600ae1144c55989b6b41335ad9e') version('1.3-1', '5415d74682588d4a6fb8ce166fc75661') version('1.2-7', 'e32cd02819682cc944c7baaac3b6f2b7') version('1.2-3', '922abc1abd8da4c6ac9830e1f2f71e84') version('1.1-03', 'f1cc9278bdb068acce4623a9d98b7b62') version('1.1-02', '6f206501b0341fb5623208d145984f5a') - depends_on('r@3.4.0:3.4.9') - depends_on('r-cluster', type=('build', 'run')) - depends_on('r-mclust', type=('build', 'run')) - depends_on('r-mvtnorm', type=('build', 'run')) - depends_on('r-sn', type=('build', 'run')) + depends_on('r@2.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tensora/package.py b/var/spack/repos/builtin/packages/r-tensora/package.py index 6735fbb829..4330b8c965 100644 --- a/var/spack/repos/builtin/packages/r-tensora/package.py +++ b/var/spack/repos/builtin/packages/r-tensora/package.py @@ -11,8 +11,11 @@ class RTensora(RPackage): with tensors and computation with datasets of tensors on a higher level abstraction.""" - homepage = "https://cran.r-project.org/web/packages/tensorA/index.html" - url = "https://cran.r-project.org/src/contrib/tensorA_0.36.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tensorA" + homepage = "https://cloud.r-project.org/package=tensorA" + url = "https://cloud.r-project.org/src/contrib/tensorA_0.36.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tensorA" + version('0.36.1', sha256='c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c') version('0.36', '01c0613491d9b46600bf403d7e3bdd80') + + depends_on('r@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py index f83669a9e8..e4a9ae9db7 100644 --- a/var/spack/repos/builtin/packages/r-testit/package.py +++ b/var/spack/repos/builtin/packages/r-testit/package.py @@ -11,9 +11,11 @@ class RTestit(RPackage): """Provides two convenience functions assert() and test_pkg() to facilitate testing R packages.""" - homepage = "https://cran.r-project.org/package=testit" - url = "https://cran.r-project.org/src/contrib/testit_0.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/testit" + homepage = "https://cloud.r-project.org/package=testit" + url = "https://cloud.r-project.org/src/contrib/testit_0.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/testit" + version('0.9', sha256='9cf6b3df9b2c700e4e7dcbd5b8cb64fabefe674e1f40346ccaf39fe7feda5e55') + version('0.8', sha256='08a9c19c962eae60f4ab58885a23e0bc239efc39da682290be436c066f8d97f7') version('0.7', 'cfc5f5c66aa644fbf53efc4b29d18e8c') version('0.5', 'f206d3cbdc5174e353d2d05ba6a12e59') diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py index 6b7c048950..baf7fced96 100644 --- a/var/spack/repos/builtin/packages/r-testthat/package.py +++ b/var/spack/repos/builtin/packages/r-testthat/package.py @@ -11,13 +11,20 @@ class RTestthat(RPackage): up.""" homepage = "https://github.com/hadley/testthat" - url = "https://cran.r-project.org/src/contrib/testthat_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/testthat" + url = "https://cloud.r-project.org/src/contrib/testthat_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/testthat" + version('2.2.1', sha256='67ee0512bb312695c81fd74338bb8ce9e2e58763681ddbcdfdf35f52dfdb0b78') + version('2.1.0', sha256='cf5fa7108111b32b86e70819352f86b57ab4e835221bb1e83642d52a1fdbcdd4') version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc') + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-digest', type=('build', 'run')) - depends_on('r-crayon', type=('build', 'run')) + depends_on('r-crayon@1.3.4:', type=('build', 'run')) depends_on('r-praise', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) - depends_on('r-r6', type=('build', 'run')) + depends_on('r-r6@2.2.0:', type=('build', 'run')) + depends_on('r-cli', when='@2.0.0:', type=('build', 'run')) + depends_on('r-rlang@0.3.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-withr@2.0.0:', when='@2.0.0:', type=('build', 'run')) + depends_on('r-evaluate', when='@2.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py index 1a305242a0..8631d5d726 100644 --- a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py +++ b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py @@ -16,9 +16,11 @@ class RTfmpvalue(RPackage): Algorithms Mol Biol:2, 15.""" homepage = "https://github.com/ge11232002/TFMPvalue" - url = "https://cran.rstudio.com/src/contrib/TFMPvalue_0.0.6.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/TFMPvalue" + url = "https://cloud.r-project.org/src/contrib/TFMPvalue_0.0.6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/TFMPvalue" + version('0.0.8', sha256='6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841') version('0.0.6', '69fdf4f9b9a0f408a5cee9ce34bea261') + depends_on('r@3.0.1:', type=('build', 'run')) depends_on('r-rcpp@0.11.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-th-data/package.py b/var/spack/repos/builtin/packages/r-th-data/package.py index 7460b5d4ee..593cb7e6ae 100644 --- a/var/spack/repos/builtin/packages/r-th-data/package.py +++ b/var/spack/repos/builtin/packages/r-th-data/package.py @@ -9,12 +9,15 @@ from spack import * class RThData(RPackage): """Contains data sets used in other packages Torsten Hothorn maintains.""" - homepage = "https://cran.r-project.org/package=TH.data" - url = "https://cran.r-project.org/src/contrib/TH.data_1.0-8.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/TH.data" + homepage = "https://cloud.r-project.org/package=TH.data" + url = "https://cloud.r-project.org/src/contrib/TH.data_1.0-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/TH.data" + version('1.0-10', sha256='618a1c67a30536d54b1e48ba3af46a6edcd6c2abef17935b5d4ba526a43aff55') + version('1.0-9', sha256='d8318a172ce2b9f7f284dc297c8a8d5093de8eccbb566c8e7580e70938dfae0f') version('1.0-8', '2cc20acc8b470dff1202749b4bea55c4') version('1.0-7', '3e8b6b1a4699544f175215aed7039a94') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py index c32f33acf9..604bbb9c2a 100644 --- a/var/spack/repos/builtin/packages/r-threejs/package.py +++ b/var/spack/repos/builtin/packages/r-threejs/package.py @@ -11,11 +11,16 @@ class RThreejs(RPackage): 'three.js' visualization library ("http://threejs.org").""" homepage = "http://bwlewis.github.io/rthreejs" - url = "https://cran.r-project.org/src/contrib/threejs_0.2.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/threejs" + url = "https://cloud.r-project.org/src/contrib/threejs_0.2.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/threejs" + + version('0.3.1', sha256='71750b741672a435ecf749b69c72f0681aa8bb795e317f4e3056d5e33f6d79e8') version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b') - depends_on('r-htmlwidgets', type=('build', 'run')) + depends_on('r@3.0.0:', type=('build', 'run')) + depends_on('r-htmlwidgets@0.3.2:', type=('build', 'run')) depends_on('r-base64enc', type=('build', 'run')) - depends_on('r-matrix', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-matrix', when='@0.2.2', type=('build', 'run')) + depends_on('r-jsonlite', when='@0.2.2', type=('build', 'run')) + depends_on('r-igraph@1.0.0:', when='@0.3.1:', type=('build', 'run')) + depends_on('r-crosstalk', when='@0.3.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py index 29b2f614cd..9e2aa5cebb 100644 --- a/var/spack/repos/builtin/packages/r-tibble/package.py +++ b/var/spack/repos/builtin/packages/r-tibble/package.py @@ -11,8 +11,10 @@ class RTibble(RPackage): capabilities than traditional data frames.""" homepage = "https://github.com/tidyverse/tibble" - url = "https://cran.rstudio.com/src/contrib/tibble_1.3.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tibble" + url = "https://cloud.r-project.org/src/contrib/tibble_1.3.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tibble" + + version('2.1.3', sha256='9a8cea9e6b5d24a7e9bf5f67ab38c40b2b6489eddb0d0edb8a48a21ba3574e1a') version('2.0.1', sha256='7ab2cc295eecf00a5310993c99853cd6622ad468e7a60d004b8a73957a713d13') version('2.0.0', sha256='05ad2d62e949909548c4bb8ac596810321f11b330afa9717d0889dc35edd99ba') version('1.4.2', sha256='11670353ff7059a55066dd075d1534d6a27bc5c3583fb9bc291bf750a75c5b17') @@ -21,13 +23,14 @@ class RTibble(RPackage): version('1.2', 'bdbc3d67aa16860741add6d6ec20ea13') version('1.1', '2fe9f806109d0b7fadafb1ffafea4cb8') - depends_on('r@3.1.2:') - - depends_on('r-assertthat', type=('build', 'run')) + depends_on('r@3.1.0:', when='@1.3.0:', type=('build', 'run')) + depends_on('r@3.1.2:', when='@:1.2', type=('build', 'run')) + depends_on('r-assertthat', type=('build', 'run'), when='@:1.3.1') depends_on('r-lazyeval@0.1.10:', type=('build', 'run'), when='@:1.3.0') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-rlang', type=('build', 'run'), when='@1.3.1:') + depends_on('r-rcpp@0.12.3:', type=('build', 'run'), when='@:1.3.4') + depends_on('r-rlang@0.3.0:', type=('build', 'run'), when='@1.3.1:') depends_on('r-cli', type=('build', 'run'), when='@1.4.2:') - depends_on('r-crayon', type=('build', 'run'), when='@1.4.2:') - depends_on('r-pillar', type=('build', 'run'), when='@1.4.2:') - depends_on('r-pkgconfig', type=('build', 'run'), when='@1.4.2:') + depends_on('r-crayon@1.3.4:', type=('build', 'run'), when='@1.4.1:') + depends_on('r-pillar@1.3.1:', type=('build', 'run'), when='@1.4.1:') + depends_on('r-pkgconfig', type=('build', 'run'), when='@2.0.0:') + depends_on('r-fansi@0.4.0:', type=('build', 'run'), when='@2.0.0:') diff --git a/var/spack/repos/builtin/packages/r-tidycensus/package.py b/var/spack/repos/builtin/packages/r-tidycensus/package.py index c6e41da83d..c6c52e3bd1 100644 --- a/var/spack/repos/builtin/packages/r-tidycensus/package.py +++ b/var/spack/repos/builtin/packages/r-tidycensus/package.py @@ -13,21 +13,23 @@ class RTidycensus(RPackage): data frames, and optionally returns a list-column with feature geometry for many geographies.""" - homepage = "https://cran.r-project.org/package=tidycensus" - url = "https://cran.rstudio.com/src/contrib/tidycensus_0.3.1.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/tidycensus" + homepage = "https://cloud.r-project.org/package=tidycensus" + url = "https://cloud.r-project.org/src/contrib/tidycensus_0.3.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tidycensus" + version('0.9.2', sha256='2454525301caff9eaaf6ebe14f58706ece1fbace6187ce8bf3fff04c842b9536') version('0.3.1', '420d046b5a408d321e775c3d410e7699') + depends_on('r@3.3.0:', type=('build', 'run')) depends_on('r-httr', type=('build', 'run')) depends_on('r-sf', type=('build', 'run')) - depends_on('r-dplyr', type=('build', 'run')) + depends_on('r-dplyr@0.7.0:', type=('build', 'run')) depends_on('r-tigris', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) - depends_on('r-jsonlite', type=('build', 'run')) + depends_on('r-jsonlite@1.5.0:', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) depends_on('r-rvest', type=('build', 'run')) - depends_on('r-tidyr', type=('build', 'run')) + depends_on('r-tidyr@0.7.0:', type=('build', 'run')) depends_on('r-rappdirs', type=('build', 'run')) depends_on('r-readr', type=('build', 'run')) depends_on('r-xml2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py index e3a5ac05e5..456a6b7931 100644 --- a/var/spack/repos/builtin/packages/r-tidyr/package.py +++ b/var/spack/repos/builtin/packages/r-tidyr/package.py @@ -12,12 +12,15 @@ class RTidyr(RPackage): pipelines.""" homepage = "https://github.com/hadley/tidyr" - url = "https://cran.r-project.org/src/contrib/tidyr_0.7.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tidyr" + url = "https://cloud.r-project.org/src/contrib/tidyr_0.7.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tidyr" + version('0.8.3', sha256='a18f54ec35124110058ab23f7e0a3c037a8d50f0405520cf5cc5443ec022cc37') + version('0.8.2', sha256='99a508d0539390364789c5f4835b36c4a383927f0ec1648e2a4636c1cc6e490f') version('0.7.2', '42d723bf04c5c1c59e27a8be14f3a6b6') version('0.5.1', '3cadc869510c054ed93d374ab44120bd') + depends_on('r@3.1:', type=('build', 'run')) depends_on('r-tibble', type=('build', 'run')) depends_on('r-dplyr@0.7.0:', type=('build', 'run')) depends_on('r-stringi', type=('build', 'run')) @@ -25,5 +28,5 @@ class RTidyr(RPackage): depends_on('r-glue', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) - depends_on('r-tidyselect', type=('build', 'run')) + depends_on('r-tidyselect@0.2.5:', type=('build', 'run')) depends_on('r-rlang', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyselect/package.py b/var/spack/repos/builtin/packages/r-tidyselect/package.py index fbcad34264..89eba20d6d 100644 --- a/var/spack/repos/builtin/packages/r-tidyselect/package.py +++ b/var/spack/repos/builtin/packages/r-tidyselect/package.py @@ -11,13 +11,16 @@ class RTidyselect(RPackage): easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.""" - homepage = "https://cran.r-project.org/package=tidyselect" - url = "https://cran.r-project.org/src/contrib/tidyselect_0.2.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tidyselect" + homepage = "https://cloud.r-project.org/package=tidyselect" + url = "https://cloud.r-project.org/src/contrib/tidyselect_0.2.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tidyselect" + version('0.2.5', sha256='5ce2e86230fa35cfc09aa71dcdd6e05e1554a5739c863ca354d241bfccb86c74') + version('0.2.4', sha256='5cb30e56ad5c1ac59786969edc8d542a7a1735a129a474f585a141aefe6a2295') version('0.2.3', 'c9dbd895ad7ce209bacfad6d19de91c9') - depends_on('r-glue', type=('build', 'run')) + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-glue@1.3.0:', type=('build', 'run')) depends_on('r-purrr', type=('build', 'run')) - depends_on('r-rlang@0.1:', type=('build', 'run')) + depends_on('r-rlang@0.2.2:', type=('build', 'run')) depends_on('r-rcpp@0.12.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tidyverse/package.py b/var/spack/repos/builtin/packages/r-tidyverse/package.py index 1f8abb3d6f..83027d7ff2 100644 --- a/var/spack/repos/builtin/packages/r-tidyverse/package.py +++ b/var/spack/repos/builtin/packages/r-tidyverse/package.py @@ -13,8 +13,8 @@ class RTidyverse(RPackage): packages in a single step.""" homepage = "http://tidyverse.tidyverse.org/" - url = "https://cran.r-project.org/src/contrib/tidyverse_1.2.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tidyverse" + url = "https://cloud.r-project.org/src/contrib/tidyverse_1.2.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tidyverse" version('1.2.1', '7e2ca0b72ab668342c02fd0f52c082e1') @@ -43,4 +43,3 @@ class RTidyverse(RPackage): depends_on('r-tibble@1.3.4:', type=('build', 'run')) depends_on('r-tidyr@0.7.2:', type=('build', 'run')) depends_on('r-xml2@1.1.1:', type=('build', 'run')) - depends_on('r-rlang@0.1.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tiff/package.py b/var/spack/repos/builtin/packages/r-tiff/package.py index 596d058754..b74693ac46 100644 --- a/var/spack/repos/builtin/packages/r-tiff/package.py +++ b/var/spack/repos/builtin/packages/r-tiff/package.py @@ -12,10 +12,11 @@ class RTiff(RPackage): write both files and in-memory raw vectors.""" homepage = "http://www.rforge.net/tiff/" - url = "https://cran.rstudio.com/src/contrib/tiff_0.1-5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tiff" + url = "https://cloud.r-project.org/src/contrib/tiff_0.1-5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tiff" version('0.1-5', '5052990b8647c77d3e27bc0ecf064e0b') + depends_on('r@2.9.0:', type=('build', 'run')) depends_on("jpeg") depends_on("libtiff") diff --git a/var/spack/repos/builtin/packages/r-tigris/package.py b/var/spack/repos/builtin/packages/r-tigris/package.py index 93ace4a3ee..19c1cef79a 100644 --- a/var/spack/repos/builtin/packages/r-tigris/package.py +++ b/var/spack/repos/builtin/packages/r-tigris/package.py @@ -10,16 +10,19 @@ class RTigris(RPackage): """Download TIGER/Line shapefiles from the United States Census Bureau and load into R as 'SpatialDataFrame' or 'sf' objects.""" - homepage = "https://cran.r-project.org/package=tigris" - url = "https://cran.rstudio.com/src/contrib/tigris_0.5.3.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/tigris" + homepage = "https://cloud.r-project.org/package=tigris" + url = "https://cloud.r-project.org/src/contrib/tigris_0.5.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tigris" + version('0.8.2', sha256='ed8d6ab25332c2cc800858d58324bd8264772d8a916a3f0a8d489250a7e7140e') version('0.5.3', 'c11cb459bf134d3deb1a641a60c86413') + depends_on('r@3.0.0:', when='@:0.5.3', type=('build', 'run')) + depends_on('r@3.3.0:', when='@0.6.1:', type=('build', 'run')) depends_on('r-stringr', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-rgdal', type=('build', 'run')) - depends_on('r-rgeos', type=('build', 'run')) + depends_on('r-rgeos', when='@:0.5.3', type=('build', 'run')) depends_on('r-sp', type=('build', 'run')) depends_on('r-rappdirs', type=('build', 'run')) depends_on('r-maptools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-timedate/package.py b/var/spack/repos/builtin/packages/r-timedate/package.py index ab31d415b0..2025d4af64 100644 --- a/var/spack/repos/builtin/packages/r-timedate/package.py +++ b/var/spack/repos/builtin/packages/r-timedate/package.py @@ -10,8 +10,12 @@ class RTimedate(RPackage): """Environment for teaching "Financial Engineering and Computational Finance". Managing chronological and calendar objects.""" - homepage = "https://cran.r-project.org/package=timeDate" - url = "https://cran.r-project.org/src/contrib/timeDate_3012.100.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/timeDate" + homepage = "https://cloud.r-project.org/package=timeDate" + url = "https://cloud.r-project.org/src/contrib/timeDate_3012.100.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/timeDate" + version('3043.102', sha256='377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473') + version('3042.101', sha256='6c8d4c7689b31c6a43555d9c7258516556ba03b132e5643691e3e317b89a8c6d') version('3012.100', '9f69d3724efbf0e125e6b8e6d3475fe4') + + depends_on('r@2.15.1:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tinytex/package.py b/var/spack/repos/builtin/packages/r-tinytex/package.py new file mode 100644 index 0000000000..e8384c0285 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-tinytex/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RTinytex(RPackage): + """Helper functions to install and maintain the 'LaTeX' distribution named + 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform, + portable, and easy-to-maintain version of 'TeX Live'. This package also + contains helper functions to compile 'LaTeX' documents, and install missing + 'LaTeX' packages automatically.""" + + homepage = "https://github.com/yihui/tinytex" + url = "https://cloud.r-project.org/src/contrib/tinytex_0.15.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tinytex" + + version('0.15', sha256='5d0988d3b7f763dfa65c722f177452a21344e428415a4b31aeb51478f0abad90') + + depends_on('r-xfun@0.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-triebeard/package.py b/var/spack/repos/builtin/packages/r-triebeard/package.py index f2d04924da..a3521c9c1b 100644 --- a/var/spack/repos/builtin/packages/r-triebeard/package.py +++ b/var/spack/repos/builtin/packages/r-triebeard/package.py @@ -10,8 +10,8 @@ class RTriebeard(RPackage): """triebeard: 'Radix' Trees in 'Rcpp'""" homepage = "https://github.com/Ironholds/triebeard/" - url = "https://cran.r-project.org/src/contrib/triebeard_0.3.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/triebeard" + url = "https://cloud.r-project.org/src/contrib/triebeard_0.3.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/triebeard" version('0.3.0', sha256='bf1dd6209cea1aab24e21a85375ca473ad11c2eff400d65c6202c0fb4ef91ec3') diff --git a/var/spack/repos/builtin/packages/r-trimcluster/package.py b/var/spack/repos/builtin/packages/r-trimcluster/package.py index d918d31439..df73e3bf94 100644 --- a/var/spack/repos/builtin/packages/r-trimcluster/package.py +++ b/var/spack/repos/builtin/packages/r-trimcluster/package.py @@ -10,9 +10,10 @@ class RTrimcluster(RPackage): """trimcluster: Cluster analysis with trimming""" homepage = "http://www.homepages.ucl.ac.uk/~ucakche" - url = "https://cran.r-project.org/src/contrib/trimcluster_0.1-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/trimcluster" + url = "https://cloud.r-project.org/src/contrib/trimcluster_0.1-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/trimcluster" + version('0.1-2.1', sha256='b64a872a6c2ad677dfeecc776c9fe5aff3e8bab6bc6a8c86957b5683fd5d2300') version('0.1-2', '7617920e224bd18f5b87db38a3116ec2') - depends_on('r@1.9.0:') + depends_on('r@1.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-truncnorm/package.py b/var/spack/repos/builtin/packages/r-truncnorm/package.py index 28929fa103..19d76beb06 100644 --- a/var/spack/repos/builtin/packages/r-truncnorm/package.py +++ b/var/spack/repos/builtin/packages/r-truncnorm/package.py @@ -10,8 +10,10 @@ class RTruncnorm(RPackage): """Density, probability, quantile and random number generation functions for the truncated normal distribution.""" - homepage = "https://cran.r-project.org/package=truncnorm" - url = "https://cran.rstudio.com/src/contrib/truncnorm_1.0-8.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/truncnorm" + homepage = "https://cloud.r-project.org/package=truncnorm" + url = "https://cloud.r-project.org/src/contrib/truncnorm_1.0-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/truncnorm" version('1.0-8', 'c60cd6555be0dd2ea91e61757439282d') + + depends_on('r@3.4.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-trust/package.py b/var/spack/repos/builtin/packages/r-trust/package.py index 2964eb6b7e..221be990b5 100644 --- a/var/spack/repos/builtin/packages/r-trust/package.py +++ b/var/spack/repos/builtin/packages/r-trust/package.py @@ -11,7 +11,9 @@ class RTrust(RPackage): Guaranteed to converge to local minimum of objective function.""" homepage = "http://www.stat.umn.edu/geyer/trust" - url = "https://cran.r-project.org/src/contrib/trust_0.1-7.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/trust" + url = "https://cloud.r-project.org/src/contrib/trust_0.1-7.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/trust" version('0.1-7', '7e218b3a6b33bd77bd7e86dc6360418d') + + depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tseries/package.py b/var/spack/repos/builtin/packages/r-tseries/package.py index 3055430340..e55c8c3b1a 100644 --- a/var/spack/repos/builtin/packages/r-tseries/package.py +++ b/var/spack/repos/builtin/packages/r-tseries/package.py @@ -9,12 +9,15 @@ from spack import * class RTseries(RPackage): """Time series analysis and computational finance.""" - homepage = "https://cran.r-project.org/package=tseries" - url = "https://cran.r-project.org/src/contrib/tseries_0.10-42.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/tseries" + homepage = "https://cloud.r-project.org/package=tseries" + url = "https://cloud.r-project.org/src/contrib/tseries_0.10-42.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tseries" + version('0.10-47', sha256='202377df56806fe611c2e12c4d9732c71b71220726e2defa7e568d2b5b62fb7b') + version('0.10-46', sha256='12940afd1d466401160e46f993ed4baf28a42cef98d3757b66ee15e916e07222') version('0.10-42', '3feaa5c463bc967d749323163d9bc836') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('r-quadprog', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) - depends_on('r-quantmod', type=('build', 'run')) + depends_on('r-quantmod@0.4-9:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-tsne/package.py b/var/spack/repos/builtin/packages/r-tsne/package.py index 11247374a9..a65ae8cfa2 100644 --- a/var/spack/repos/builtin/packages/r-tsne/package.py +++ b/var/spack/repos/builtin/packages/r-tsne/package.py @@ -9,12 +9,10 @@ from spack import * class RTsne(RPackage): """A "pure R" implementation of the t-SNE algorithm.""" - homepage = "https://cran.r-project.org/web/packages/tsne/index.html" - url = "https://cran.r-project.org/src/contrib/tsne_0.1-3.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/tnse" + homepage = "https://cloud.r-project.org/package=tsne" + url = "https://cloud.r-project.org/src/contrib/tsne_0.1-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/tnse" version('0.1-3', '00974d4b3fd5f1100d0ebd24e03b0af9') version('0.1-2', 'd96d8dce6ffeda68e2b25ec1ff52ea61') version('0.1-1', '8197e5c61dec916b7a31b74e658b632d') - - depends_on('r@3.4.0:3.4.9') diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py index 8e81f13825..08583bb6db 100644 --- a/var/spack/repos/builtin/packages/r-ttr/package.py +++ b/var/spack/repos/builtin/packages/r-ttr/package.py @@ -10,10 +10,13 @@ class RTtr(RPackage): """Functions and data to construct technical trading rules with R.""" homepage = "https://github.com/joshuaulrich/TTR" - url = "https://cran.r-project.org/src/contrib/TTR_0.23-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/TTR" + url = "https://cloud.r-project.org/src/contrib/TTR_0.23-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/TTR" + version('0.23-4', sha256='eb17604da986213b3b924f0af65c3d089502a658a253ee34f6b8f6caccf6bfa2') + version('0.23-3', sha256='2136032c7a2cd2a82518a4412fc655ecb16597b123dbdebe5684caef9f15261f') version('0.23-1', '35f693ac0d97e8ec742ebea2da222986') - depends_on('r-xts', type=('build', 'run')) + depends_on('r-xts@0.10-0:', type=('build', 'run')) depends_on('r-zoo', type=('build', 'run')) + depends_on('r-curl', when='@0.23-4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-ucminf/package.py b/var/spack/repos/builtin/packages/r-ucminf/package.py new file mode 100644 index 0000000000..a0ddaaa7b1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ucminf/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RUcminf(RPackage): + """An algorithm for general-purpose unconstrained non-linear optimization. + The algorithm is of quasi-Newton type with BFGS updating of the inverse + Hessian and soft line search with a trust region type monitoring of the + input to the line search algorithm. The interface of 'ucminf' is designed + for easy interchange with 'optim'.""" + + homepage = "https://cloud.r-project.org/package=ucminf" + url = "https://cloud.r-project.org/src/contrib/ucminf_1.1-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/ucminf" + + version('1.1-4', sha256='a2eb382f9b24e949d982e311578518710f8242070b3aa3314a331c1e1e7f6f07') diff --git a/var/spack/repos/builtin/packages/r-udunits2/package.py b/var/spack/repos/builtin/packages/r-udunits2/package.py index b72b7224ab..0adfcef4b3 100644 --- a/var/spack/repos/builtin/packages/r-udunits2/package.py +++ b/var/spack/repos/builtin/packages/r-udunits2/package.py @@ -10,9 +10,10 @@ class RUdunits2(RPackage): """Provides simple bindings to Unidata's udunits library.""" homepage = "https://github.com/pacificclimate/Rudunits2" - url = "https://cran.r-project.org/src/contrib/udunits2_0.13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/udunits2" + url = "https://cloud.r-project.org/src/contrib/udunits2_0.13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/udunits2" version('0.13', 'c8717808c740ef70eed7aea93c7c4c7d') + depends_on('r@2.10.0:', type=('build', 'run')) depends_on('udunits2') diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py index 0dcf8c35d9..49ae88dcba 100644 --- a/var/spack/repos/builtin/packages/r-units/package.py +++ b/var/spack/repos/builtin/packages/r-units/package.py @@ -15,9 +15,14 @@ class RUnits(RPackage): conversion.""" homepage = "https://github.com/edzer/units/" - url = "https://cran.r-project.org/src/contrib/units_0.4-6.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/units" + url = "https://cloud.r-project.org/src/contrib/units_0.4-6.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/units" + version('0.6-3', sha256='03de88d9dcfe80d22dd3813413f33657c576aed24a8091dbfc7f68602020a64f') + version('0.6-2', sha256='5e286775d0712c8e15b6ae3a533d4c4349b0f6410c2d9d897ca519c3d0e5f170') version('0.4-6', '0bb90dde5dad7608fa6feb1599381bf2') - depends_on('r-udunits2', type=('build', 'run')) + depends_on('r@3.0.2:', type=('build', 'run')) + depends_on('r-udunits2@0.13:', when='@:0.5-1', type=('build', 'run')) + depends_on('r-rcpp@0.12.10:', type=('build', 'run')) + depends_on('udunits2', when='@0.6-0:') diff --git a/var/spack/repos/builtin/packages/r-urca/package.py b/var/spack/repos/builtin/packages/r-urca/package.py new file mode 100644 index 0000000000..1dc5753a43 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-urca/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RUrca(RPackage): + """Unit root and cointegration tests encountered in applied econometric + analysis are implemented.""" + + homepage = "https://cloud.r-project.org/package=urca" + url = "https://cloud.r-project.org/src/contrib/urca_1.3-0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/urca" + + version('1.3-0', sha256='621cc82398e25b58b4a16edf000ed0a1484d9a0bc458f734e97b6f371cc76aaa') + + depends_on('r@2.0.0:', type=('build', 'run')) + depends_on('r-nlme', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-urltools/package.py b/var/spack/repos/builtin/packages/r-urltools/package.py index 6c1b78deb2..5187a31288 100644 --- a/var/spack/repos/builtin/packages/r-urltools/package.py +++ b/var/spack/repos/builtin/packages/r-urltools/package.py @@ -10,8 +10,8 @@ class RUrltools(RPackage): """urltools: Vectorised Tools for URL Handling and Parsing""" homepage = "https://github.com/Ironholds/urltools/" - url = "https://cran.r-project.org/src/contrib/urltools_1.7.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/urltools" + url = "https://cloud.r-project.org/src/contrib/urltools_1.7.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/urltools" version('1.7.3', sha256='6020355c1b16a9e3956674e5dea9ac5c035c8eb3eb6bbdd841a2b5528cafa313') diff --git a/var/spack/repos/builtin/packages/r-usethis/package.py b/var/spack/repos/builtin/packages/r-usethis/package.py new file mode 100644 index 0000000000..4f7cfc743c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-usethis/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RUsethis(RPackage): + """Automate package and project setup tasks that are otherwise performed + manually. This includes setting up unit testing, test coverage, continuous + integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and + more.""" + + homepage = "https://usethis.r-lib.org/" + url = "https://cloud.r-project.org/src/contrib/usethis_1.5.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/usethis" + + version('1.5.1', sha256='9e3920a04b0df82adf59eef2c1b2b4d835c4a757a51b3c163b8fc619172f561d') + + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-clipr@0.3.0:', type=('build', 'run')) + depends_on('r-clisymbols', type=('build', 'run')) + depends_on('r-crayon', type=('build', 'run')) + depends_on('r-curl@2.7:', type=('build', 'run')) + depends_on('r-desc', type=('build', 'run')) + depends_on('r-fs@1.3.0:', type=('build', 'run')) + depends_on('r-gh', type=('build', 'run')) + depends_on('r-git2r@0.23:', type=('build', 'run')) + depends_on('r-glue@1.3.0:', type=('build', 'run')) + depends_on('r-purrr', type=('build', 'run')) + depends_on('r-rlang', type=('build', 'run')) + depends_on('r-rprojroot@1.2:', type=('build', 'run')) + depends_on('r-rstudioapi', type=('build', 'run')) + depends_on('r-whisker', type=('build', 'run')) + depends_on('r-withr', type=('build', 'run')) + depends_on('r-yaml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-utf8/package.py b/var/spack/repos/builtin/packages/r-utf8/package.py index 2e40f83bfa..8a00a26db6 100644 --- a/var/spack/repos/builtin/packages/r-utf8/package.py +++ b/var/spack/repos/builtin/packages/r-utf8/package.py @@ -10,12 +10,15 @@ class RUtf8(RPackage): """Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.""" - homepage = "https://cran.r-project.org/package=utf8" - url = "https://cran.r-project.org/src/contrib/utf8_1.1.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/utf8" + homepage = "https://cloud.r-project.org/package=utf8" + url = "https://cloud.r-project.org/src/contrib/utf8_1.1.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/utf8" + version('1.1.4', sha256='f6da9cadfc683057d45f54b43312a359cf96ec2731c0dda18a8eae31d1e31e54') version('1.1.3', sha256='43b394c3274ba0f66719d28dc4a7babeb87187e766de8d8ca716e0548091440f') version('1.1.2', sha256='148517aadb75d82aba61f63afe2a30d254abebbdc7e32dd0830e12ff443915b9') version('1.1.1', sha256='0e30c824e43cdc0a3339f4688e3271737d02ea10768a46137e0e41936051cb3d') version('1.1.0', sha256='6a8ae2c452859800c3ef12993a55892588fc35df8fa1360f3d182ed97244dc4f') version('1.0.0', sha256='7562a80262cbc2017eee76c0d3c9575f240fab291f868a11724fa04a116efb80') + + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-utils/package.py b/var/spack/repos/builtin/packages/r-utils/package.py deleted file mode 100644 index 45caeafb93..0000000000 --- a/var/spack/repos/builtin/packages/r-utils/package.py +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class RUtils(RPackage): - """Utility functions useful when programming and - developing R packages.""" - - homepage = "https://github.com/HenrikBengtsson/R.utils" - url = "https://cran.rstudio.com/src/contrib/R.utils_2.5.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/R.utils" - - version('2.5.0', 'a728ef3ceb35cafc4c39ea577cecc38b') - - depends_on('r-oo', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py index d161948c05..d68b08fc99 100644 --- a/var/spack/repos/builtin/packages/r-uuid/package.py +++ b/var/spack/repos/builtin/packages/r-uuid/package.py @@ -12,6 +12,9 @@ class RUuid(RPackage): Identifiers).""" homepage = "http://www.rforge.net/uuid" - url = "https://cran.rstudio.com/src/contrib/uuid_0.1-2.tar.gz" + url = "https://cloud.r-project.org/src/contrib/uuid_0.1-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/uuid" version('0.1-2', 'f97d000c0b16bca455fb5bf2cd668ddf') + + depends_on('r@2.9.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-uwot/package.py b/var/spack/repos/builtin/packages/r-uwot/package.py new file mode 100644 index 0000000000..092288646d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-uwot/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RUwot(RPackage): + """An implementation of the Uniform Manifold Approximation and Projection + dimensionality reduction by McInnes et al. (2018) <arXiv:1802.03426>. It + also provides means to transform new data and to carry out supervised + dimensionality reduction. An implementation of the related LargeVis method + of Tang et al. (2016) <arXiv:1602.00370> is also provided. This is a + complete re-implementation in R (and C++, via the 'Rcpp' package): no + Python installation is required. See the uwot website + (<https://github.com/jlmelville/uwot>) for more documentation and + examples.""" + + homepage = "https://github.com/jlmelville/uwot" + url = "https://cloud.r-project.org/src/contrib/uwot_0.1.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/uwot" + + version('0.1.3', sha256='4936e6922444cae8a71735e945b6bb0828a1012232eb94568054f78451c406d7') + + depends_on('r-matrix', type=('build', 'run')) + depends_on('r-rcpp', type=('build', 'run')) + depends_on('r-fnn', type=('build', 'run')) + depends_on('r-rspectra', type=('build', 'run')) + depends_on('r-rcppannoy@0.0.11:', type=('build', 'run')) + depends_on('r-rcppparallel', type=('build', 'run')) + depends_on('r-irlba', type=('build', 'run')) + depends_on('r-rcppprogress', type=('build', 'run')) + depends_on('r-dqrng', type=('build', 'run')) + depends_on('gmake', type='build') diff --git a/var/spack/repos/builtin/packages/r-varselrf/package.py b/var/spack/repos/builtin/packages/r-varselrf/package.py index b187f4a542..03fedb632a 100644 --- a/var/spack/repos/builtin/packages/r-varselrf/package.py +++ b/var/spack/repos/builtin/packages/r-varselrf/package.py @@ -15,8 +15,10 @@ class RVarselrf(RPackage): and other genomics and proteomics applications).""" homepage = "http://ligarto.org/rdiaz/Software/Software.html" - url = "https://cran.rstudio.com/src/contrib/varSelRF_0.7-8.tar.gz" + url = "https://cloud.r-project.org/src/contrib/varSelRF_0.7-8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/varSelRF" version('0.7-8', '103c460d0734bd38ae13496c839d3435') + depends_on('r@2.0.0:', type=('build', 'run')) depends_on('r-randomforest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py index 6980e5459a..f342ec5770 100644 --- a/var/spack/repos/builtin/packages/r-vcd/package.py +++ b/var/spack/repos/builtin/packages/r-vcd/package.py @@ -14,12 +14,15 @@ class RVcd(RPackage): the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).""" - homepage = "https://cran.r-project.org/package=vcd" - url = "https://cran.r-project.org/src/contrib/vcd_1.4-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/vcd" + homepage = "https://cloud.r-project.org/package=vcd" + url = "https://cloud.r-project.org/src/contrib/vcd_1.4-1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/vcd" + version('1.4-4', sha256='a561adf120b5ce41b66e0c0c321542fcddc772eb12b3d7020d86e9cd014ce9d2') + version('1.4-3', sha256='17ce89927421d9cd01285b6093eeaaecb1e7252388007f66d3b9222e58cc5f15') version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02') + depends_on('r@2.4.0:', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) depends_on('r-lmtest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vctrs/package.py b/var/spack/repos/builtin/packages/r-vctrs/package.py new file mode 100644 index 0000000000..0dc05227c5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-vctrs/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RVctrs(RPackage): + """Defines new notions of prototype and size that are used to provide tools + for consistent and well-founded type-coercion and size-recycling, and are + in turn connected to ideas of type- and size-stability useful for analyzing + function interfaces.""" + + homepage = "https://github.com/r-lib/vctrs" + url = "https://cloud.r-project.org/src/contrib/vctrs_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/vctrs" + + version('0.2.0', sha256='5bce8f228182ecaa51230d00ad8a018de9cf2579703e82244e0931fe31f20016') + + depends_on('r@3.2:', type=('build', 'run')) + depends_on('r-backports', type=('build', 'run')) + depends_on('r-ellipsis@0.2.0:', type=('build', 'run')) + depends_on('r-digest', type=('build', 'run')) + depends_on('r-glue', type=('build', 'run')) + depends_on('r-rlang@0.4.0:', type=('build', 'run')) + depends_on('r-zeallot', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vegan/package.py b/var/spack/repos/builtin/packages/r-vegan/package.py index 1410129e62..2248bfd9e1 100644 --- a/var/spack/repos/builtin/packages/r-vegan/package.py +++ b/var/spack/repos/builtin/packages/r-vegan/package.py @@ -11,10 +11,19 @@ class RVegan(RPackage): community and vegetation ecologists.""" homepage = "https://github.com/vegandevs/vegan" - url = "https://cran.r-project.org/src/contrib/vegan_2.4-3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/vegan" + url = "https://cloud.r-project.org/src/contrib/vegan_2.4-3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/vegan" + version('2.5-5', sha256='876b5266f29f3034fed881020d16f476e62d145a00cb450a1a213e019e056971') + version('2.5-4', sha256='5116a440111fca49b5f95cfe888b180ff29a112e6301d5e2ac5cae0e628493e0') version('2.4-3', 'db17d4c4b9a4d421246abd5b36b00fec') - depends_on('r@3.0:') + depends_on('r@3.0.0:', when='@:2.4-6', type=('build', 'run')) + depends_on('r@3.1.0:', when='@2.5-1', type=('build', 'run')) + depends_on('r@3.2.0:', when='@2.5-2:2.5-4', type=('build', 'run')) + depends_on('r@3.4.0:', when='@2.5-5:', type=('build', 'run')) depends_on('r-permute@0.9-0:', type=('build', 'run')) + depends_on('r-lattice', type=('build', 'run')) + depends_on('r-mass', type=('build', 'run')) + depends_on('r-cluster', type=('build', 'run')) + depends_on('r-mgcv', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vfs/package.py b/var/spack/repos/builtin/packages/r-vfs/package.py index 0e5d8c0a72..d6c52c2c50 100644 --- a/var/spack/repos/builtin/packages/r-vfs/package.py +++ b/var/spack/repos/builtin/packages/r-vfs/package.py @@ -9,15 +9,12 @@ from spack import * class RVfs(RPackage): """VFS: Vegetated Filter Strip and Erosion Model""" - homepage = "https://cran.r-project.org/package=VFS" - url = "https://cran.r-project.org/src/contrib/VFS_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/VFS" + homepage = "https://cloud.r-project.org/package=VFS" + url = "https://cloud.r-project.org/src/contrib/VFS_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/VFS" version('1.0.2', sha256='8ff7e7e13919ff21f10c7c693ef596a2c7b57c7ca37d79278e443ed122a21aad') depends_on('r@3.4.0:', type=('build', 'run')) depends_on('r-e1071', type=('build', 'run')) depends_on('r-nleqslv@3.3.0:', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) - depends_on('r-rmarkdown', type=('build', 'run')) - depends_on('r-testthat', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vgam/package.py b/var/spack/repos/builtin/packages/r-vgam/package.py index 236de33f3a..3039bbbd6c 100644 --- a/var/spack/repos/builtin/packages/r-vgam/package.py +++ b/var/spack/repos/builtin/packages/r-vgam/package.py @@ -10,16 +10,18 @@ class RVgam(RPackage): """An implementation of about 6 major classes of statistical regression models.""" - homepage = "https://cran.r-project.org/web/packages/VGAM/index.html" - url = "https://cran.r-project.org/src/contrib/VGAM_1.0-4.tar.gz" - list_url = "https://cran.rstudio.com/src/contrib/Archive/VGAM" + homepage = "https://cloud.r-project.org/package=VGAM" + url = "https://cloud.r-project.org/src/contrib/VGAM_1.0-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/VGAM" + version('1.1-1', sha256='de192bd65a7e8818728008de8e60e6dd3b61a13616c887a43e0ccc8147c7da52') + version('1.0-6', sha256='121820a167411e847b41bdcb0028b55842d0ccc0c3471755c67449837e0fe3b9') version('1.0-4', '9d30736842db6d9dcec83df49f11d3c1') version('1.0-3', 'a158cd0a6ff956b4bf21d610df361b18') version('1.0-2', '813b303d5d956914cf8910db3fa1ba14') version('1.0-1', '778182585c774036ac3d10240cf63b40') version('1.0-0', '81da7b3a797b5e26b9e859dc2f373b7b') - depends_on('r@3.4.0:3.4.9') - depends_on('r-mass', type=('build', 'run')) - depends_on('r-mgcv', type=('build', 'run')) + depends_on('r@3.0.0:', when='@:1.0-1', type=('build', 'run')) + depends_on('r@3.1.0:', when='@1.0-2:1.0-3', type=('build', 'run')) + depends_on('r@3.4.0:', when='@1.0-4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-vipor/package.py b/var/spack/repos/builtin/packages/r-vipor/package.py index 354305221f..e4deb92f86 100644 --- a/var/spack/repos/builtin/packages/r-vipor/package.py +++ b/var/spack/repos/builtin/packages/r-vipor/package.py @@ -9,9 +9,9 @@ from spack import * class RVipor(RPackage): """Plot Categorical Data Using Quasirandom Noise and Density Estimates""" - homepage = "https://cran.r-project.org/package=vipor" - url = "https://cran.r-project.org/src/contrib/vipor_0.4.5.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/vipor" + homepage = "https://cloud.r-project.org/package=vipor" + url = "https://cloud.r-project.org/src/contrib/vipor_0.4.5.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/vipor" version('0.4.5', 'd08bc95b3aaf1574bf41b7eb41b67ce4') version('0.4.4', '834212e3971787809ba9737744d54dee') diff --git a/var/spack/repos/builtin/packages/r-viridis/package.py b/var/spack/repos/builtin/packages/r-viridis/package.py index 5492e1451c..82f5578b1a 100644 --- a/var/spack/repos/builtin/packages/r-viridis/package.py +++ b/var/spack/repos/builtin/packages/r-viridis/package.py @@ -10,12 +10,14 @@ class RViridis(RPackage): """viridis: Default Color Maps from 'matplotlib'""" homepage = "https://github.com/sjmgarnier/viridis" - url = "https://cran.r-project.org/src/contrib/viridis_0.4.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/viridis" + url = "https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/viridis" + version('0.5.1', sha256='ddf267515838c6eb092938133035cee62ab6a78760413bfc28b8256165701918') + version('0.5.0', sha256='fea477172c1e11be40554545260b36d6ddff3fe6bc3bbed87813ffb77c5546cd') version('0.4.0', 'f874384cbedf459f6c309ddb40b354ea') - depends_on('r@2.1.0:') - depends_on('r-viridislite@0.2.0:', type=('build', 'run')) + depends_on('r@2.10:', type=('build', 'run')) + depends_on('r-viridislite@0.3.0:', type=('build', 'run')) depends_on('r-ggplot2@1.0.1:', type=('build', 'run')) depends_on('r-gridextra', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-viridislite/package.py b/var/spack/repos/builtin/packages/r-viridislite/package.py index 8b73a9f6c0..5ff479d2f4 100644 --- a/var/spack/repos/builtin/packages/r-viridislite/package.py +++ b/var/spack/repos/builtin/packages/r-viridislite/package.py @@ -10,9 +10,10 @@ class RViridislite(RPackage): """viridisLite: Default Color Maps from 'matplotlib' (Lite Version)""" homepage = "https://github.com/sjmgarnier/viridisLite" - url = "https://cran.r-project.org/src/contrib/viridisLite_0.2.0.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/viridisLite" + url = "https://cloud.r-project.org/src/contrib/viridisLite_0.2.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/viridisLite" + version('0.3.0', sha256='780ea12e7c4024d5ba9029f3a107321c74b8d6d9165262f6e64b79e00aa0c2af') version('0.2.0', '04a04415cf651a2b5f964b261896c0fb') - depends_on('r@2.1.0:') + depends_on('r@2.10:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py index 80e254de0c..bbf78d7372 100644 --- a/var/spack/repos/builtin/packages/r-visnetwork/package.py +++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py @@ -11,11 +11,14 @@ class RVisnetwork(RPackage): allows an interactive visualization of networks.""" homepage = "https://github.com/datastorm-open/visNetwork" - url = "https://cran.r-project.org/src/contrib/visNetwork_1.0.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/visNetwork" + url = "https://cloud.r-project.org/src/contrib/visNetwork_1.0.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/visNetwork" + version('2.0.7', sha256='15ad01636a3a19e1901be6743052805a5b6a9ac1240fb3dab765252b1e865128') + version('2.0.6', sha256='ec2478e6a2af446569ef2d5210a2bc6b2600bcb7fd9908cef8f8c80b01e9c8aa') version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7') + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-htmlwidgets', type=('build', 'run')) depends_on('r-htmltools', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-webshot/package.py b/var/spack/repos/builtin/packages/r-webshot/package.py index 5821e2949c..987dd60c2c 100644 --- a/var/spack/repos/builtin/packages/r-webshot/package.py +++ b/var/spack/repos/builtin/packages/r-webshot/package.py @@ -10,11 +10,12 @@ class RWebshot(RPackage): """webshot: Take Screenshots of Web Pages""" homepage = "https://github.com/wch/webshot/" - url = "https://cran.r-project.org/src/contrib/webshot_0.5.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/webshot/" + url = "https://cloud.r-project.org/src/contrib/webshot_0.5.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/webshot/" version('0.5.1', sha256='b9750d206c6fa0f1f16cc212b0a34f4f4bfa916962d2c877f0ee9a33620f4b23') + depends_on('r@3.0:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-jsonlite', type=('build', 'run')) depends_on('r-callr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-wgcna/package.py b/var/spack/repos/builtin/packages/r-wgcna/package.py index 14c6d8b8a6..7b21e756ed 100644 --- a/var/spack/repos/builtin/packages/r-wgcna/package.py +++ b/var/spack/repos/builtin/packages/r-wgcna/package.py @@ -9,10 +9,12 @@ from spack import * class RWgcna(RPackage): """WGCNA: Weighted Correlation Network Analysis""" - homepage = "https://cran.r-project.org/package=WGCNA" - url = "https://cran.r-project.org/src/contrib/WGCNA_1.66.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/WGCNA/" + homepage = "https://cloud.r-project.org/package=WGCNA" + url = "https://cloud.r-project.org/src/contrib/WGCNA_1.66.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/WGCNA/" + version('1.68', sha256='0a04f15a20817f9260ae1896eda3be83a7f4855a27a348df85c7f4d376f1efe8') + version('1.67', sha256='c9cc9989763b2c80835489eabd38d9ee35b204305044d115ca7c775a103f6824') version('1.64-1', sha256='961a890cda40676ba533cd6de2b1d4f692addd16363f874c82ba8b65dd2d0db6') depends_on('r@3.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py index 55b3a4f1ba..951e64faba 100644 --- a/var/spack/repos/builtin/packages/r-whisker/package.py +++ b/var/spack/repos/builtin/packages/r-whisker/package.py @@ -11,7 +11,7 @@ class RWhisker(RPackage): including R""" homepage = "http://github.com/edwindj/whisker" - url = "https://cran.r-project.org/src/contrib/whisker_0.3-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/whisker" + url = "https://cloud.r-project.org/src/contrib/whisker_0.3-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/whisker" version('0.3-2', 'c4b9bf9a22e69ce003fe68663ab5e8e6') diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py index fffb8ee84a..f1e50a2ec4 100644 --- a/var/spack/repos/builtin/packages/r-withr/package.py +++ b/var/spack/repos/builtin/packages/r-withr/package.py @@ -13,11 +13,11 @@ class RWithr(RPackage): dependencies to provide access to these functions.""" homepage = "http://github.com/jimhester/withr" - url = "https://cran.r-project.org/src/contrib/withr_1.0.2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/withr" + url = "https://cloud.r-project.org/src/contrib/withr_1.0.2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/withr" version('2.1.2', sha256='41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686') version('1.0.2', 'ca52b729af9bbaa14fc8b7bafe38663c') version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598') - depends_on('r@3.0.2:') + depends_on('r@3.0.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xfun/package.py b/var/spack/repos/builtin/packages/r-xfun/package.py new file mode 100644 index 0000000000..9ffb8f618e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xfun/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RXfun(RPackage): + """Miscellaneous functions commonly used in other packages maintained by + 'Yihui Xie'.""" + + homepage = "https://github.com/yihui/xfun" + url = "https://cloud.r-project.org/src/contrib/xfun_0.8.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/xfun" + + version('0.8', sha256='c2f8ecf8b57ddec02f9be7f417d9e22fc1ae2c7db8d70aa703fc62bf4a5c5416') diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py index 581c442a05..13cc2d6139 100644 --- a/var/spack/repos/builtin/packages/r-xgboost/package.py +++ b/var/spack/repos/builtin/packages/r-xgboost/package.py @@ -18,14 +18,17 @@ class RXgboost(RPackage): users are also allowed to define their own objectives easily.""" homepage = "https://github.com/dmlc/xgboost" - url = "https://cran.r-project.org/src/contrib/xgboost_0.6-4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/xgboost" + url = "https://cloud.r-project.org/src/contrib/xgboost_0.6-4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/xgboost" + version('0.90.0.2', sha256='240584c1b4d54a95b4fef9074480752fae9a5b096e8f84747457d641decfc9bf') + version('0.81.0.1', sha256='3e7ada32e66881ea5c90aeafdab948927014c76cfff60a8e3d7f9e1f8a9ed7ce') version('0.6-4', '86e517e3ce39f8a01de796920f6b425e') version('0.4-4', 'c24d3076058101a71de4b8af8806697c') - depends_on('r@3.3.0:') - + depends_on('r@2.10:', when='@:0.4-4', type=('build', 'run')) + depends_on('r@2.15.1:', when='@0.6-0:0.6-2', type=('build', 'run')) + depends_on('r@3.3.0:', when='@0.6-3:', type=('build', 'run')) depends_on('r-matrix@1.1-0:', type=('build', 'run')) depends_on('r-data-table@1.9.6:', type=('build', 'run')) depends_on('r-magrittr@1.5:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py index 0d2b658537..a6b1d4619d 100644 --- a/var/spack/repos/builtin/packages/r-xlconnect/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -11,11 +11,15 @@ class RXlconnect(RPackage): data.""" homepage = "http://miraisolutions.wordpress.com/" - url = "https://cran.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnect" + url = "https://cloud.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/XLConnect" + version('0.2-15', sha256='26e1d8db65974719adbc25f1327c584003eb562dc1bb2121bffc2550cf3178b3') + version('0.2-14', sha256='d1013ed26947572bad97d62a3d66346f74993cf96c6408d21d5b6ee567468819') version('0.2-12', '3340d05d259f0a41262eab4ed32617ad') version('0.2-11', '9d1769a103cda05665df399cc335017d') - depends_on('r-xlconnectjars', type=('build', 'run')) + depends_on('r@2.10.0:', type=('build', 'run')) + depends_on('r-xlconnectjars@0.2-15', type=('build', 'run')) depends_on('r-rjava', type=('build', 'run')) + depends_on('java@6:') diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py index ce529fe6be..57edc703ae 100644 --- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -10,10 +10,13 @@ class RXlconnectjars(RPackage): """Provides external JAR dependencies for the XLConnect package.""" homepage = "http://miraisolutions.wordpress.com/" - url = "https://cran.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnectJars" + url = "https://cloud.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/XLConnectJars" + version('0.2-15', sha256='bd6f48a72c3a02b7a5e9373bcfc671614bc793f41d7bb8f4f34115a89ff4f8c6') + version('0.2-14', sha256='c675f0ccff0c3e56b2b1cc00d4d28bf8fdfa508266ac0ffab5c0641151dd7332') version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81') version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') depends_on('r-rjava', type=('build', 'run')) + depends_on('java@6:') diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index af4ec6f739..06f3b7e916 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -11,9 +11,12 @@ class RXlsx(RPackage): 97/2000/XP/2003 file formats.""" homepage = "http://code.google.com/p/rexcel/" - url = "https://cran.rstudio.com/src/contrib/xlsx_0.5.7.tar.gz" + url = "https://cloud.r-project.org/src/contrib/xlsx_0.5.7.tar.gz" + listurl = "https://cloud.r-project.org/src/contrib/Archive/xlsx" + version('0.6.1', sha256='a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4') version('0.5.7', '36b1b16f29c54b6089b1dae923180dd5') depends_on('r-rjava', type=('build', 'run')) depends_on('r-xlsxjars', type=('build', 'run')) + depends_on('java@1.6:') diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py index 541028a873..ad383b3fef 100644 --- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py +++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py @@ -10,8 +10,9 @@ class RXlsxjars(RPackage): """The xlsxjars package collects all the external jars required for the xlxs package. This release corresponds to POI 3.10.1.""" - homepage = "https://cran.rstudio.com/web/packages/xlsxjars/index.html" - url = "https://cran.rstudio.com/src/contrib/xlsxjars_0.6.1.tar.gz" + homepage = "https://cloud.r-project.org/package=xlsxjars" + url = "https://cloud.r-project.org/src/contrib/xlsxjars_0.6.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/xlsxjars" version('0.6.1', '5a1721d5733cb42f3a29e3f353e39166') diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py index 1454226466..954c1c7633 100644 --- a/var/spack/repos/builtin/packages/r-xml/package.py +++ b/var/spack/repos/builtin/packages/r-xml/package.py @@ -11,11 +11,15 @@ class RXml(RPackage): (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".""" - homepage = "https://cran.r-project.org/web/packages/XML/index.html" - url = "https://cran.r-project.org/src/contrib/XML_3.98-1.9.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/XML" + homepage = "https://cloud.r-project.org/package=XML" + url = "https://cloud.r-project.org/src/contrib/XML_3.98-1.9.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/XML" + + version('3.98-1.20', sha256='46af86376ea9a0fb1b440cf0acdf9b89178686a05c4b77728fcff1f023aa4858') + version('3.98-1.19', sha256='81b1c4a2df24c5747fa8b8ec2d76b4e9c3649b56ca94f6c93fbd106c8a72beab') version('3.98-1.9', '70dd9d711cf3cbd218eb2b870aee9503') version('3.98-1.5', 'd1cfcd56f7aec96a84ffca91aea507ee') version('3.98-1.4', '1a7f3ce6f264eeb109bfa57bedb26c14') - depends_on('libxml2') + depends_on('r@2.13.0:', type=('build', 'run')) + depends_on('libxml2@2.6.3:') diff --git a/var/spack/repos/builtin/packages/r-xml2/package.py b/var/spack/repos/builtin/packages/r-xml2/package.py index 80c748ef86..cf355c7f6f 100644 --- a/var/spack/repos/builtin/packages/r-xml2/package.py +++ b/var/spack/repos/builtin/packages/r-xml2/package.py @@ -10,12 +10,15 @@ class RXml2(RPackage): """Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.""" - homepage = "https://cran.r-project.org/package=xml2" - url = "https://cran.r-project.org/src/contrib/xml2_1.1.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/xml2" + homepage = "https://cloud.r-project.org/package=xml2" + url = "https://cloud.r-project.org/src/contrib/xml2_1.1.1.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/xml2" + version('1.2.2', sha256='3050f147c4335be2925a576557bbda36bd52a5bba3110d47b740a2dd811a78f4') + version('1.2.1', sha256='5615bbc94607efc3bc192551992b349091df802ae34b855cfa817733f2690605') version('1.1.1', '768f7edc39c4baab6b6b9e7c7ec79fee') - depends_on('r-rcpp', type=('build', 'run')) - depends_on('r-bh', type=('build', 'run')) + depends_on('r@3.1.0:', type=('build', 'run')) + depends_on('r-rcpp@0.12.12:', type=('build', 'run')) + depends_on('r-bh', when='@:1.1.1', type=('build', 'run')) depends_on('libxml2') diff --git a/var/spack/repos/builtin/packages/r-xnomial/package.py b/var/spack/repos/builtin/packages/r-xnomial/package.py index 348245d267..609340c966 100644 --- a/var/spack/repos/builtin/packages/r-xnomial/package.py +++ b/var/spack/repos/builtin/packages/r-xnomial/package.py @@ -11,11 +11,10 @@ class RXnomial(RPackage): """XNomial: Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities""" - homepage = "https://cran.r-project.org/package=XNomial" - url = "https://cran.r-project.org/src/contrib/XNomial_1.0.4.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/XNomial/" + homepage = "https://cloud.r-project.org/package=XNomial" + url = "https://cloud.r-project.org/src/contrib/XNomial_1.0.4.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/XNomial/" version('1.0.4', sha256='e6237f79d96f02bb30af1cf055ae9f70541abba34ce045a9d4359b5304189dd7') depends_on('r@2.14:', type=('build', 'run')) - depends_on('r-knitr', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xopen/package.py b/var/spack/repos/builtin/packages/r-xopen/package.py new file mode 100644 index 0000000000..4365dff7e1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xopen/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RXopen(RPackage): + """Cross platform solution to open files, directories or 'URLs' with their + associated programs.""" + + homepage = "https://github.com/r-lib/xopen#readme" + url = "https://cloud.r-project.org/src/contrib/xopen_1.0.0.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/xopen" + + version('1.0.0', sha256='e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef') + + depends_on('r@3.1:', type=('build', 'run')) + depends_on('r-processx', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py index 0265a5e3f2..96eeedcaba 100644 --- a/var/spack/repos/builtin/packages/r-xtable/package.py +++ b/var/spack/repos/builtin/packages/r-xtable/package.py @@ -10,7 +10,11 @@ class RXtable(RPackage): """Coerce data to LaTeX and HTML tables.""" homepage = "http://xtable.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/xtable" + url = "https://cloud.r-project.org/src/contrib/xtable_1.8-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/xtable" + version('1.8-4', sha256='5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c') + version('1.8-3', sha256='53b2b0fff8d7a8bba434063c2a01b867f510a4389ded2691fbedbc845f08c325') version('1.8-2', '239e4825cd046156a67efae3aac01d86') + + depends_on('r@2.10.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py index 2e657117ea..d698110be7 100644 --- a/var/spack/repos/builtin/packages/r-xts/package.py +++ b/var/spack/repos/builtin/packages/r-xts/package.py @@ -13,10 +13,10 @@ class RXts(RPackage): cross-class interoperability.""" homepage = "http://r-forge.r-project.org/projects/xts/" - url = "https://cran.r-project.org/src/contrib/xts_0.11-2.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/xts" + url = "https://cloud.r-project.org/src/contrib/xts_0.11-2.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/xts" version('0.11-2', sha256='12772f6a66aab5b84b0665c470f11a3d8d8a992955c027261cfe8e6077ee13b8') version('0.9-7', 'a232e94aebfa654653a7d88a0503537b') - depends_on('r-zoo', type=('build', 'run')) + depends_on('r-zoo@1.7-12:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py index a7d537e094..9454402e20 100644 --- a/var/spack/repos/builtin/packages/r-yaml/package.py +++ b/var/spack/repos/builtin/packages/r-yaml/package.py @@ -10,9 +10,11 @@ class RYaml(RPackage): """This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.""" - homepage = "https://cran.r-project.org/web/packages/yaml/index.html" - url = "https://cran.r-project.org/src/contrib/yaml_2.1.13.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/yaml" + homepage = "https://cloud.r-project.org/package=yaml" + url = "https://cloud.r-project.org/src/contrib/yaml_2.1.13.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/yaml" + version('2.2.0', sha256='55bcac87eca360ab5904914fcff473a6981a1f5e6d2215d2634344d0ac30c546') + version('2.1.19', sha256='e5db035693ac765e4b5fe1fc2e9711f8ca73e398e3f2bf27cc60def59ccd7f11') version('2.1.14', '2de63248e6a122c368f8e4537426e35c') version('2.1.13', 'f2203ea395adaff6bd09134666191d9a') diff --git a/var/spack/repos/builtin/packages/r-zeallot/package.py b/var/spack/repos/builtin/packages/r-zeallot/package.py new file mode 100644 index 0000000000..7276bff255 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-zeallot/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RZeallot(RPackage): + """Provides a %<-% operator to perform multiple, unpacking, and + destructuring assignment in R. The operator unpacks the right-hand side of + an assignment into multiple values and assigns these values to variables on + the left-hand side of the assignment.""" + + homepage = "https://github.com/nteetor/zeallot" + url = "https://cloud.r-project.org/src/contrib/zeallot_0.1.0.tar.gz" + listurl = "https://cloud.r-project.org/src/contrib/Archive/zeallot" + + version('0.1.0', sha256='439f1213c97c8ddef9a1e1499bdf81c2940859f78b76bc86ba476cebd88ba1e9') diff --git a/var/spack/repos/builtin/packages/r-zip/package.py b/var/spack/repos/builtin/packages/r-zip/package.py new file mode 100644 index 0000000000..13270d7b32 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-zip/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class RZip(RPackage): + """Cross-Platform 'zip' Compression Library. A replacement for the 'zip' + function, that does not require any additional external tools on any + platform.""" + + homepage = "https://github.com/r-lib/zip#readme" + url = "https://cloud.r-project.org/src/contrib/zip_2.0.3.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/zip" + + version('2.0.3', sha256='4a8cb8e41eb630bbf448a0fd56bcaeb752b8484fef98c6419334edf46401317e') diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py index 50b38f8aa9..fe845adea5 100644 --- a/var/spack/repos/builtin/packages/r-zoo/package.py +++ b/var/spack/repos/builtin/packages/r-zoo/package.py @@ -14,10 +14,14 @@ class RZoo(RPackage): methods to extend standard generics.""" homepage = "http://zoo.r-forge.r-project.org/" - url = "https://cran.r-project.org/src/contrib/zoo_1.7-14.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/zoo" + url = "https://cloud.r-project.org/src/contrib/zoo_1.7-14.tar.gz" + list_url = "https://cloud.r-project.org/src/contrib/Archive/zoo" + version('1.8-6', sha256='2217a4f362f2201443b5fdbfd9a77d9a6caeecb05f02d703ee8b3b9bf2af37cc') + version('1.8-5', sha256='8773969973d28d7d1a48f74b73be1dbd97acb3b22a4668a102e8bb585a7de826') version('1.7-14', '8c577a7c1e535c899ab14177b1039c32') version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30') - depends_on('r-lattice', type=('build', 'run')) + depends_on('r@2.10.0:', when='@:1.8-1', type=('build', 'run')) + depends_on('r@3.1.0:', when='@1.8-2:', type=('build', 'run')) + depends_on('r-lattice@0.20-27:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/swftools/configure.patch b/var/spack/repos/builtin/packages/swftools/configure.patch new file mode 100644 index 0000000000..fdaff87aa4 --- /dev/null +++ b/var/spack/repos/builtin/packages/swftools/configure.patch @@ -0,0 +1,17 @@ +--- a/configure 2019-08-07 20:44:13.708133253 -0500 ++++ b/configure 2019-08-07 20:44:27.334099579 -0500 +@@ -2640,10 +2640,10 @@ + + # ------------------------------------------------------------------ + +-if test "x${srcdir}" != "x."; then +- echo "--srcdir is not supported" +- exit 1 +-fi ++#if test "x${srcdir}" != "x."; then ++# echo "--srcdir is not supported" ++# exit 1 ++#fi + + WARNINGS="-Wimplicit -Wreturn-type -Wno-write-strings -Wformat" + if test "x$ENABLE_WARNINGS" '!=' "x";then diff --git a/var/spack/repos/builtin/packages/swftools/package.py b/var/spack/repos/builtin/packages/swftools/package.py new file mode 100644 index 0000000000..779358df74 --- /dev/null +++ b/var/spack/repos/builtin/packages/swftools/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Swftools(AutotoolsPackage): + """SWFTools is a collection of utilities for working with Adobe Flash files + (SWF files). The tool collection includes programs for reading SWF files, + combining them, and creating them from other content (like images, sound + files, videos or sourcecode). SWFTools is released under the GPL. + """ + + homepage = "http://swftools.org" + url = "http://swftools.org/swftools-0.9.2.tar.gz" + + version('0.9.2', sha256='bf6891bfc6bf535a1a99a485478f7896ebacbe3bbf545ba551298080a26f01f1') + + patch('configure.patch') + patch('swfs_Makefile.in.patch') + patch('https://aur.archlinux.org/cgit/aur.git/plain/giflib-5.1.patch?h=swftools', + sha256='6a995dfd674c5954f5b967e3d45d6845a186872fcaa4223d725902fd4d679f1b', + level=0) + + depends_on('giflib') + depends_on('lame') + depends_on('poppler') + depends_on('freetype') + depends_on('jpeg') + depends_on('fftw') diff --git a/var/spack/repos/builtin/packages/swftools/swfs_Makefile.in.patch b/var/spack/repos/builtin/packages/swftools/swfs_Makefile.in.patch new file mode 100644 index 0000000000..c53f3dbfa3 --- /dev/null +++ b/var/spack/repos/builtin/packages/swftools/swfs_Makefile.in.patch @@ -0,0 +1,14 @@ +--- a/swfs/Makefile.ing 2019-08-07 21:53:26.077931626 -0500 ++++ b/swfs/Makefile.in 2019-08-07 21:54:18.845809017 -0500 +@@ -41,9 +41,9 @@ + $(INSTALL_DATA) ./PreLoaderTemplate.swf $(pkgdatadir)/swfs/PreLoaderTemplate.swf + $(INSTALL_DATA) ./tessel_loader.swf $(pkgdatadir)/swfs/tessel_loader.swf + $(INSTALL_DATA) ./swft_loader.swf $(pkgdatadir)/swfs/swft_loader.swf +- rm -f $(pkgdatadir)/swfs/default_viewer.swf -o -L $(pkgdatadir)/swfs/default_viewer.swf ++ #rm -f $(pkgdatadir)/swfs/default_viewer.swf -o -L $(pkgdatadir)/swfs/default_viewer.swf + $(LN_S) $(pkgdatadir)/swfs/simple_viewer.swf $(pkgdatadir)/swfs/default_viewer.swf +- rm -f $(pkgdatadir)/swfs/default_loader.swf -o -L $(pkgdatadir)/swfs/default_loader.swf ++ #rm -f $(pkgdatadir)/swfs/default_loader.swf -o -L $(pkgdatadir)/swfs/default_loader.swf + $(LN_S) $(pkgdatadir)/swfs/tessel_loader.swf $(pkgdatadir)/swfs/default_loader.swf + + uninstall: |