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.

1 files changed, 5 insertions, 4 deletions

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'))