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2019-09-02refactor: clean up `spack find`, make `spack find -dp` work properlyTodd Gamblin4-153/+132
Refactor `spack.cmd.display_specs()` and `spack find` so that any options can be used together with -d. This cleans up the display logic considerably, as there are no longer multiple "modes".
2019-09-02docs: add docs for `spack find --format` and `spack find --json`Todd Gamblin3-9/+119
- add docs for `spack find --format` - add docs for `spack find --json` - update references to Spec.format() docs and add links
2019-09-02command: add `spack find --json`Todd Gamblin4-4/+52
This is another machine-readable version of `spack find`. Supplying the `--json` argument causes specs to be written out as json records, easily filered with tools like jq. e.g.: $ spack find --json python | jq -C ".[] | { name, version } " [ { "name": "python", "version": "2.7.16" }, { "name": "bzip2", "version": "1.0.8" } ]
2019-09-02command: add `spack find --format`Todd Gamblin2-23/+53
- spack find --format allows you to supply a format string and have specs output in a more machine-readable way, without dedcoration e.g.: spack find --format "{name}-{version}-{hash}" autoconf-2.69-icynozk7ti6h4ezzgonqe6jgw5f3ulx4 automake-1.16.1-o5v3tc77kesgonxjbmeqlwfmb5qzj7zy bzip2-1.0.6-syohzw57v2jfag5du2x4bowziw3m5p67 ... or: spack find --format "{hash}" icynozk7ti6h4ezzgonqe6jgw5f3ulx4 o5v3tc77kesgonxjbmeqlwfmb5qzj7zy syohzw57v2jfag5du2x4bowziw3m5p67 ... This is intended to make it much easier to script with `spack find`
2019-09-02esmf: Fix build with gcc@8: (#12678)Michael Kuhn3-12/+161
2019-09-02Add XSSP recipe (#12679)asmaahassan901-0/+41
2019-09-02icu4c: Add missing python dependency (#12683)Michael Kuhn1-0/+7
2019-09-02Add fpocket (#12675)asmaahassan901-0/+26
* Add fpocket * fix recipe break down the description to pass lint * update license * make changes as per maintainer's review
2019-09-01Install the newest version of ncbi-rmblastn (#12580)asmaahassan902-3/+251
* Install the newest version of ncbi-rmblastn Version ncbi-rmblastn 2.2.28 coonfiguration fails for gcc compiler on ubuntu 16.04 due to some compatibility issues that requires manual intervention to keep the installation going. However you still stumble upon other issues while compiling it. Using Intel compiler passes the configuration step but fails for the compilation process as well. Here I'm using the latest version and patch, and the recommended configuration option as mention in http://www.repeatmasker.org/RMBlast.html * uploading ncbi-blast patch
2019-09-01IDBA: package does not need conflicts with other compilers (#12674)Kevin Manalo1-8/+0
2019-09-01Add Vesta recipe (#12581)asmaahassan901-0/+29
* Add Vesta recipe * Break down description to pass lint * Make changes as maintainers' review * remove whitespaces
2019-09-01A new package: fastp. (#12671)健美猞猁1-0/+20
* A new package: fastp. * Flake8. * Flake8.
2019-08-31new package: py-requests-oauthlib (#12548)Sinan1-0/+24
* new package: py-requests-oauthlib * add a version * fix typo
2019-08-31new package: py-systemd-python (#12595)Sinan1-0/+15
2019-08-31Add MKL variant to Julia (#12602)Glenn Johnson1-0/+5
This PR provides an option to build Julia with Intel MKL.
2019-08-31new package: optipng (#12608)Sinan1-0/+20
2019-08-31new package: pngquant (#12609)Sinan1-0/+18
2019-08-31new package: pktools (#12611)Sinan1-0/+42
* new package: pktools * rename and enable utilities * enable build with FANN * add variants, dependencies * expcitly turn off options when not in use
2019-08-31new package: FANN (#12614)Sinan1-0/+26
2019-08-31Add int64 variant to pumi and zoltan (#12630)Cameron Smith2-1/+9
* pumi and zoltan: add int64 variant * typo
2019-08-31add variant for building RTREE module (#12668)Sinan1-0/+6
2019-08-31new package: libwebp (#12669)Sinan1-0/+19
2019-08-31Add conflicts statement to mariadb (#12670)Glenn Johnson1-0/+2
The mariadb-5.5 series can not be compiled with gcc-9.1.0 and above. Add a conflicts statement to reflect that. The error is due to -Werror=address-of-packed-member, a warning that is new in gcc-9.
2019-08-31A new package: py-gdc-client. (#12672)健美猞猁1-0/+18
* A new package: py-gdc-client. * Flake8.
2019-08-30p4est package: add version 2.2 (#12603)Ruben Di Battista1-1/+2
2019-08-30new package: attrSinan811-0/+26
2019-08-30salmon package: add version 0.14.1 (#12646)Justin S1-0/+5
2019-08-30Update R CRAN packages (#12019)Glenn Johnson579-1835/+4618
* 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.
2019-08-30Add athena package (#12663)Adam J. Stewart2-0/+239
* Add athena package * Flake8 fix * Fix missing separator error * Add master branch
2019-08-30gtkplus package: add variant for CUPS support (#12566)brietzke1-0/+5
Default is ~cups (no CUPS support). Before this option, gtkplus would potentially use a system-installed version of CUPS.
2019-08-30extrae package: add 3.7.1, optionalise dyninst, papi (#11978)Phil Tooley1-35/+57
* Convert to Autotools package * dyninst and papi are now optional (off by default) * limit dyninst version to < 10 (see https://github.com/bsc-performance-tools/extrae/issues/30) * Add numactl dependency * Enable parallel installs for 3.7 and later * Set EXTRAE_HOME in module files and for dependent package installs * Generalize cxx11 support flag (previously it was using a specific syntax and this updates it to use the cxx11 support flag for the compiler in use).
2019-08-30kaldi package: fix installation of libraries (#12177)Jimmy Tang1-3/+9
* The install for kaldi was copying library symlinks but not the actual library files, this makes sure to copy the libraries * All libraries are installed to 'prefix.lib' (the original library directory structure is no longer maintained) * The install step for executables did not account for the different dynamic library suffix on MacOS
2019-08-30New package: py-oauthlib (#12528)Sinan1-0/+36
2019-08-30gtkplus: package cairo dependency must be +gobject (#12655)George Hartzell1-1/+1
e891cc4 updated the cairo package to make gobject support optional and disabled it by default. gtkplus requires gobject support so this explicitly enables +gobject on the cairo dependency of gtkplus.
2019-08-30Add py-pytest 5.1.1 (#12660)Adam J. Stewart1-15/+36
2019-08-30Add py-packaging 19.1 (#12659)Adam J. Stewart1-4/+6
2019-08-30Add py-pluggy 0.12.0 (#12658)Adam J. Stewart1-1/+3
2019-08-30Add py-importlib-metadata package (#12657)Adam J. Stewart1-0/+23
2019-08-30Add py-zipp package (#12656)Adam J. Stewart1-0/+20
2019-08-30Archive all patches in a package after install (#12653)Peter Scheibel1-1/+4
When Spack installs a package it writes the package.py file and patches to a separate repository (which reflects the state of the package at the time it was installed). Previously, Spack only wrote patches that were used at installation time. This updates the archiving step to include all patch files that are relevant to the package (in case that repository is used in another context).
2019-08-30Fujitsu compiler: Add flags for c11/c99 (#12622)t-karatsu2-0/+10
* Fujitsu compiler: Add flags for c11/c99 * Add unit tests about supported flags
2019-08-29OpenSceneGraph package: add version 3.6.4; update URL and checksums (#12626)Sinan1-3/+4
Replace old checksums with sha256 checksums
2019-08-29hpctoolkit: tighten some dependenciesMark W. Krentel1-4/+4
Change the depends_on type from default (build + link) to just 'link' for binutils and a few other packages. We don't use the binutils utilities (only libs). On cori at NERSC (Cray), this was breaking the build by covering up the system ld.
2019-08-29elpa package: add version 2018.11.001 (#12645)Janne Blomqvist1-1/+3
Remove designation of 2017.11.001 as preferred version
2019-08-29emacs package: add version 26.2, jpeg dependency (#12632)brietzke1-0/+2
2019-08-29Scalpel package: remove CMake dependency (#12631)健美猞猁1-1/+0
Scalpel does not depend on CMake
2019-08-29NAMD package: add version 2.13 (#12616)Kevin Manalo1-0/+1
2019-08-29ABINIT package: add version 8.10.3 (#12615)Kevin Manalo1-0/+1
2019-08-29mc package: add version 4.8.23 (#12605)Matthias Diener1-0/+1
2019-08-29New package: py-ecdsa (#12598)Sinan1-0/+20
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