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copyright: update license headers for 2013-2019 copyright.
2019-01-01 14:04:23 +08:00
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-08 04:52:23 +08:00
# Spack Project Developers. See the top-level COPYRIGHT file for details.
New package - RStan This PR creates the RStan package and its dependencies.
2016-07-05 06:30:05 +08:00
#
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-08 04:52:23 +08:00
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
New package - RStan This PR creates the RStan package and its dependencies.
2016-07-05 06:30:05 +08:00
from spack import *
Preliminary RPackage class (#2761)
2017-01-08 08:28:52 +08:00
class RPlyr(RPackage):
New package - RStan This PR creates the RStan package and its dependencies.
2016-07-05 06:30:05 +08:00
"""A set of tools that solves a common set of problems: you need to break a
big problem down into manageable pieces, operate on each piece and then put
all the pieces back together. For example, you might want to fit a model to
each spatial location or time point in your study, summarise data by panels
or collapse high-dimensional arrays to simpler summary statistics. The
Fix flake errors
2016-07-05 06:55:10 +08:00
development of 'plyr' has been generously supported by 'Becton
Dickinson'."""
New package - RStan This PR creates the RStan package and its dependencies.
2016-07-05 06:30:05 +08:00
homepage = "http://had.co.nz/plyr"
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.
2019-08-31 07:22:13 +08:00
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"
New package - RStan This PR creates the RStan package and its dependencies.
2016-07-05 06:30:05 +08:00
checksums: use sha256 checksums everywhere We'd like to use a consistent checksum scheme everywhere so that we can: a) incorporate archive checksums into our specs and have a consistent hashing algorithm across all specs. b) index mirrors with a consistent type of checksum, and not one that is dependent on how spack packages are written. - [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
2019-10-11 13:44:41 +08:00
version('1.8.4', sha256='60b522d75961007658c9806f8394db27989f1154727cb0bb970062c96ec9eac5')
New package - RStan This PR creates the RStan package and its dependencies.
2016-07-05 06:30:05 +08:00
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.
2019-08-31 07:22:13 +08:00
depends_on('r@3.1.0:', type=('build', 'run'))
depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
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