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| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2016-06-05 20:12:11 -0500 |
|---|---|---|
| committer | Glenn Johnson <glenn-johnson@uiowa.edu> | 2016-06-16 23:08:55 -0500 |
| commit | 7213b123245895ab3fe588c7b5656b68f648b99d (patch) | |
| tree | 3b10e4b769d90ed36878198038c9f6281433d77d /var | |
| parent | 0e64c25ffc09d764eaeb11ffb0db93bb8baaf34a (diff) | |
| download | spack-7213b123245895ab3fe588c7b5656b68f648b99d.tar.gz spack-7213b123245895ab3fe588c7b5656b68f648b99d.tar.bz2 spack-7213b123245895ab3fe588c7b5656b68f648b99d.tar.xz spack-7213b123245895ab3fe588c7b5656b68f648b99d.zip | |
Tweak how R packages are built.
Add bzip2 as a dependency to base R.
Switch from installing the R packages from tar files to installing from
the extracted directory. This is more in line with a standard install
and also allows installing from VCS.
Use the Bioconductor version for BiocGenerics and future Bioconductor
packages. Suffix the package with 'bioc-$version' to indicate which
Bioconductor release the package is a part of. This is actually more
important than the actual version attached to individual packages
although those are subject to change within the Bioconductor branch.
Diffstat (limited to 'var')
5 files changed, 14 insertions, 10 deletions
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index af520082ec..74dd95e5c2 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -61,6 +61,7 @@ class R(Package): depends_on('icu') depends_on('glib') depends_on('zlib') + depends_on('bzip2') depends_on('libtiff') depends_on('jpeg') depends_on('cairo') diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py index d509bc3d84..ffd578a42c 100644 --- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py +++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py @@ -29,12 +29,15 @@ class RBiocgenerics(Package): """S4 generic functions needed by many Bioconductor packages.""" homepage = 'https://bioconductor.org/packages/BiocGenerics/' - url = 'https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.18.0.tar.gz' - - version('0.18.0', 'baaff00eb2c2b15396fed2f7f43e634c', expand=False) + version('bioc-3.3', + git='https://github.com/Bioconductor-mirror/BiocGenerics.git', + branch='release-3.3') + version('bioc-3.2', + git='https://github.com/Bioconductor-mirror/BiocGenerics.git', + branch='release-3.2') extends('R') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library=%s' % - self.module.r_lib_dir, '%s' % self.stage.archive_file) + self.module.r_lib_dir, '%s' % self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index f9ac684aa4..b67a06d9b5 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -34,11 +34,11 @@ class RAbind(Package): homepage = "https://cran.r-project.org/" url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz" - version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False) + version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5') extends('R') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library=%s' % - self.module.r_lib_dir, '%s' % self.stage.archive_file) + self.module.r_lib_dir, '%s' % self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index e59ba18fa3..924066e063 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -39,10 +39,10 @@ class RFilehash(Package): homepage = 'https://cran.r-project.org/' url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz" - version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False) + version('2.3', '01fffafe09b148ccadc9814c103bdc2f') extends('R') def install(self, spec, prefix): R('CMD', 'INSTALL', '--library=%s' % - self.module.r_lib_dir, '%s' % self.stage.archive_file) + self.module.r_lib_dir, '%s' % self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index ec4b9b9e41..31dab3b8af 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -34,7 +34,7 @@ class RMagic(Package): homepage = "https://cran.r-project.org/" url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz" - version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False) + version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029') extends('R') @@ -42,4 +42,4 @@ class RMagic(Package): def install(self, spec, prefix): R('CMD', 'INSTALL', '--library=%s' % - self.module.r_lib_dir, '%s' % self.stage.archive_file) + self.module.r_lib_dir, '%s' % self.stage.source_path) |