From 64acbbfcf03393eab99301f1e7843618c5547cf0 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sat, 28 May 2016 20:19:45 -0500
Subject: Clean up R package files
- remove unused imports
- apply pep8
- reformat text strings
---
var/spack/repos/builtin/packages/R/package.py | 44 ++++++++++++---------------
1 file changed, 19 insertions(+), 25 deletions(-)
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 0177fe1a2b..727cd38461 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -22,28 +22,22 @@
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
-import functools
-import glob
-import inspect
import os
-import re
-from contextlib import closing
-import spack
-from llnl.util.lang import match_predicate
from spack import *
from spack.util.environment import *
class R(Package):
- """
- R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a
- wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series
- analysis, classification, clustering, etc. Please consult the R project homepage for further information.
- """
+ """R is 'GNU S', a freely available language and environment for
+ statistical computing and graphics which provides a wide variety of
+ statistical and graphical techniques: linear and nonlinear modelling,
+ statistical tests, time series analysis, classification, clustering, etc.
+ Please consult the R project homepage for further information."""
+
homepage = "https://www.r-project.org"
url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
-
+
extendable = True
version('3.2.3', '1ba3dac113efab69e706902810cc2970')
@@ -53,7 +47,8 @@ class R(Package):
version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4')
version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
- variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK')
+ variant('external-lapack', default=False,
+ description='Links to externally installed BLAS/LAPACK')
# Virtual dependencies
depends_on('blas', when='+external-lapack')
@@ -106,25 +101,24 @@ class R(Package):
r_libs_path = ':'.join(r_libs_path)
spack_env.set('R_LIBS', r_libs_path)
- # For run time environment set only the path for extension_spec and prepend it to R_LIBS
+ # For run time environment set only the path for extension_spec and
+ # prepend it to R_LIBS
if extension_spec.package.extends(self.spec):
- run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir))
-
+ run_env.prepend_path('R_LIBS', os.path.join(
+ extension_spec.prefix, self.r_lib_dir))
def setup_dependent_package(self, module, ext_spec):
- """
- Called before R modules' install() methods.
-
- In most cases, extensions will only need to have one line::
-
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
- """
+ """Called before R modules' install() methods. In most cases,
+ extensions will only need to have one line:
+ R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' %
+ self.stage.archive_file)"""
# R extension builds can have a global R executable function
module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
# Add variable for library directry
module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir)
- # Make the site packages directory for extensions, if it does not exist already.
+ # Make the site packages directory for extensions, if it does not exist
+ # already.
if ext_spec.package.is_extension:
mkdirp(module.r_lib_dir)
--
cgit v1.2.3-70-g09d2
From 6649f9edc226742b4184b73106df5496ad66406a Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sat, 28 May 2016 22:25:32 -0500
Subject: Add version 3.3.0 of R
This commit adds the 3.3.0 version of R and adds dependencies on curl
and pcre.
---
var/spack/repos/builtin/packages/R/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 727cd38461..f4728bfd64 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -40,6 +40,7 @@ class R(Package):
extendable = True
+ version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
version('3.2.3', '1ba3dac113efab69e706902810cc2970')
version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
@@ -67,6 +68,8 @@ class R(Package):
depends_on('freetype')
depends_on('tcl')
depends_on('tk')
+ depends_on('curl')
+ depends_on('pcre')
def install(self, spec, prefix):
rlibdir = join_path(prefix, 'rlib')
--
cgit v1.2.3-70-g09d2
From cb3505769b57e9f7c06f42faf8b88dfb40db7ec9 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sat, 28 May 2016 22:31:47 -0500
Subject: Clean up R extensions
Run the existing R extension packages through autopep8 to clean up.
---
var/spack/repos/builtin/packages/r-BiocGenerics/package.py | 6 ++++--
var/spack/repos/builtin/packages/r-abind/package.py | 6 ++++--
var/spack/repos/builtin/packages/r-filehash/package.py | 6 ++++--
var/spack/repos/builtin/packages/r-magic/package.py | 6 ++++--
4 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
index 0d3b6a3e57..1d994cc2ef 100644
--- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
@@ -24,15 +24,17 @@
##############################################################################
from spack import *
+
class RBiocgenerics(Package):
"""S4 generic functions needed by many Bioconductor packages."""
homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html'
- url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz"
+ url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz"
version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False)
extends('R')
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ R('CMD', 'INSTALL', '--library=%s' %
+ self.module.r_lib_dir, '%s' % self.stage.archive_file)
diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py
index 34a1eee79f..f9ac684aa4 100644
--- a/var/spack/repos/builtin/packages/r-abind/package.py
+++ b/var/spack/repos/builtin/packages/r-abind/package.py
@@ -24,6 +24,7 @@
##############################################################################
from spack import *
+
class RAbind(Package):
"""Combine multidimensional arrays into a single array. This is a
generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and
@@ -31,7 +32,7 @@ class RAbind(Package):
'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"
+ url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz"
version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False)
@@ -39,4 +40,5 @@ class RAbind(Package):
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ R('CMD', 'INSTALL', '--library=%s' %
+ self.module.r_lib_dir, '%s' % self.stage.archive_file)
diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py
index fffae68019..e59ba18fa3 100644
--- a/var/spack/repos/builtin/packages/r-filehash/package.py
+++ b/var/spack/repos/builtin/packages/r-filehash/package.py
@@ -24,6 +24,7 @@
##############################################################################
from spack import *
+
class RFilehash(Package):
"""Implements a simple key-value style database where character string keys
are associated with data values that are stored on the disk. A simple
@@ -36,11 +37,12 @@ class RFilehash(Package):
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"
+ url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz"
version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False)
extends('R')
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ R('CMD', 'INSTALL', '--library=%s' %
+ self.module.r_lib_dir, '%s' % self.stage.archive_file)
diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py
index f86917ec0c..ec4b9b9e41 100644
--- a/var/spack/repos/builtin/packages/r-magic/package.py
+++ b/var/spack/repos/builtin/packages/r-magic/package.py
@@ -24,6 +24,7 @@
##############################################################################
from spack import *
+
class RMagic(Package):
"""A collection of efficient, vectorized algorithms for the creation and
investigation of magic squares and hypercubes, including a variety of
@@ -31,7 +32,7 @@ class RMagic(Package):
arrays."""
homepage = "https://cran.r-project.org/"
- url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz"
+ url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz"
version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False)
@@ -40,4 +41,5 @@ class RMagic(Package):
depends_on('r-abind')
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ R('CMD', 'INSTALL', '--library=%s' %
+ self.module.r_lib_dir, '%s' % self.stage.archive_file)
--
cgit v1.2.3-70-g09d2
From fe256870b47d8b0381c918e54a45c46229506bad Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 29 May 2016 15:26:34 -0500
Subject: Add variant for UTF support to pcre
This will build PCRE with UTF support by default. That seems to be
reasonable for most environments.
---
var/spack/repos/builtin/packages/pcre/package.py | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py
index 8e0f83110e..53b23a203d 100644
--- a/var/spack/repos/builtin/packages/pcre/package.py
+++ b/var/spack/repos/builtin/packages/pcre/package.py
@@ -29,6 +29,7 @@ class Pcre(Package):
"""The PCRE package contains Perl Compatible Regular Expression
libraries. These are useful for implementing regular expression
pattern matching using the same syntax and semantics as Perl 5."""
+
homepage = "http://www.pcre.org"""
url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.36.tar.bz2"
@@ -37,7 +38,14 @@ class Pcre(Package):
patch("intel.patch")
+ variant('utf', default=True,
+ description='Enable support for UTF-8/16/32, incompatible with EBCDIC.')
+
def install(self, spec, prefix):
- configure("--prefix=%s" % prefix)
+ configure_args = ['--prefix=%s' % prefix]
+ if '+utf' in spec:
+ configure_args.append('--enable-utf')
+
+ configure(*configure_args)
make()
make("install")
--
cgit v1.2.3-70-g09d2
From 8704a4ed35b5868a62cde613d85c3eeae27e5a5e Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 29 May 2016 16:06:03 -0500
Subject: Use configure_args rather than options
Replaced 'options' with 'configure_args'. That seems like a better name
and is consistent with the packaging guide.
---
var/spack/repos/builtin/packages/R/package.py | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index f4728bfd64..af520082ec 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -73,15 +73,15 @@ class R(Package):
def install(self, spec, prefix):
rlibdir = join_path(prefix, 'rlib')
- options = ['--prefix=%s' % prefix,
- '--libdir=%s' % rlibdir,
- '--enable-R-shlib',
- '--enable-BLAS-shlib',
- '--enable-R-framework=no']
+ configure_args = ['--prefix=%s' % prefix,
+ '--libdir=%s' % rlibdir,
+ '--enable-R-shlib',
+ '--enable-BLAS-shlib',
+ '--enable-R-framework=no']
if '+external-lapack' in spec:
- options.extend(['--with-blas', '--with-lapack'])
+ configure_args.extend(['--with-blas', '--with-lapack'])
- configure(*options)
+ configure(*configure_args)
make()
make('install')
@@ -111,7 +111,7 @@ class R(Package):
extension_spec.prefix, self.r_lib_dir))
def setup_dependent_package(self, module, ext_spec):
- """Called before R modules' install() methods. In most cases,
+ """Called before R modules' install() methods. In most cases,
extensions will only need to have one line:
R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' %
self.stage.archive_file)"""
--
cgit v1.2.3-70-g09d2
From 37dc13edaf92c9fa45c0b82c736f5b40ed8172f7 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 29 May 2016 17:03:38 -0500
Subject: Update version of BiocGenerics
The BioConductor repositories only keep the most recent version so this
has to be bumped.
---
var/spack/repos/builtin/packages/r-BiocGenerics/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
index 1d994cc2ef..16a8027e3c 100644
--- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
@@ -31,7 +31,7 @@ class RBiocgenerics(Package):
homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html'
url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz"
- version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False)
+ version('0.18.0', 'baaff00eb2c2b15396fed2f7f43e634c', expand=False)
extends('R')
--
cgit v1.2.3-70-g09d2
From 0e64c25ffc09d764eaeb11ffb0db93bb8baaf34a Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 29 May 2016 17:40:26 -0500
Subject: Fix flake8 errors
Use Bioconductor provided Short URL for homepage in BiocGenerics.
Wrap description text for utf variant in pcre.
---
var/spack/repos/builtin/packages/pcre/package.py | 3 ++-
var/spack/repos/builtin/packages/r-BiocGenerics/package.py | 4 ++--
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py
index 53b23a203d..a43729a1ac 100644
--- a/var/spack/repos/builtin/packages/pcre/package.py
+++ b/var/spack/repos/builtin/packages/pcre/package.py
@@ -39,7 +39,8 @@ class Pcre(Package):
patch("intel.patch")
variant('utf', default=True,
- description='Enable support for UTF-8/16/32, incompatible with EBCDIC.')
+ description='Enable support for UTF-8/16/32, '
+ 'incompatible with EBCDIC.')
def install(self, spec, prefix):
configure_args = ['--prefix=%s' % prefix]
diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
index 16a8027e3c..d509bc3d84 100644
--- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
@@ -28,8 +28,8 @@ from spack import *
class RBiocgenerics(Package):
"""S4 generic functions needed by many Bioconductor packages."""
- homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html'
- url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz"
+ 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)
--
cgit v1.2.3-70-g09d2
From 7213b123245895ab3fe588c7b5656b68f648b99d Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 5 Jun 2016 20:12:11 -0500
Subject: 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.
---
var/spack/repos/builtin/packages/R/package.py | 1 +
var/spack/repos/builtin/packages/r-BiocGenerics/package.py | 11 +++++++----
var/spack/repos/builtin/packages/r-abind/package.py | 4 ++--
var/spack/repos/builtin/packages/r-filehash/package.py | 4 ++--
var/spack/repos/builtin/packages/r-magic/package.py | 4 ++--
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)
--
cgit v1.2.3-70-g09d2
From 7da405e630b6b0e65f4ec8d551a4ed988f32ac74 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Mon, 6 Jun 2016 17:06:50 -0500
Subject: Add validator for bioconductor packages
This commit adds a validator function to make sure the versions of R and
bioconductor are in sync.
---
var/spack/repos/builtin/packages/r-BiocGenerics/package.py | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
index ffd578a42c..5a6ce72a4b 100644
--- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
@@ -38,6 +38,19 @@ class RBiocgenerics(Package):
extends('R')
+ def validate(self, spec):
+ """
+ Checks that the version of R is appropriate for the Bioconductor
+ version.
+ """
+ if spec.satisfies('@bioc-3.3'):
+ if not spec.satisfies('^R@3.3.0:3.3.9'):
+ raise InstallError('Must use R-3.3 for Bioconductor-3.3')
+ elif spec.satisfies('@bioc-3.2'):
+ if not spec.satisfies('^R@3.2.0:3.2.9'):
+ raise InstallError('Must use R-3.2 for Bioconductor-3.2')
+
def install(self, spec, prefix):
+ self.validate(spec)
R('CMD', 'INSTALL', '--library=%s' %
self.module.r_lib_dir, '%s' % self.stage.source_path)
--
cgit v1.2.3-70-g09d2
From 4850b9d4d1446f96732e27053df50c16629ec448 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Mon, 6 Jun 2016 17:30:35 -0500
Subject: Make install comment consistent with actual call.
---
var/spack/repos/builtin/packages/R/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 74dd95e5c2..c7d8f89906 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -115,7 +115,7 @@ class R(Package):
"""Called before R modules' install() methods. In most cases,
extensions will only need to have one line:
R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' %
- self.stage.archive_file)"""
+ self.stage.source_path)"""
# R extension builds can have a global R executable function
module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
--
cgit v1.2.3-70-g09d2
From a813f03955397140104b7d926f0fddf925e672bc Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sat, 11 Jun 2016 16:18:54 -0500
Subject: Add list_url for old versions.
---
var/spack/repos/builtin/packages/r-abind/package.py | 8 ++++----
var/spack/repos/builtin/packages/r-filehash/package.py | 7 ++++---
var/spack/repos/builtin/packages/r-magic/package.py | 7 ++++---
3 files changed, 12 insertions(+), 10 deletions(-)
diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py
index b67a06d9b5..96f623a096 100644
--- a/var/spack/repos/builtin/packages/r-abind/package.py
+++ b/var/spack/repos/builtin/packages/r-abind/package.py
@@ -32,13 +32,13 @@ class RAbind(Package):
'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"
+ 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"
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.source_path)
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ 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 924066e063..a09b458eaf 100644
--- a/var/spack/repos/builtin/packages/r-filehash/package.py
+++ b/var/spack/repos/builtin/packages/r-filehash/package.py
@@ -37,12 +37,13 @@ class RFilehash(Package):
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"
+ url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/filehash"
version('2.3', '01fffafe09b148ccadc9814c103bdc2f')
extends('R')
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' %
- self.module.r_lib_dir, '%s' % self.stage.source_path)
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ 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 31dab3b8af..f6ba97740b 100644
--- a/var/spack/repos/builtin/packages/r-magic/package.py
+++ b/var/spack/repos/builtin/packages/r-magic/package.py
@@ -32,7 +32,8 @@ class RMagic(Package):
arrays."""
homepage = "https://cran.r-project.org/"
- url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz"
+ 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"
version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029')
@@ -41,5 +42,5 @@ class RMagic(Package):
depends_on('r-abind')
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' %
- self.module.r_lib_dir, '%s' % self.stage.source_path)
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
--
cgit v1.2.3-70-g09d2
From 8970785d33e07105f47bca390d846127d7e5ce7b Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Mon, 13 Jun 2016 17:22:44 -0500
Subject: Add 'jdk' as a dependency.
Add jdk as a dependency so that R has support for java and allow
packages that need java to work.
---
var/spack/repos/builtin/packages/R/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index c7d8f89906..001dde5329 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -71,6 +71,7 @@ class R(Package):
depends_on('tk')
depends_on('curl')
depends_on('pcre')
+ depends_on('jdk')
def install(self, spec, prefix):
rlibdir = join_path(prefix, 'rlib')
--
cgit v1.2.3-70-g09d2