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

@@ -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')

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('bioc-3.3',
-
+            git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
-    version('0.18.0', 'baaff00eb2c2b15396fed2f7f43e634c', expand=False)
+            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)

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)

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)

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)