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authorGlenn Johnson <glenn-johnson@uiowa.edu>2020-02-13 19:47:37 -0600
committerGitHub <noreply@github.com>2020-02-13 19:47:37 -0600
commit725336ee48422be487747c08e0dff58f23a3b7ad (patch)
tree023e4b40b18b26f0bc54e6de6294da81d80bde1b /var
parent0d0ab601503c238986a49e0c764639044b393cfe (diff)
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Update and fix the r-rhtslib package (#14863)
This PR adds an updated version to the r-rhtslib package as well as fix the build. - add patches to use compiler flags from R - add variables for bzip2 and xz dependencies - use the spack Makeconf file when building the in-tree htslib - make patchelf available to allow R to remove reference to temporary installation directory in htslib shared object - Add new version of r-rsamtools as the r-rsamtools and r-rhtlib packages are closely paired.
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/r-rhtslib/find_deps-1.12.patch19
-rw-r--r--var/spack/repos/builtin/packages/r-rhtslib/find_deps-1.16.patch18
-rw-r--r--var/spack/repos/builtin/packages/r-rhtslib/package.py17
-rw-r--r--var/spack/repos/builtin/packages/r-rhtslib/use_spack_Makeconf.patch11
-rw-r--r--var/spack/repos/builtin/packages/r-rsamtools/package.py4
5 files changed, 68 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/find_deps-1.12.patch b/var/spack/repos/builtin/packages/r-rhtslib/find_deps-1.12.patch
new file mode 100644
index 0000000000..224eb5fdf8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rhtslib/find_deps-1.12.patch
@@ -0,0 +1,19 @@
+--- a/src/htslib-1.7/Makefile.Rhtslib 2020-02-08 17:12:30.000000000 -0600
++++ b/src/htslib-1.7/Makefile.Rhtslib 2020-02-08 19:08:45.969675431 -0600
+@@ -37,13 +37,13 @@
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+
+-CPPFLAGS =
++CPPFLAGS += $(BZIP2_INCLUDE) $(XZ_INCLUDE)
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+ # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+ #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
+-CFLAGS = -g -Wall -O2
++CFLAGS += -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS =
++LDFLAGS += $(BZIP2_LIB) $(XZ_LIB)
+ LIBS = $(htslib_default_libs)
+
+ prefix = /usr/local
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/find_deps-1.16.patch b/var/spack/repos/builtin/packages/r-rhtslib/find_deps-1.16.patch
new file mode 100644
index 0000000000..ae3ec24d2c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rhtslib/find_deps-1.16.patch
@@ -0,0 +1,18 @@
+--- a/src/htslib-1.7/Makefile.Rhtslib 2020-02-08 13:25:34.000000000 -0600
++++ b/src/htslib-1.7/Makefile.Rhtslib 2020-02-08 21:02:01.434363322 -0600
+@@ -37,13 +37,13 @@
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+
+-CPPFLAGS += -D_FILE_OFFSET_BITS=64
++CPPFLAGS += -D_FILE_OFFSET_BITS=64 $(BZIP2_INCLUDE) $(XZ_INCLUDE)
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+ # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+ #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
+ CFLAGS += -fpic
+ EXTRA_CFLAGS_PIC =
+-#LDFLAGS =
++LDFLAGS += $(BZIP2_LIB) $(XZ_LIB)
+ LIBS = $(htslib_default_libs)
+
+ prefix = /usr/local
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py
index 2ee01f0ac9..03539a56ba 100644
--- a/var/spack/repos/builtin/packages/r-rhtslib/package.py
+++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py
@@ -18,6 +18,7 @@ class RRhtslib(RPackage):
homepage = "https://bioconductor.org/packages/Rhtslib"
git = "https://git.bioconductor.org/packages/Rhtslib.git"
+ version('1.18.1', commit='751a2ebaed43b7991204b27bd6c7870645001d82')
version('1.16.3', commit='3ed0b5db2ee3cf0df1c6096fde8855c8485eebd4')
version('1.14.1', commit='4be260720f845a34d0ac838278fce1363f645230')
version('1.12.1', commit='e3487b1355995d09b28fde5d0a7504a3e79a7203')
@@ -30,3 +31,19 @@ class RRhtslib(RPackage):
depends_on('xz', type=('build', 'link', 'run'))
depends_on('curl', type=('build', 'link', 'run'))
depends_on('gmake', type='build')
+
+ # Some versions of this package will leave the temporary installation
+ # directory in the htslib shared object. R will fix this if patchelf is
+ # available
+ depends_on('patchelf', when='@1.12:1.14', type='build')
+
+ patch('use_spack_Makeconf.patch', when='@1.12:')
+ patch('find_deps-1.12.patch', when='@1.12:1.14')
+ patch('find_deps-1.16.patch', when='@1.16:')
+
+ @when('@1.12:')
+ def setup_build_environment(self, env):
+ env.set('BZIP2_INCLUDE', self.spec['bzip2'].headers.include_flags)
+ env.set('XZ_INCLUDE', self.spec['xz'].headers.include_flags)
+ env.set('BZIP2_LIB', self.spec['bzip2'].libs.search_flags)
+ env.set('XZ_LIB', self.spec['xz'].libs.search_flags)
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/use_spack_Makeconf.patch b/var/spack/repos/builtin/packages/r-rhtslib/use_spack_Makeconf.patch
new file mode 100644
index 0000000000..d8b8ef5acf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rhtslib/use_spack_Makeconf.patch
@@ -0,0 +1,11 @@
+--- a/src/Makevars.common 2020-02-08 17:12:30.000000000 -0600
++++ b/src/Makevars.common 2020-02-08 20:34:49.573031195 -0600
+@@ -3,7 +3,7 @@
+ INCLUDE_DIR=${R_PACKAGE_DIR}/include
+ USRLIB_DIR=${R_PACKAGE_DIR}/usrlib${R_ARCH}
+
+-R_ETC_MAKECONF=${R_HOME}/etc${R_ARCH}/Makeconf
++R_ETC_MAKECONF=${R_HOME}/etc${R_ARCH}/Makeconf.spack
+
+ ## Preprocessor options. Keep Rhtslib::pkgconfig() function (defined in
+ ## R/zzz.R) in sync with this.
diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py
index d988fbb9a8..d0046d5186 100644
--- a/var/spack/repos/builtin/packages/r-rsamtools/package.py
+++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py
@@ -18,6 +18,7 @@ class RRsamtools(RPackage):
homepage = "https://bioconductor.org/packages/Rsamtools"
git = "https://git.bioconductor.org/packages/Rsamtools.git"
+ version('2.2.1', commit='f10084658b4c9744961fcacd79c0ae9a7a40cd30')
version('2.0.3', commit='17d254cc026574d20db67474260944bf60befd70')
version('1.34.1', commit='0ec1d45c7a14b51d019c3e20c4aa87c6bd2b0d0c')
version('1.32.3', commit='0aa3f134143b045aa423894de81912becf64e4c2')
@@ -42,6 +43,7 @@ class RRsamtools(RPackage):
depends_on('r-iranges@2.13.12:', when='@1.32.3:', type=('build', 'run'))
depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run'))
- depends_on('r-rhtslib@1.16.3:', when='@2.0.3:', type=('build', 'run'))
+ depends_on('r-rhtslib@1.16.3', when='@2.0.3', type=('build', 'run'))
+ depends_on('r-rhtslib@1.17.7:', when='@2.2.1:', type=('build', 'run'))
depends_on('gmake', type='build')