commit: e4dbb5c139e2c3dfe8a7d6eaa7f19a08da9b88b0 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Sep 2 18:34:46 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Sep 2 18:35:42 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4dbb5c1
sci-biology/pysam: Fix broken relative -I Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670 Package-Manager: Portage-2.3.8, Repoman-2.3.3 .../pysam/files/pysam-0.12-fix-buildsystem.patch | 63 ++++++++++++++++++++++ sci-biology/pysam/pysam-0.12.ebuild | 6 ++- 2 files changed, 68 insertions(+), 1 deletion(-) diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch new file mode 100644 index 00000000000..8b323a63fba --- /dev/null +++ b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch @@ -0,0 +1,63 @@ +The build system is not designed with partial out-of-source +builds in mind. This is evident by using relative includes +such as '-Isamtools' instead of proper relative or absolute +paths. + +Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670 + +--- a/setup.py ++++ b/setup.py +@@ -359,6 +359,8 @@ + + define_macros = [] + ++samtools_include_dirs = [os.path.abspath("samtools")] ++ + chtslib = Extension( + "pysam.libchtslib", + [source_pattern % "htslib", +@@ -385,7 +387,7 @@ + htslib_sources + + os_c_files, + library_dirs=htslib_library_dirs, +- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, ++ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", + extra_compile_args=extra_compile_args, +@@ -404,7 +406,7 @@ + htslib_sources + + os_c_files, + library_dirs=htslib_library_dirs, +- include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs, ++ include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", + extra_compile_args=extra_compile_args, +@@ -423,7 +425,7 @@ + htslib_sources + + os_c_files, + library_dirs=htslib_library_dirs, +- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, ++ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", + extra_compile_args=extra_compile_args, +@@ -467,7 +469,7 @@ + htslib_sources + + os_c_files, + library_dirs=["pysam"] + htslib_library_dirs, +- include_dirs=["samtools", "pysam", "."] + ++ include_dirs=["pysam", "."] + samtools_include_dirs + + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", +@@ -482,7 +484,7 @@ + htslib_sources + + os_c_files, + library_dirs=["pysam"] + htslib_library_dirs, +- include_dirs=["bcftools", "pysam", "."] + ++ include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs + + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", diff --git a/sci-biology/pysam/pysam-0.12.ebuild b/sci-biology/pysam/pysam-0.12.ebuild index e181e06ac9b..1f4f58fdfe2 100644 --- a/sci-biology/pysam/pysam-0.12.ebuild +++ b/sci-biology/pysam/pysam-0.12.ebuild @@ -22,10 +22,14 @@ DEPEND="${RDEPEND} dev-python/cython[${PYTHON_USEDEP}] dev-python/setuptools[${PYTHON_USEDEP}]" +PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch ) + python_prepare_all() { + # unbundle htslib + export HTSLIB_MODE="external" export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) - export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl" + rm -r htslib || die # prevent setup.py from adding RPATHs sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
