diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
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committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/pysam/files |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/pysam/files')
-rw-r--r-- | sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch | 63 |
1 files changed, 63 insertions, 0 deletions
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 000000000000..8b323a63fba5 --- /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", |