| 1 |
commit: e4dbb5c139e2c3dfe8a7d6eaa7f19a08da9b88b0 |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sat Sep 2 18:34:46 2017 +0000 |
| 4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sat Sep 2 18:35:42 2017 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4dbb5c1 |
| 7 |
|
| 8 |
sci-biology/pysam: Fix broken relative -I |
| 9 |
|
| 10 |
Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670 |
| 11 |
Package-Manager: Portage-2.3.8, Repoman-2.3.3 |
| 12 |
|
| 13 |
.../pysam/files/pysam-0.12-fix-buildsystem.patch | 63 ++++++++++++++++++++++ |
| 14 |
sci-biology/pysam/pysam-0.12.ebuild | 6 ++- |
| 15 |
2 files changed, 68 insertions(+), 1 deletion(-) |
| 16 |
|
| 17 |
diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch |
| 18 |
new file mode 100644 |
| 19 |
index 00000000000..8b323a63fba |
| 20 |
--- /dev/null |
| 21 |
+++ b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch |
| 22 |
@@ -0,0 +1,63 @@ |
| 23 |
+The build system is not designed with partial out-of-source |
| 24 |
+builds in mind. This is evident by using relative includes |
| 25 |
+such as '-Isamtools' instead of proper relative or absolute |
| 26 |
+paths. |
| 27 |
+ |
| 28 |
+Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670 |
| 29 |
+ |
| 30 |
+--- a/setup.py |
| 31 |
++++ b/setup.py |
| 32 |
+@@ -359,6 +359,8 @@ |
| 33 |
+ |
| 34 |
+ define_macros = [] |
| 35 |
+ |
| 36 |
++samtools_include_dirs = [os.path.abspath("samtools")] |
| 37 |
++ |
| 38 |
+ chtslib = Extension( |
| 39 |
+ "pysam.libchtslib", |
| 40 |
+ [source_pattern % "htslib", |
| 41 |
+@@ -385,7 +387,7 @@ |
| 42 |
+ htslib_sources + |
| 43 |
+ os_c_files, |
| 44 |
+ library_dirs=htslib_library_dirs, |
| 45 |
+- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, |
| 46 |
++ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, |
| 47 |
+ libraries=external_htslib_libraries + internal_htslib_libraries, |
| 48 |
+ language="c", |
| 49 |
+ extra_compile_args=extra_compile_args, |
| 50 |
+@@ -404,7 +406,7 @@ |
| 51 |
+ htslib_sources + |
| 52 |
+ os_c_files, |
| 53 |
+ library_dirs=htslib_library_dirs, |
| 54 |
+- include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs, |
| 55 |
++ include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs, |
| 56 |
+ libraries=external_htslib_libraries + internal_htslib_libraries, |
| 57 |
+ language="c", |
| 58 |
+ extra_compile_args=extra_compile_args, |
| 59 |
+@@ -423,7 +425,7 @@ |
| 60 |
+ htslib_sources + |
| 61 |
+ os_c_files, |
| 62 |
+ library_dirs=htslib_library_dirs, |
| 63 |
+- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, |
| 64 |
++ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, |
| 65 |
+ libraries=external_htslib_libraries + internal_htslib_libraries, |
| 66 |
+ language="c", |
| 67 |
+ extra_compile_args=extra_compile_args, |
| 68 |
+@@ -467,7 +469,7 @@ |
| 69 |
+ htslib_sources + |
| 70 |
+ os_c_files, |
| 71 |
+ library_dirs=["pysam"] + htslib_library_dirs, |
| 72 |
+- include_dirs=["samtools", "pysam", "."] + |
| 73 |
++ include_dirs=["pysam", "."] + samtools_include_dirs + |
| 74 |
+ include_os + htslib_include_dirs, |
| 75 |
+ libraries=external_htslib_libraries + internal_htslib_libraries, |
| 76 |
+ language="c", |
| 77 |
+@@ -482,7 +484,7 @@ |
| 78 |
+ htslib_sources + |
| 79 |
+ os_c_files, |
| 80 |
+ library_dirs=["pysam"] + htslib_library_dirs, |
| 81 |
+- include_dirs=["bcftools", "pysam", "."] + |
| 82 |
++ include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs + |
| 83 |
+ include_os + htslib_include_dirs, |
| 84 |
+ libraries=external_htslib_libraries + internal_htslib_libraries, |
| 85 |
+ language="c", |
| 86 |
|
| 87 |
diff --git a/sci-biology/pysam/pysam-0.12.ebuild b/sci-biology/pysam/pysam-0.12.ebuild |
| 88 |
index e181e06ac9b..1f4f58fdfe2 100644 |
| 89 |
--- a/sci-biology/pysam/pysam-0.12.ebuild |
| 90 |
+++ b/sci-biology/pysam/pysam-0.12.ebuild |
| 91 |
@@ -22,10 +22,14 @@ DEPEND="${RDEPEND} |
| 92 |
dev-python/cython[${PYTHON_USEDEP}] |
| 93 |
dev-python/setuptools[${PYTHON_USEDEP}]" |
| 94 |
|
| 95 |
+PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch ) |
| 96 |
+ |
| 97 |
python_prepare_all() { |
| 98 |
+ # unbundle htslib |
| 99 |
+ export HTSLIB_MODE="external" |
| 100 |
export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include |
| 101 |
export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) |
| 102 |
- export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl" |
| 103 |
+ rm -r htslib || die |
| 104 |
|
| 105 |
# prevent setup.py from adding RPATHs |
| 106 |
sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \ |
Archives