Date: Thu, 25 May 2023 09:44:07 GMT From: Robert Clausecker <fuz@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 41cce74a9e4c - main - biology/py-pysam: unbundle biology/htslib Message-ID: <202305250944.34P9i7rg001265@gitrepo.freebsd.org>
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The branch main has been updated by fuz: URL: https://cgit.FreeBSD.org/ports/commit/?id=41cce74a9e4c1727c4120517724059f68f27404f commit 41cce74a9e4c1727c4120517724059f68f27404f Author: Robert Clausecker <fuz@FreeBSD.org> AuthorDate: 2023-05-24 07:09:35 +0000 Commit: Robert Clausecker <fuz@FreeBSD.org> CommitDate: 2023-05-25 09:39:33 +0000 biology/py-pysam: unbundle biology/htslib This fixes the build on armv7 by picking up our custom fixed libhts over the bundled unfixed version. The CFLAGS workaround is now no longer required either. Approved by: yuri (maintainer) Differential Revision: https://reviews.freebsd.org/D40251 --- biology/py-pysam/Makefile | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile index 5cd1b27a49a0..10e1d55b786e 100644 --- a/biology/py-pysam/Makefile +++ b/biology/py-pysam/Makefile @@ -1,5 +1,6 @@ PORTNAME= pysam DISTVERSION= 0.20.0 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,12 +12,15 @@ WWW= https://github.com/pysam-developers/pysam LICENSE= MIT LICENSE_FILE= ${WRKSRC}/COPYING +LIB_DEPENDS= libhts.so:biology/htslib + USES= gmake python:3.6-3.9 USE_PYTHON= autoplist distutils cython cython_run pytest -CFLAGS+= -fPIC # workaround for https://github.com/pysam-developers/pysam/issues/1146 - BINARY_ALIAS= make=${GMAKE} +MAKE_ENV= HTSLIB_MODE=external \ + HTSLIB_LIBRARY_DIR=${LOCALBASE}/lib \ + HTSLIB_INCLUDE_DIR=${LOCALBASE}/include post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/lib*${PYTHON_EXT_SUFFIX}.so
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