Date: Tue, 19 Feb 2019 23:03:41 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r493399 - in head/biology/pbbam: . files Message-ID: <201902192303.x1JN3fVr065061@repo.freebsd.org>
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Author: jwb Date: Tue Feb 19 23:03:41 2019 New Revision: 493399 URL: https://svnweb.freebsd.org/changeset/ports/493399 Log: biology/pbbam: Upgrade to 0.18.0 release In preparation for unanimity upgrade Added: head/biology/pbbam/files/ head/biology/pbbam/files/patch-meson__options.txt (contents, props changed) Modified: head/biology/pbbam/Makefile head/biology/pbbam/distinfo head/biology/pbbam/pkg-plist Modified: head/biology/pbbam/Makefile ============================================================================== --- head/biology/pbbam/Makefile Tue Feb 19 22:52:11 2019 (r493398) +++ head/biology/pbbam/Makefile Tue Feb 19 23:03:41 2019 (r493399) @@ -1,8 +1,7 @@ # $FreeBSD$ PORTNAME= pbbam -DISTVERSION= g20180416 -PORTREVISION= 3 +DISTVERSION= 0.18.0 # Test with biology/unanimity before upgrading! CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -11,26 +10,24 @@ COMMENT= PacBio BAM C++ library, with SWIG bindings LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt -BUILD_DEPENDS= boost-libs>=1.60.0:devel/boost-libs LIB_DEPENDS= libhts.so:biology/htslib \ libboost_regex.so:devel/boost-libs -USES= cmake compiler:c++14-lang pkgconfig +# Meson needs BOOST_ROOT=${LOCALBASE} +# https://github.com/mesonbuild/meson/issues/2239 +USES= compiler:c++14-lang localbase meson pkgconfig python +USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= PacificBiosciences -GH_TAGNAME= c6b8113adb5104948879e9ff69f739121f12a09f -# Disable tests for now. Bound to bundled googletest. -CMAKE_ARGS+= -DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \ - -DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \ - -DPacBioBAM_build_tests:BOOL=OFF \ - -DPacBioBAM_build_docs:BOOL=OFF +pre-configure: + @${REINPLACE_CMD} -e "s|'python'|'${PYTHON_VERSION}'|g" \ + ${WRKSRC}/meson.build -do-install: - ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin - ${INSTALL_DATA} ${BUILD_WRKSRC}/lib/* ${STAGEDIR}${PREFIX}/lib - cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include - ${MV} ${STAGEDIR}${PREFIX}/include/meson.build \ - ${STAGEDIR}${PREFIX}/include/pbbam +post-install: + ${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \ + ${STAGEDIR}${PREFIX}/lib/libpbbam.so.0.18 + ${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \ + ${STAGEDIR}${PREFIX}/lib/libpbbam.so.0 .include <bsd.port.mk> Modified: head/biology/pbbam/distinfo ============================================================================== --- head/biology/pbbam/distinfo Tue Feb 19 22:52:11 2019 (r493398) +++ head/biology/pbbam/distinfo Tue Feb 19 23:03:41 2019 (r493399) @@ -1,3 +1,3 @@ -TIMESTAMP = 1524331626 -SHA256 (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = f7ede42417110db4fcc3fbc4b837911a0e2242e541a88c8ac34b4c26b4e5aad4 -SIZE (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = 8105156 +TIMESTAMP = 1550453627 +SHA256 (PacificBiosciences-pbbam-0.18.0_GH0.tar.gz) = 45286e5f7deb7ff629e0643c8a416155915aec7b85d54c60b5cdc07f4d7b234a +SIZE (PacificBiosciences-pbbam-0.18.0_GH0.tar.gz) = 8136503 Added: head/biology/pbbam/files/patch-meson__options.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/pbbam/files/patch-meson__options.txt Tue Feb 19 23:03:41 2019 (r493399) @@ -0,0 +1,11 @@ +--- meson_options.txt.orig 2019-02-17 01:55:33 UTC ++++ meson_options.txt +@@ -15,7 +15,7 @@ option('auto-validate', + + option('tests', + type : 'boolean', +- value : true, ++ value : false, + description : 'Enable dependencies required for testing') + + option('permissive-cigar', Modified: head/biology/pbbam/pkg-plist ============================================================================== --- head/biology/pbbam/pkg-plist Tue Feb 19 22:52:11 2019 (r493398) +++ head/biology/pbbam/pkg-plist Tue Feb 19 23:03:41 2019 (r493399) @@ -118,7 +118,19 @@ include/pbbam/internal/ReadGroupInfo.inl include/pbbam/internal/SequenceInfo.inl include/pbbam/internal/Tag.inl include/pbbam/internal/Validator.inl -include/pbbam/meson.build +include/pbbam/vcf/VcfFile.h +include/pbbam/vcf/VcfFormat.h +include/pbbam/vcf/VcfHeader.h +include/pbbam/vcf/VcfHeaderTypes.h +include/pbbam/vcf/VcfQuery.h +include/pbbam/vcf/VcfReader.h +include/pbbam/vcf/VcfSort.h +include/pbbam/vcf/VcfVariant.h +include/pbbam/vcf/VcfWriter.h +include/pbbam/vcf/internal/VcfFile.inl +include/pbbam/vcf/internal/VcfHeader.inl +include/pbbam/vcf/internal/VcfHeaderTypes.inl +include/pbbam/vcf/internal/VcfVariant.inl include/pbbam/virtual/VirtualPolymeraseBamRecord.h include/pbbam/virtual/VirtualPolymeraseCompositeReader.h include/pbbam/virtual/VirtualPolymeraseReader.h @@ -129,4 +141,8 @@ include/pbbam/virtual/VirtualZmwBamRecord.h include/pbbam/virtual/WhitelistedZmwReadStitcher.h include/pbbam/virtual/ZmwReadStitcher.h include/pbbam/virtual/ZmwWhitelistVirtualReader.h -lib/libpbbam.a +lib/libpbbam.so +lib/libpbbam.so.0 +lib/libpbbam.so.0.18 +lib/libpbbam.so.0.18.0 +libdata/pkgconfig/pbbam.pc
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