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Bacon" Date: Wed, 20 Feb 2019 01:36:51 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r493402 - in head/biology/unanimity: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/unanimity: . files X-SVN-Commit-Revision: 493402 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 5187585E5A X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.98 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.98)[-0.977,0]; NEURAL_HAM_LONG(-1.00)[-0.999,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 20 Feb 2019 01:36:54 -0000 Author: jwb Date: Wed Feb 20 01:36:51 2019 New Revision: 493402 URL: https://svnweb.freebsd.org/changeset/ports/493402 Log: biology/unanimity: Upgrade to 3.4.0 Switch from cmake to new meson build system Tests disabled for now pending work on unbundling googletest Added: head/biology/unanimity/files/patch-meson.build (contents, props changed) head/biology/unanimity/files/patch-meson__options.txt (contents, props changed) head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp (contents, props changed) head/biology/unanimity/pkg-plist (contents, props changed) Deleted: head/biology/unanimity/files/patch-CMakeLists.txt head/biology/unanimity/files/patch-cmake_uny-config.cmake head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake head/biology/unanimity/files/patch-src_CMakeLists.txt Modified: head/biology/unanimity/Makefile head/biology/unanimity/distinfo Modified: head/biology/unanimity/Makefile ============================================================================== --- head/biology/unanimity/Makefile Wed Feb 20 00:50:37 2019 (r493401) +++ head/biology/unanimity/Makefile Wed Feb 20 01:36:51 2019 (r493402) @@ -2,8 +2,7 @@ PORTNAME= unanimity DISTVERSIONPREFIX= v -DISTVERSION= 3.1.0 -PORTREVISION= 2 +DISTVERSION= 3.4.0 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -14,30 +13,31 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_aarch64= fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? -# Sensitive to dependency versions, use latest commit for everything -BUILD_DEPENDS= pbseqan>=g20171002:biology/pbseqan \ - pbbam>=g20180416:biology/pbbam \ - pbcopper>=g20180413:biology/pbcopper +# Very sensitive to pbbam and pbcopper versions! +# Fully test new combinations and upgrade them together. +BUILD_DEPENDS= seqan>=2.4.0:biology/seqan \ + swig30>=3.0:devel/swig30 \ + ${PYNUMPY} LIB_DEPENDS= libhts.so:biology/htslib \ - libboost_regex.so:devel/boost-libs + libboost_regex.so:devel/boost-libs \ + libpbbam.so.0.18.0:biology/pbbam \ + libpbcopper.so.0.4.1:biology/pbcopper +RUN_DEPENDS= ${PYNUMPY} -USES= cmake:insource compiler:c++14-lang pkgconfig python +# Meson needs BOOST_ROOT=${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 -CMAKE_ARGS+= -DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \ - -DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \ - -DPacBioBAM_INCLUDE_DIRS:STRING=${LOCALBASE}/include/pbbam \ - -DPacBioBAM_LIBRARIES:STRING="-L${LOCALBASE}/lib -lpbbam" \ - -DSEQAN_INCLUDE_DIRS:STRING=${LOCALBASE}/include/PacBio \ - -Dpbcopper_INCLUDE_DIRS=${LOCALBASE}/include \ - -Dpbcopper_LIBRARIES="-L${LOCALBASE}/lib -lpbcopper" CFLAGS_i386= -msse2 -Wno-c++11-narrowing +LDFLAGS+= -lexecinfo -PLIST_FILES= bin/arrow bin/ccs bin/gcpp lib/libcc2.a lib/libunanimity.a - post-install: - ${INSTALL_DATA} ${WRKSRC}/src/libcc2.a ${WRKSRC}/src/libunanimity.a \ - ${STAGEDIR}${PREFIX}/lib + ${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \ + ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0 + ${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \ + ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3 .include Modified: head/biology/unanimity/distinfo ============================================================================== --- head/biology/unanimity/distinfo Wed Feb 20 00:50:37 2019 (r493401) +++ head/biology/unanimity/distinfo Wed Feb 20 01:36:51 2019 (r493402) @@ -1,3 +1,3 @@ -TIMESTAMP = 1534907295 -SHA256 (PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz) = 355866bd3f83bf1f7c322269c01d3c2f943e30942455741d6e802b0ad3f89912 -SIZE (PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz) = 6493202 +TIMESTAMP = 1550617512 +SHA256 (PacificBiosciences-unanimity-v3.4.0_GH0.tar.gz) = cb2fd361b2cae1196e710e4d0b8af3b03a7f09145f96ce8aa7d2aef2401ca8e0 +SIZE (PacificBiosciences-unanimity-v3.4.0_GH0.tar.gz) = 6493566 Added: head/biology/unanimity/files/patch-meson.build ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-meson.build Wed Feb 20 01:36:51 2019 (r493402) @@ -0,0 +1,11 @@ +--- meson.build.orig 2019-02-17 22:59:57 UTC ++++ meson.build +@@ -90,7 +90,7 @@ subdir('src') + + if (not meson.is_subproject()) and get_option('swig') + uny_python_interp = find_program(get_option('PYTHON'), required : true) +- uny_swig = find_program('swig', required : true) ++ uny_swig = find_program('swig3.0', required : true) + + uny_pv_ver = run_command(uny_python_interp, ['-c', 'import sys; sys.stdout.write(sys.version[:3])']).stdout() + message('Python version: ' + uny_pv_ver) Added: head/biology/unanimity/files/patch-meson__options.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-meson__options.txt Wed Feb 20 01:36:51 2019 (r493402) @@ -0,0 +1,8 @@ +--- meson_options.txt.orig 2019-02-17 22:53:47 UTC ++++ meson_options.txt +@@ -1,4 +1,4 @@ +-option('tests', type : 'boolean', value : true, description : 'Enable dependencies required for testing') ++option('tests', type : 'boolean', value : false, description : 'Enable dependencies required for testing') + + # python: + option('swig', type : 'boolean', value : true, description : 'Build UNANMITIY\'s SWIG interfacing code') Added: head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp Wed Feb 20 01:36:51 2019 (r493402) @@ -0,0 +1,9 @@ +--- src/variantCaller/variantCaller.cpp.orig 2019-02-17 23:15:10 UTC ++++ src/variantCaller/variantCaller.cpp +@@ -1,5 +1,6 @@ + // Author: David Seifert + ++#include + #include + #include + Added: head/biology/unanimity/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/unanimity/pkg-plist Wed Feb 20 01:36:51 2019 (r493402) @@ -0,0 +1,82 @@ +bin/ChimeraLabeler +bin/arrow +bin/ccs +bin/ccs_sim +bin/gcpp +bin/genomic_sim +bin/variantCaller +include/pacbio/UnanimityConfig.h +include/pacbio/UnanimityVersion.h +include/pacbio/align/AffineAlignment.h +include/pacbio/align/AlignConfig.h +include/pacbio/align/BandedAligner.h +include/pacbio/align/BandedChainAlignment.h +include/pacbio/align/ChainScorer.h +include/pacbio/align/ChainSeeds.h +include/pacbio/align/ChainSeedsConfig.h +include/pacbio/align/FilterSeeds.h +include/pacbio/align/FindSeeds.h +include/pacbio/align/FindSeedsConfig.h +include/pacbio/align/HomopolymerHasher.h +include/pacbio/align/LinearAlignment.h +include/pacbio/align/LocalAlignment.h +include/pacbio/align/PairwiseAlignment.h +include/pacbio/align/SeedScorer.h +include/pacbio/align/SparseAlignment.h +include/pacbio/align/internal/BCAlignBlocks.h +include/pacbio/align/internal/BCAlignImpl.h +include/pacbio/ccs/Consensus.h +include/pacbio/ccs/ConsensusSettings.h +include/pacbio/ccs/SparseAlignment.h +include/pacbio/ccs/Whitelist.h +include/pacbio/chimera/ChimeraLabel.h +include/pacbio/chimera/ChimeraLabeler.h +include/pacbio/chimera/ChimeraResultWriter.h +include/pacbio/consensus/AbstractMatrix.h +include/pacbio/consensus/Coverage.h +include/pacbio/consensus/EasyReadScorer.h +include/pacbio/consensus/Evaluator.h +include/pacbio/consensus/Integrator.h +include/pacbio/consensus/IntervalMask.h +include/pacbio/consensus/MatrixViewConvention.h +include/pacbio/consensus/ModelConfig.h +include/pacbio/consensus/ModelSelection.h +include/pacbio/consensus/Mutation.h +include/pacbio/consensus/Polish.h +include/pacbio/consensus/PolishResult.h +include/pacbio/consensus/Template.h +include/pacbio/consensus/internal/ModelInternalInitializer.h +include/pacbio/data/ChemistryMapping.h +include/pacbio/data/ChemistryTriple.h +include/pacbio/data/Interval.h +include/pacbio/data/IntervalTree.h +include/pacbio/data/PlainOption.h +include/pacbio/data/Read.h +include/pacbio/data/ReadId.h +include/pacbio/data/Sequence.h +include/pacbio/data/State.h +include/pacbio/data/StrandType.h +include/pacbio/data/SubreadResultCounter.h +include/pacbio/data/internal/BaseEncoding.h +include/pacbio/data/internal/ConversionFunctions.h +include/pacbio/denovo/PoaConsensus.h +include/pacbio/denovo/PoaGraph.h +include/pacbio/denovo/RangeFinder.h +include/pacbio/denovo/SparsePoa.h +include/pacbio/exception/CCSExceptions.h +include/pacbio/exception/InvalidEvaluatorException.h +include/pacbio/exception/ModelError.h +include/pacbio/exception/StateError.h +include/pacbio/io/Utility.h +include/pacbio/parallel/WorkQueue.h +include/pacbio/util/ExecUtils.h +include/pacbio/util/Timer.h +lib/libunanimity.so +lib/libunanimity.so.3 +lib/libunanimity.so.3.0 +lib/libunanimity.so.3.0.0 +%%PYTHON_SITELIBDIR%%/ConsensusCore2.py +%%PYTHON_SITELIBDIR%%/ConsensusCore2.pyc +%%PYTHON_SITELIBDIR%%/ConsensusCore2.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/_ConsensusCore2.so +libdata/pkgconfig/unanimity.pc