Date: Sat, 2 Mar 2024 20:36:07 GMT From: Nuno Teixeira <eduardo@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 44f5f66effbc - main - biology/vcflib: Move man pages to share/man Message-ID: <202403022036.422Ka7ec025566@gitrepo.freebsd.org>
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The branch main has been updated by eduardo: URL: https://cgit.FreeBSD.org/ports/commit/?id=44f5f66effbcd759bce03421231713a9b7c0e170 commit 44f5f66effbcd759bce03421231713a9b7c0e170 Author: Nuno Teixeira <eduardo@FreeBSD.org> AuthorDate: 2024-03-02 20:20:37 +0000 Commit: Nuno Teixeira <eduardo@FreeBSD.org> CommitDate: 2024-03-02 20:35:56 +0000 biology/vcflib: Move man pages to share/man Approved by: portmgr (blanket) --- biology/vcflib/Makefile | 1 + biology/vcflib/files/patch-CMakeLists.txt | 12 +- biology/vcflib/pkg-plist | 178 +++++++++++++++--------------- 3 files changed, 99 insertions(+), 92 deletions(-) diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index 26105d1a65ba..7adcd1d6051d 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,6 +1,7 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v DISTVERSION= 1.0.7 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt index 263e3dbee0f9..4203916395af 100644 --- a/biology/vcflib/files/patch-CMakeLists.txt +++ b/biology/vcflib/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2023-01-29 04:57:02 UTC +--- CMakeLists.txt.orig 2023-02-07 17:22:46 UTC +++ CMakeLists.txt -@@ -9,7 +9,7 @@ +@@ -9,7 +9,7 @@ project(vcflib) cmake_minimum_required(VERSION 3.16) project(vcflib) @@ -9,7 +9,7 @@ include(ExternalProject) include(FeatureSummary) -@@ -69,7 +69,7 @@ if(NOT CMAKE_BUILD_TYPE) +@@ -69,7 +69,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release) endif() if (${CMAKE_BUILD_TYPE} MATCHES Release) @@ -18,3 +18,9 @@ # set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast endif() +@@ -570,4 +570,4 @@ install(FILES ${INCLUDES} DESTINATION include) + + install(FILES ${INCLUDES} DESTINATION include) + +-install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1) ++install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1) diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index 297ee6aaa750..b612a8ab875b 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -159,92 +159,92 @@ include/veclib_types.h lib/libvcflib.a %%ZIG%%lib/libzig.a lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so -man/man1/abba-baba.1.gz -man/man1/bFst.1.gz -man/man1/dumpContigsFromHeader.1.gz -man/man1/genotypeSummary.1.gz -man/man1/hapLrt.1.gz -man/man1/iHS.1.gz -man/man1/meltEHH.1.gz -man/man1/normalize-iHS.1.gz -man/man1/pFst.1.gz -man/man1/pVst.1.gz -man/man1/permuteGPAT++.1.gz -man/man1/permuteSmooth.1.gz -man/man1/plotHaps.1.gz -man/man1/popStats.1.gz -man/man1/pyvcflib.1.gz -man/man1/segmentFst.1.gz -man/man1/segmentIhs.1.gz -man/man1/sequenceDiversity.1.gz -man/man1/smoother.1.gz -man/man1/vcf2dag.1.gz -man/man1/vcf2fasta.1.gz -man/man1/vcf2tsv.1.gz -man/man1/vcfaddinfo.1.gz -man/man1/vcfafpath.1.gz -man/man1/vcfallelicprimitives.1.gz -man/man1/vcfaltcount.1.gz -man/man1/vcfannotate.1.gz -man/man1/vcfannotategenotypes.1.gz -man/man1/vcfbreakmulti.1.gz -man/man1/vcfcat.1.gz -man/man1/vcfcheck.1.gz -man/man1/vcfclassify.1.gz -man/man1/vcfcleancomplex.1.gz -man/man1/vcfcombine.1.gz -man/man1/vcfcommonsamples.1.gz -man/man1/vcfcountalleles.1.gz -man/man1/vcfcreatemulti.1.gz -man/man1/vcfdistance.1.gz -man/man1/vcfecho.1.gz -man/man1/vcfentropy.1.gz -man/man1/vcfevenregions.1.gz -man/man1/vcffilter.1.gz -man/man1/vcffixup.1.gz -man/man1/vcfflatten.1.gz -man/man1/vcfgeno2alleles.1.gz -man/man1/vcfgeno2haplo.1.gz -man/man1/vcfgenosamplenames.1.gz -man/man1/vcfgenosummarize.1.gz -man/man1/vcfgenotypecompare.1.gz -man/man1/vcfgenotypes.1.gz -man/man1/vcfglbound.1.gz -man/man1/vcfglxgt.1.gz -man/man1/vcfhetcount.1.gz -man/man1/vcfhethomratio.1.gz -man/man1/vcfindex.1.gz -man/man1/vcfinfo2qual.1.gz -man/man1/vcfinfosummarize.1.gz -man/man1/vcfintersect.1.gz -man/man1/vcfkeepgeno.1.gz -man/man1/vcfkeepinfo.1.gz -man/man1/vcfkeepsamples.1.gz -man/man1/vcfld.1.gz -man/man1/vcfleftalign.1.gz -man/man1/vcflength.1.gz -man/man1/vcflib-api.1.gz -man/man1/vcflib.1.gz -man/man1/vcfnulldotslashdot.1.gz -man/man1/vcfnullgenofields.1.gz -man/man1/vcfnumalt.1.gz -man/man1/vcfoverlay.1.gz -man/man1/vcfparsealts.1.gz -man/man1/vcfprimers.1.gz -man/man1/vcfqual2info.1.gz -man/man1/vcfrandom.1.gz -man/man1/vcfrandomsample.1.gz -man/man1/vcfremap.1.gz -man/man1/vcfremoveaberrantgenotypes.1.gz -man/man1/vcfremovesamples.1.gz -man/man1/vcfroc.1.gz -man/man1/vcfsample2info.1.gz -man/man1/vcfsamplediff.1.gz -man/man1/vcfsamplenames.1.gz -man/man1/vcfsitesummarize.1.gz -man/man1/vcfstats.1.gz -man/man1/vcfstreamsort.1.gz -man/man1/vcfuniq.1.gz -man/man1/vcfuniqalleles.1.gz -man/man1/vcfwave.1.gz -man/man1/wcFst.1.gz +share/man/man1/abba-baba.1.gz +share/man/man1/bFst.1.gz +share/man/man1/dumpContigsFromHeader.1.gz +share/man/man1/genotypeSummary.1.gz +share/man/man1/hapLrt.1.gz +share/man/man1/iHS.1.gz +share/man/man1/meltEHH.1.gz +share/man/man1/normalize-iHS.1.gz +share/man/man1/pFst.1.gz +share/man/man1/pVst.1.gz +share/man/man1/permuteGPAT++.1.gz +share/man/man1/permuteSmooth.1.gz +share/man/man1/plotHaps.1.gz +share/man/man1/popStats.1.gz +share/man/man1/pyvcflib.1.gz +share/man/man1/segmentFst.1.gz +share/man/man1/segmentIhs.1.gz +share/man/man1/sequenceDiversity.1.gz +share/man/man1/smoother.1.gz +share/man/man1/vcf2dag.1.gz +share/man/man1/vcf2fasta.1.gz +share/man/man1/vcf2tsv.1.gz +share/man/man1/vcfaddinfo.1.gz +share/man/man1/vcfafpath.1.gz +share/man/man1/vcfallelicprimitives.1.gz +share/man/man1/vcfaltcount.1.gz +share/man/man1/vcfannotate.1.gz +share/man/man1/vcfannotategenotypes.1.gz +share/man/man1/vcfbreakmulti.1.gz +share/man/man1/vcfcat.1.gz +share/man/man1/vcfcheck.1.gz +share/man/man1/vcfclassify.1.gz +share/man/man1/vcfcleancomplex.1.gz +share/man/man1/vcfcombine.1.gz +share/man/man1/vcfcommonsamples.1.gz +share/man/man1/vcfcountalleles.1.gz +share/man/man1/vcfcreatemulti.1.gz +share/man/man1/vcfdistance.1.gz +share/man/man1/vcfecho.1.gz +share/man/man1/vcfentropy.1.gz +share/man/man1/vcfevenregions.1.gz +share/man/man1/vcffilter.1.gz +share/man/man1/vcffixup.1.gz +share/man/man1/vcfflatten.1.gz +share/man/man1/vcfgeno2alleles.1.gz +share/man/man1/vcfgeno2haplo.1.gz +share/man/man1/vcfgenosamplenames.1.gz +share/man/man1/vcfgenosummarize.1.gz +share/man/man1/vcfgenotypecompare.1.gz +share/man/man1/vcfgenotypes.1.gz +share/man/man1/vcfglbound.1.gz +share/man/man1/vcfglxgt.1.gz +share/man/man1/vcfhetcount.1.gz +share/man/man1/vcfhethomratio.1.gz +share/man/man1/vcfindex.1.gz +share/man/man1/vcfinfo2qual.1.gz +share/man/man1/vcfinfosummarize.1.gz +share/man/man1/vcfintersect.1.gz +share/man/man1/vcfkeepgeno.1.gz +share/man/man1/vcfkeepinfo.1.gz +share/man/man1/vcfkeepsamples.1.gz +share/man/man1/vcfld.1.gz +share/man/man1/vcfleftalign.1.gz +share/man/man1/vcflength.1.gz +share/man/man1/vcflib-api.1.gz +share/man/man1/vcflib.1.gz +share/man/man1/vcfnulldotslashdot.1.gz +share/man/man1/vcfnullgenofields.1.gz +share/man/man1/vcfnumalt.1.gz +share/man/man1/vcfoverlay.1.gz +share/man/man1/vcfparsealts.1.gz +share/man/man1/vcfprimers.1.gz +share/man/man1/vcfqual2info.1.gz +share/man/man1/vcfrandom.1.gz +share/man/man1/vcfrandomsample.1.gz +share/man/man1/vcfremap.1.gz +share/man/man1/vcfremoveaberrantgenotypes.1.gz +share/man/man1/vcfremovesamples.1.gz +share/man/man1/vcfroc.1.gz +share/man/man1/vcfsample2info.1.gz +share/man/man1/vcfsamplediff.1.gz +share/man/man1/vcfsamplenames.1.gz +share/man/man1/vcfsitesummarize.1.gz +share/man/man1/vcfstats.1.gz +share/man/man1/vcfstreamsort.1.gz +share/man/man1/vcfuniq.1.gz +share/man/man1/vcfuniqalleles.1.gz +share/man/man1/vcfwave.1.gz +share/man/man1/wcFst.1.gz
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