Date: Sun, 6 Feb 2022 20:25:42 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 09167ae22b66 - main - biology/freebayes: Update to 1.3.6 Message-ID: <202202062025.216KPgDB083744@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=09167ae22b6631ec9a9d52fb66c3b177976d4c2c commit 09167ae22b6631ec9a9d52fb66c3b177976d4c2c Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2022-02-06 20:23:45 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2022-02-06 20:23:45 +0000 biology/freebayes: Update to 1.3.6 Minor dependency updates, but mostly build system improvements Changes: https://github.com/freebayes/freebayes/tags Reported by: portscout --- biology/freebayes/Makefile | 23 ++++++++++------------- biology/freebayes/distinfo | 30 +++++++++++++----------------- 2 files changed, 23 insertions(+), 30 deletions(-) diff --git a/biology/freebayes/Makefile b/biology/freebayes/Makefile index b3ba5491d42a..a30487d291b1 100644 --- a/biology/freebayes/Makefile +++ b/biology/freebayes/Makefile @@ -1,6 +1,6 @@ PORTNAME= freebayes DISTVERSIONPREFIX= v -DISTVERSION= 1.3.5 +DISTVERSION= 1.3.6 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -8,32 +8,29 @@ COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping LICENSE= MIT -# These should be rechecked: Same error resolved on aarch64 in 1.3.5 update. -BROKEN_armv6= fails to compile: invalid conversion between vector type and integer type - LIB_DEPENDS= libhts.so:biology/htslib \ libtabix.so:biology/tabixpp # Submodules use older versions than the ports, so we cannot safely unbundle # No shared libs are built by the submodules so there will be no conflicts +# Yes, there are actually 2 versions of intervaltree required USES= compiler:c++14-lang localbase meson perl5 pkgconfig USE_GITHUB= yes GH_ACCOUNT= ekg -GH_TUPLE= ekg:vcflib:d4073c3:vcflib/vcflib-temp \ - ekg:smithwaterman:2610e25:smithwaterman/vcflib/smithwaterman \ - ekg:multichoose:68733cd:multichoose/vcflib/multichoose \ +GH_TUPLE= ekg:intervaltree:b90527f:intervaltree/vcflib/intervaltree \ + ekg:vcflib:d4073c3:vcflib/vcflib-temp \ ekg:fastahack:bb33265:fastahack/vcflib/fastahack \ - ekg:intervaltree:17ddd57:intervaltree/vcflib/intervaltree \ - ekg:fsom:a6ef318:fsom/vcflib/fsom \ ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \ + ekg:fsom:a6ef318:fsom/vcflib/fsom \ google:googletest:d225acc:googletest/vcflib/googletest \ + ekg:intervaltree:17ddd57:intervaltree/vcflib/intervaltree \ edawson:libVCFH:615a06b:libVCFH/vcflib/libVCFH \ - simd-everywhere:simde-no-tests:2931676:simd/vcflib/src/simde \ - ekg:intervaltree:b90527f:intervaltree2/intervaltree \ + ekg:multichoose:68733cd:multichoose/vcflib/multichoose \ + ekg:smithwaterman:2610e25:smithwaterman/vcflib/smithwaterman \ ekg:tabixpp:b255df1:tabixpp/vcflib/tabixpp \ + simd-everywhere:simde-no-tests:2931676:simd/vcflib/src/simde \ ingydotnet:test-simple-bash:124673f:testsimplebash/test/test-simple-bash \ - illusori:bash-tap:c38fbfa:bashtap/test/bash-tap \ - samtools:htslib:b581944:htslib/contrib/htslib + illusori:bash-tap:c38fbfa:bashtap/test/bash-tap USE_PERL5= build LDFLAGS+= -lexecinfo diff --git a/biology/freebayes/distinfo b/biology/freebayes/distinfo index 1b22d3cb70ab..22a8193e42eb 100644 --- a/biology/freebayes/distinfo +++ b/biology/freebayes/distinfo @@ -1,33 +1,29 @@ -TIMESTAMP = 1635952798 -SHA256 (ekg-freebayes-v1.3.5_GH0.tar.gz) = af195a8c54b742d01af5a7e1fd1781a89290d726b310216c83e78c650d7aee49 -SIZE (ekg-freebayes-v1.3.5_GH0.tar.gz) = 2890213 +TIMESTAMP = 1644155282 +SHA256 (ekg-freebayes-v1.3.6_GH0.tar.gz) = d668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044 +SIZE (ekg-freebayes-v1.3.6_GH0.tar.gz) = 2898209 +SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1 +SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488 SHA256 (ekg-vcflib-d4073c3_GH0.tar.gz) = 27ed96714eeaa871b8036bcb308db5256b8266cadd2689fbd1dbf3771611b879 SIZE (ekg-vcflib-d4073c3_GH0.tar.gz) = 19215364 -SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce -SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160 -SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297 -SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 -SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1 -SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488 -SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b -SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686 SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070 SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053 +SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b +SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686 SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815 SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223 SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295 -SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63 -SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996 -SHA256 (ekg-intervaltree-b90527f_GH0.tar.gz) = 4d9272046972e595e4ac771fe6958b4c166a35e2ac727fc977fc4e0b9f8e887c -SIZE (ekg-intervaltree-b90527f_GH0.tar.gz) = 72540 +SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297 +SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558 +SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce +SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160 SHA256 (ekg-tabixpp-b255df1_GH0.tar.gz) = 96d9aa41f55f74498e267b582e93e986605913fbd830dca6bf4cac5d9f927bb9 SIZE (ekg-tabixpp-b255df1_GH0.tar.gz) = 3739 +SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63 +SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996 SHA256 (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 19b5c27402d955909fcbf601ed02bcd7d9f2aa841e2158ecd93b9ff8f7ec1d98 SIZE (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 6609 SHA256 (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5e658965f7c8730d7f29642ebb40b0e0beb701f992e391a1273af3b132ff66b8 SIZE (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5826 -SHA256 (samtools-htslib-b581944_GH0.tar.gz) = 940f0acd7037af262e15388eff9a6d696d03966fef1bae19d663130926c365f4 -SIZE (samtools-htslib-b581944_GH0.tar.gz) = 1501311
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