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To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org,
dev-commits-ports-main@FreeBSD.org
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Subject: git: 09167ae22b66 - main - biology/freebayes: Update to 1.3.6
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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