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

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