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-rw-r--r--biology/bifrost/Makefile13
-rw-r--r--biology/bifrost/files/patch-CMakeLists.txt4
-rw-r--r--biology/hyphy/Makefile2
-rw-r--r--biology/hyphy/distinfo6
-rw-r--r--biology/hyphy/pkg-plist9
-rw-r--r--biology/kallisto/Makefile12
-rw-r--r--biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt13
-rw-r--r--biology/paml/Makefile3
-rw-r--r--biology/paml/distinfo6
-rw-r--r--biology/paml/files/patch-src_Makefile15
-rw-r--r--biology/paml/pkg-plist2
-rw-r--r--biology/vcftools/Makefile8
-rw-r--r--biology/vcftools/distinfo6
13 files changed, 63 insertions, 36 deletions
diff --git a/biology/bifrost/Makefile b/biology/bifrost/Makefile
index 8820ddfa0631..082d27df32e6 100644
--- a/biology/bifrost/Makefile
+++ b/biology/bifrost/Makefile
@@ -18,6 +18,17 @@ USE_GITHUB= yes
CMAKE_ARGS= -DCOMPILATION_ARCH=${CPUTYPE:UOFF}
+CXXFLAGS+= -Wno-unqualified-std-cast-call
+
GH_ACCOUNT= pmelsted
-.include <bsd.port.mk>
+.include <bsd.port.pre.mk>
+
+# Build fails with clang19, but succeeds with gcc13
+# Have not figured out where this sz_link member is even supposed to come from
+# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>'
+.if ${OSVERSION} > 1500000
+USE_GCC= yes
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/biology/bifrost/files/patch-CMakeLists.txt b/biology/bifrost/files/patch-CMakeLists.txt
index 27893b9ec44d..4d49c5a270cc 100644
--- a/biology/bifrost/files/patch-CMakeLists.txt
+++ b/biology/bifrost/files/patch-CMakeLists.txt
@@ -1,6 +1,6 @@
---- CMakeLists.txt.orig 2023-08-12 14:26:29 UTC
+--- CMakeLists.txt.orig 2024-03-15 15:20:17 UTC
+++ CMakeLists.txt
-@@ -46,7 +46,6 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
+@@ -56,7 +56,6 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
set(CMAKE_EXE_LINKER_FLAGS "-pg")
else(CMAKE_BUILD_TYPE MATCHES Profile)
message("Build type: Release")
diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index 55476ed67c9b..f281649f9c47 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,5 +1,5 @@
PORTNAME= hyphy
-DISTVERSION= 2.5.70
+DISTVERSION= 2.5.73
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
index 7b906e8bb328..ae85017d004d 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1742777609
-SHA256 (veg-hyphy-2.5.70_GH0.tar.gz) = 38c2549dcaec9f7df63b5e3aab965794484edc11a221fa0c0d909f7c68614de3
-SIZE (veg-hyphy-2.5.70_GH0.tar.gz) = 5617978
+TIMESTAMP = 1747240205
+SHA256 (veg-hyphy-2.5.73_GH0.tar.gz) = efc64adb9f270aa6c284dbee22a16132f4e59126e9df071c5267cd79e2883969
+SIZE (veg-hyphy-2.5.73_GH0.tar.gz) = 4161304
diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist
index 2f58e0cb50d2..cea5332c2742 100644
--- a/biology/hyphy/pkg-plist
+++ b/biology/hyphy/pkg-plist
@@ -11,6 +11,7 @@ bin/hyphy
%%DATADIR%%/GeneticCodes/Thraustochytrium_mtDNA.cod
%%DATADIR%%/GeneticCodes/Vertebratemtdna.cod
%%DATADIR%%/GeneticCodes/Yeast_mtDNA.cod
+%%DATADIR%%/README.md
%%DATADIR%%/SubstitutionClasses/AAEFV/Equal
%%DATADIR%%/SubstitutionClasses/AAEFV/Estimated
%%DATADIR%%/SubstitutionClasses/AAEFV/Observed In Data Set
@@ -177,6 +178,7 @@ bin/hyphy
%%DATADIR%%/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf
%%DATADIR%%/TemplateBatchFiles/Samplers/srs.ibf
%%DATADIR%%/TemplateBatchFiles/SandNSAmbigs.bf
+%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BUSTED-PH.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FADE.bf
@@ -333,7 +335,6 @@ bin/hyphy
%%DATADIR%%/TemplateBatchFiles/Utility/BranchLengthFitters.bf
%%DATADIR%%/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
%%DATADIR%%/TemplateBatchFiles/Utility/CodonTools.bf
-%%DATADIR%%/TemplateBatchFiles/Utility/DBTools.ibf
%%DATADIR%%/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
%%DATADIR%%/TemplateBatchFiles/Utility/GrabBag.bf
%%DATADIR%%/TemplateBatchFiles/Utility/HXB2Mapper.bf
@@ -371,6 +372,10 @@ bin/hyphy
%%DATADIR%%/TemplateBatchFiles/globalChecker.ibf
%%DATADIR%%/TemplateBatchFiles/heuristicMethodNPBootstrap.bf
%%DATADIR%%/TemplateBatchFiles/last.date
+%%DATADIR%%/TemplateBatchFiles/lib/label-tree.bf
+%%DATADIR%%/TemplateBatchFiles/lib/remove-duplicates.bf
+%%DATADIR%%/TemplateBatchFiles/lib/trim-label-tree.bf
+%%DATADIR%%/TemplateBatchFiles/lib/trim-tree.bf
%%DATADIR%%/TemplateBatchFiles/libv3/IOFunctions.bf
%%DATADIR%%/TemplateBatchFiles/libv3/UtilityFunctions.bf
%%DATADIR%%/TemplateBatchFiles/libv3/all-terms.bf
@@ -393,6 +398,7 @@ bin/hyphy
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf
+%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES_BSREL.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MSS.bf
%%DATADIR%%/TemplateBatchFiles/libv3/models/frequencies.bf
@@ -421,6 +427,7 @@ bin/hyphy
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/mpi.bf
%%DATADIR%%/TemplateBatchFiles/libv3/tasks/trees.bf
%%DATADIR%%/TemplateBatchFiles/molclockBootstrap.bf
+%%DATADIR%%/TemplateBatchFiles/molerate.bf
%%DATADIR%%/TemplateBatchFiles/pairwiseDistanceEstimator.ibf
%%DATADIR%%/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf
%%DATADIR%%/TemplateBatchFiles/partitionSequences.ibf
diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 91193aa7facc..c2d33ef3ce82 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -37,12 +37,22 @@ CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON
# WIP: Remove before committing
CMAKE_ARGS+= -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
MAKE_JOBS_UNSAFE= yes
+CXXFLAGS+= -Wno-unqualified-std-cast-call
LDFLAGS+= -lhts -lz
OPTIONS_DEFINE= EXAMPLES
+.include <bsd.port.pre.mk>
+
+# Build fails with clang19, but succeeds with gcc13
+# Have not figured out where this sz_link member is even supposed to come from
+# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>'
+.if ${OSVERSION} > 1500000
+USE_GCC= yes
+.endif
+
post-install-EXAMPLES-on:
${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
index d25cf028cfdd..c662b37881c9 100644
--- a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
+++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
@@ -1,8 +1,8 @@
---- ext/bifrost/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC
+--- ext/bifrost/CMakeLists.txt.orig 2024-09-17 05:40:08 UTC
+++ ext/bifrost/CMakeLists.txt
-@@ -7,18 +7,12 @@ find_package(Threads REQUIRED)
+@@ -6,18 +6,12 @@ SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX
+
# To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.
- SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE")
SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE")
-# Enable architecture optimizations
-SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
@@ -12,7 +12,8 @@
# Set some default compile flags
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11")
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wno-unqualified-std-cast-call")
-set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops")
-
@@ -20,7 +21,7 @@
#check if we are on arm64 and apple, if so, disable AVX2
if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
message("Disabling AVX2 instructions on arm64")
-@@ -30,8 +24,6 @@ if(COMPILATION_ARCH MATCHES "OFF")
+@@ -29,8 +23,6 @@ else(COMPILATION_ARCH MATCHES "OFF")
message("Disabling native architecture compilation (including AVX2)")
else(COMPILATION_ARCH MATCHES "OFF")
message("Compilation architecture: ${COMPILATION_ARCH}")
@@ -29,7 +30,7 @@
endif(COMPILATION_ARCH MATCHES "OFF")
if(ENABLE_AVX2 MATCHES "OFF")
-@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
+@@ -55,7 +47,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
set(CMAKE_EXE_LINKER_FLAGS "-pg")
else(CMAKE_BUILD_TYPE MATCHES Profile)
message("Build type: Release")
diff --git a/biology/paml/Makefile b/biology/paml/Makefile
index 7ba18e506f72..4a6375689d5e 100644
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@@ -1,5 +1,6 @@
PORTNAME= paml
-DISTVERSION= 4.10.7
+DISTVERSIONPREFIX= v
+DISTVERSION= 4.10.9
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org
diff --git a/biology/paml/distinfo b/biology/paml/distinfo
index cd64f0e34127..7dd47591a370 100644
--- a/biology/paml/distinfo
+++ b/biology/paml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1688759942
-SHA256 (abacus-gene-paml-4.10.7_GH0.tar.gz) = 0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3
-SIZE (abacus-gene-paml-4.10.7_GH0.tar.gz) = 5250841
+TIMESTAMP = 1747232666
+SHA256 (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 19ca9d484d729324748b9c86453e4c8f4a1fa79ad6fa3ac7cdbfaa7d0bfb8c22
+SIZE (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 3920159
diff --git a/biology/paml/files/patch-src_Makefile b/biology/paml/files/patch-src_Makefile
index 4a9bd7ed2da6..1fd048a0594b 100644
--- a/biology/paml/files/patch-src_Makefile
+++ b/biology/paml/files/patch-src_Makefile
@@ -1,10 +1,11 @@
---- src/Makefile.orig 2023-07-08 03:40:50 UTC
+--- src/Makefile.orig 2025-05-14 14:29:51 UTC
+++ src/Makefile
-@@ -1,6 +1,6 @@ CC = cc # cc, gcc, cl
+@@ -1,6 +1,6 @@ PRGS = baseml codeml basemlg mcmctree pamp evolver yn
PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2
- CC = cc # cc, gcc, cl
--CFLAGS = -O3 -Wall -Wno-unused-result -Wmemset-elt-size
-+CFLAGS = -O3 -Wall -Wno-unused-result
- #CC = icc
- #CFLAGS = -fast -Wall
+-CC = gcc
+-CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result
++#CC = gcc
++#CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result
+
+ LIBS = -lm
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
index 544b761367c3..02f053d2563e 100644
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@@ -199,8 +199,6 @@ bin/yn00
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/data-MCU0.95-rep1.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo4.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo5.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo4.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo5.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo4.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo5.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl
diff --git a/biology/vcftools/Makefile b/biology/vcftools/Makefile
index e7d8ab338312..5c3b2d72c47b 100644
--- a/biology/vcftools/Makefile
+++ b/biology/vcftools/Makefile
@@ -1,7 +1,6 @@
PORTNAME= vcftools
-PORTVERSION= 0.1.16
+PORTVERSION= 0.1.17
DISTVERSIONPREFIX= v
-PORTREVISION= 2
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
@@ -11,11 +10,10 @@ WWW= https://github.com/vcftools/vcftools
LICENSE= LGPL3
USES= autoreconf cpe gmake perl5 pkgconfig
-
-GNU_CONFIGURE= yes
-GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share
USE_GITHUB= yes
+GNU_CONFIGURE= yes
+GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share
CXXFLAGS+= -std=c++14
CPE_VENDOR= vcftools_project
diff --git a/biology/vcftools/distinfo b/biology/vcftools/distinfo
index 14a425bfc4c0..5a5c2ff84384 100644
--- a/biology/vcftools/distinfo
+++ b/biology/vcftools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1533330712
-SHA256 (vcftools-vcftools-v0.1.16_GH0.tar.gz) = 575c13073efe65cbff6e2ab99eef12fe04536f5dc1f98de6674c848ca83cf302
-SIZE (vcftools-vcftools-v0.1.16_GH0.tar.gz) = 246933
+TIMESTAMP = 1747310968
+SHA256 (vcftools-vcftools-v0.1.17_GH0.tar.gz) = 00b54fc7349179c2efbdab0e4dcb65a69e7b0ab0d0d29b59cc823140d0b40bff
+SIZE (vcftools-vcftools-v0.1.17_GH0.tar.gz) = 247685
generated by cgit v1.2.3 (git 2.25.1) at 2025-05-15 13:27:34 +0000