diff options
Diffstat (limited to 'biology')
43 files changed, 227 insertions, 325 deletions
diff --git a/biology/bamtools/Makefile b/biology/bamtools/Makefile index 8ba4a4d667ec..775c1f88cb59 100644 --- a/biology/bamtools/Makefile +++ b/biology/bamtools/Makefile @@ -1,7 +1,6 @@ PORTNAME= bamtools DISTVERSIONPREFIX= v -DISTVERSION= 2.5.2 -PORTREVISION= 2 +DISTVERSION= 2.5.3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -19,4 +18,6 @@ GH_ACCOUNT= pezmaster31 CMAKE_ON+= BUILD_SHARED_LIBS +PLIST_SUB= PORTVERSION=${PORTVERSION} + .include <bsd.port.mk> diff --git a/biology/bamtools/distinfo b/biology/bamtools/distinfo index e36197452212..dd64a579b51b 100644 --- a/biology/bamtools/distinfo +++ b/biology/bamtools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1625529459 -SHA256 (pezmaster31-bamtools-v2.5.2_GH0.tar.gz) = 4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8 -SIZE (pezmaster31-bamtools-v2.5.2_GH0.tar.gz) = 245729 +TIMESTAMP = 1747676701 +SHA256 (pezmaster31-bamtools-v2.5.3_GH0.tar.gz) = 7d4e59bac7c03bde488fe43e533692f78b5325a097328785ec31373ffac08344 +SIZE (pezmaster31-bamtools-v2.5.3_GH0.tar.gz) = 245648 diff --git a/biology/bamtools/pkg-descr b/biology/bamtools/pkg-descr index 632f635d85bd..e5116b7fbba8 100644 --- a/biology/bamtools/pkg-descr +++ b/biology/bamtools/pkg-descr @@ -1,6 +1,5 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. - BAM is the binary alternative to the sequence alignment/map (SAM) format used for storing genetic sequence data. It uses BGZF block compression implemented on top of the standard gzip file format to provide good compression while diff --git a/biology/bamtools/pkg-plist b/biology/bamtools/pkg-plist index a976799fd806..df5a98027cbe 100644 --- a/biology/bamtools/pkg-plist +++ b/biology/bamtools/pkg-plist @@ -21,5 +21,5 @@ include/bamtools/api/api_global.h include/bamtools/api/bamtools_api_export.h include/bamtools/shared/bamtools_global.h lib/libbamtools.so -lib/libbamtools.so.2.5.2 +lib/libbamtools.so.%%PORTVERSION%% libdata/pkgconfig/bamtools-1.pc diff --git a/biology/bifrost/Makefile b/biology/bifrost/Makefile index 8820ddfa0631..082d27df32e6 100644 --- a/biology/bifrost/Makefile +++ b/biology/bifrost/Makefile @@ -18,6 +18,17 @@ USE_GITHUB= yes CMAKE_ARGS= -DCOMPILATION_ARCH=${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/haplohseq/Makefile b/biology/haplohseq/Makefile index 8da67ec49753..128b5317242d 100644 --- a/biology/haplohseq/Makefile +++ b/biology/haplohseq/Makefile @@ -1,16 +1,15 @@ PORTNAME= haplohseq -DISTVERSION= 0.1.2 -PORTREVISION= 13 +DISTVERSION= 0.1.2-3 +DISTVERSIONSUFFIX= -gfeb9267 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Identify regions of allelic imbalance -WWW= https://sites.google.com/site/integrativecancergenomics/software/haplohseq +WWW= https://github.com/outpaddling/haplohseq \ + https://sites.google.com/site/integrativecancergenomics/software/haplohseq LICENSE= MIT -BROKEN= fails to build with Boost>=1.87 - LIB_DEPENDS= libboost_system.so:devel/boost-libs RUN_DEPENDS= R-cran-optparse>0:devel/R-cran-optparse diff --git a/biology/haplohseq/distinfo b/biology/haplohseq/distinfo index 7af7556d5596..ab9872a8d79f 100644 --- a/biology/haplohseq/distinfo +++ b/biology/haplohseq/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1611421648 -SHA256 (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 64f61023a6795decb680c23d142b1a349988d4c0e3bef8c7d52ca33bf42f29f0 -SIZE (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 12084603 +TIMESTAMP = 1747762325 +SHA256 (outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz) = a23691f16f1c03e0dfd833896068e05eaa139d488a7094a49033aeacba948cb1 +SIZE (outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz) = 12085111 diff --git a/biology/haplohseq/files/patch-makefile b/biology/haplohseq/files/patch-makefile deleted file mode 100644 index 5387716aa503..000000000000 --- a/biology/haplohseq/files/patch-makefile +++ /dev/null @@ -1,105 +0,0 @@ ---- makefile.orig 2019-08-29 18:03:23 UTC -+++ makefile -@@ -7,23 +7,32 @@ - # - - # Constants --CXX=g++ -+# Default to g++ if not set by make args or environment -+CXX?=g++ - #-O0 -g will turn on debugging - #The rule of thumb: - #When you need to debug, use -O0 (and -g to generate debugging symbols.) - #When you are preparing to ship it, use -O2. - #When you use gentoo, use -O3...! - #When you need to put it on an embedded system, use -Os (optimize for size, not for efficiency.) --CXX_FLAGS=-Wall -g -stdlib=libstdc++ -+# Use canonincal compiler variables, which may be provided by build env -+CXXFLAGS?=-Wall -g -stdlib=libstdc++ - SRC=src - CONF=conf - HMM_SRC=$(SRC)/hmm - UTIL_SRC=$(SRC)/util --BOOST=/usr/local/boost_1_52_0 -+BOOST?=/usr/local/boost_1_52_0 - INCLUDES=-I./$(SRC) -I./$(HMM_SRC) -I./$(UTIL_SRC) -isystem$(BOOST) --LIBRARY_PATHS=-Llib/macosx -+LIBRARY_PATHS?=-Llib/macosx - LIBRARIES=-lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread - -+# Installation target with destdir support -+DESTDIR?=. -+PREFIX?=/usr/local -+MKDIR?=mkdir -+INSTALL?=install -+STRIP?= # empty, set to -s to install stripped binary -+ - # Generated directories which are generated in this script and cleaned up with 'make clean' - BUILD=build - OBJ=$(BUILD)/obj -@@ -35,18 +44,21 @@ directories: - - # Create object files into the OBJ directory from cpp files in the SRC directory. - $(OBJ)/%.o: $(SRC)/%.cpp directories -- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< -+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< - $(OBJ)/%.o: $(HMM_SRC)/%.cpp directories -- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< -+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< - $(OBJ)/%.o: $(UTIL_SRC)/%.cpp directories -- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< -+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< - --all: clean haplohseq -+all: haplohseq test - - haplohseq: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o -- $(CXX) -o $(BIN)/$@ $(CXX_FLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) -- cp -r $(CONF) $(BIN)/. -- -+ $(CXX) -o $(BIN)/$@ $(CXXFLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) -+ -+install: -+ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin -+ $(INSTALL) -c $(STRIP) $(BIN)/* $(DESTDIR)$(PREFIX)/bin -+ - clean: - rm -rf $(BUILD) - -@@ -74,28 +86,28 @@ test: FreqPhaseTest HaplohSeqTest HmmTest InputProcess - - # Create test object files into the OBJ directory from cpp files in the SRC directory. - $(TEST_BIN)/%.o: $(TEST_SRC)/%.cpp directories test_directory -- $(CXX) $(CXX_FLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $< -+ $(CXX) $(CXXFLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $< - - HaplohSeqTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - FreqPhaseTest: $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - HmmTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - InputProcessorTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - MathUtilTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - ReporterTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - ThreadPoolTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - ############################## END TEST LOGIC ############################## - - diff --git a/biology/haplohseq/files/patch-scripts_ldmap.py b/biology/haplohseq/files/patch-scripts_ldmap.py deleted file mode 100644 index f9fb588048b1..000000000000 --- a/biology/haplohseq/files/patch-scripts_ldmap.py +++ /dev/null @@ -1,42 +0,0 @@ ---- scripts/ldmap.py.orig 2021-01-23 17:32:15 UTC -+++ scripts/ldmap.py -@@ -29,10 +29,10 @@ class MapMaker: - coordinates of the haplotype marker genomic positions. - ''' - def __init__(self, markerFilename, haplotypesFilename): -- print "reading haplotype base coordinates ...." -+ print("reading haplotype base coordinates ....") - self.coords, self.coordIndexes, self.refs, self.alts = self.readMarkers(markerFilename) - # self.haplotypes = self.readHaplotypes(haplotypesFilename) -- print "reading haplotype panel ...." -+ print("reading haplotype panel ....") - self.markerCalls = self.readHaplotypes(haplotypesFilename, transpose = True) - - # reads from a vcf file of defined positions representing the haplotype data -@@ -118,7 +118,7 @@ class MapMaker: - # 1) COLLECT MARGINALS AND IDENTIFY SITES THAT ARE POLYMORPHIC - # If a site has only one allele in the haplotype panel it is not informative, so it won't be used - # in LD calculations. We may want to consider setting some minimum threshold for a minor allele frequency. -- print "collecting marginal allele counts and identifying polymorphic sites from haplotype panel ...." -+ print("collecting marginal allele counts and identifying polymorphic sites from haplotype panel ....") - for index in range(0,len(self.markerCalls)): - ref = self.refs[index] - alt = self.alts[index] -@@ -152,7 +152,7 @@ class MapMaker: - log.write("Num non-polymorphic sites: " + str(numNonpolymorphicSites) + "\n") - - # 2) CALCULATE D FOR POLYMORPHIC SITES COMPARED WITH N SITES TO THE RIGHT THAT ARE POLYMORPHIC -- print "calculating D between polymorphic sites and their neighbors ...." -+ print("calculating D between polymorphic sites and their neighbors ....") - dVals = [] - for i in range(0, len(polymorphicIndexes)): # the last coordinate won't have any partners - index_i = polymorphicIndexes[i] -@@ -244,7 +244,7 @@ class LDMap: - return ldMap - - def save(self, filename): -- print "saving ldmap to " + filename -+ print("saving ldmap to " + filename) - ldMapFile = open(filename, 'w') - ldMapFile.write("\t".join(["COORD","REF","ALT","PAIRED_ALLELES"]) + "\n") - for i in range(0,len(self.coords)): diff --git a/biology/haplohseq/files/patch-scripts_simple__phaser.py b/biology/haplohseq/files/patch-scripts_simple__phaser.py deleted file mode 100644 index c6c5941ee00d..000000000000 --- a/biology/haplohseq/files/patch-scripts_simple__phaser.py +++ /dev/null @@ -1,31 +0,0 @@ ---- scripts/simple_phaser.py.orig 2021-01-23 17:25:56 UTC -+++ scripts/simple_phaser.py -@@ -108,7 +108,7 @@ class SimplePhaser: - return informativeHets, informativeCoords, informativeIndexes - - def getRefPairedAllele(self, anchorIndex, pairedIndex): --# print "\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts -+# print("\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts) - if (pairedIndex - anchorIndex - 1) >= len(self.ldMap.dVals[anchorIndex]): - pRef = random.uniform(0,1) - if pRef > 0.5: -@@ -166,8 +166,8 @@ class SimplePhaser: - altHap = temp - - if pairedAllele not in [ref,alt]: -- print "pairedAllele not ref or alt " + ref + " " + alt -- print pairedAllele -+ print("pairedAllele not ref or alt " + ref + " " + alt) -+ print(pairedAllele) - - return phasedAlleles, informativeCoords - -@@ -182,7 +182,7 @@ class SimplePhaser: - elif candidateHap[i].upper() == phasedHaps[1][i].upper(): - currentMatch = 1 - else: -- print "ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i] -+ print("ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i]) - # # randomly assign match - # p0 = random.uniform(0,1) - # if p0 > 0.5: diff --git a/biology/haplohseq/files/patch-src_FreqPhase.cpp b/biology/haplohseq/files/patch-src_FreqPhase.cpp deleted file mode 100644 index 9bab76aee2f5..000000000000 --- a/biology/haplohseq/files/patch-src_FreqPhase.cpp +++ /dev/null @@ -1,29 +0,0 @@ ---- src/FreqPhase.cpp.orig 2019-11-13 14:19:06 UTC -+++ src/FreqPhase.cpp -@@ -5,6 +5,7 @@ - * Email: sanlucas@gmail.com - */ - -+#include <sysexits.h> - #include "FreqPhase.h" - - namespace haplohseq { -@@ -180,10 +181,17 @@ double FreqPhase::meanValue(const std::v - double FreqPhase::medianValue(const std::vector<double>& values) { - double median; - size_t size = values.size(); -+ -+ // We can probably detect this condition earlier while loading the VCF -+ if ( size == 0 ) { -+ std::cerr << "FreqPhase::medianValue(): values vector is empty." << std::endl; -+ std::cerr << "Make sure your VCF has all of GT:AD:DP in the FORMAT column." << std::endl; -+ exit(EX_DATAERR); -+ } - std::vector<double> tempFreqs(values); - sort(tempFreqs.begin(), tempFreqs.end()); - -- if (size % 2 == 0) { -+ if (size % 2 == 0) { - median = (tempFreqs[size / 2 - 1] + tempFreqs[size / 2]) / 2; - } - else { diff --git a/biology/haplohseq/files/patch-src_HaplohSeq.cpp b/biology/haplohseq/files/patch-src_HaplohSeq.cpp deleted file mode 100644 index a80ce577f747..000000000000 --- a/biology/haplohseq/files/patch-src_HaplohSeq.cpp +++ /dev/null @@ -1,20 +0,0 @@ ---- src/HaplohSeq.cpp.orig 2019-09-01 14:58:30 UTC -+++ src/HaplohSeq.cpp -@@ -202,7 +202,7 @@ void HaplohSeq::runBafHaplohseq( std::string& obsType, - - // Spawn worker threads - for (std::size_t t = 0; t < numThreads; t++) { -- threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); -+ threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); - } - - std::map<std::string, boost::shared_ptr<Hmm> > chrHmms; -@@ -420,7 +420,7 @@ void HaplohSeq::runVcfHaplohseq( std::string& obsType, - - // Spawn worker threads - for (std::size_t t = 0; t < numThreads; t++) { -- threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); -+ threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); - } - - std::map<std::string, boost::shared_ptr<Hmm> > chrHmms; diff --git a/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp b/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp deleted file mode 100644 index 21ea56a8f600..000000000000 --- a/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- src/test/InputProcessorTest.cpp.orig 2019-09-01 12:33:22 UTC -+++ src/test/InputProcessorTest.cpp -@@ -82,7 +82,7 @@ BOOST_AUTO_TEST_CASE(isHetTest) { - BOOST_REQUIRE_EQUAL(inputProc.isHet('A','?'), false); - BOOST_REQUIRE_EQUAL(inputProc.isHet('A','.'), false); - BOOST_REQUIRE_EQUAL(inputProc.isHet('A',' '), false); -- BOOST_REQUIRE_EQUAL(inputProc.isHet('C', NULL), true); -+ BOOST_REQUIRE_EQUAL(inputProc.isHet('C','\0'), true); - } - - BOOST_AUTO_TEST_CASE(readAllelesTest) { 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/kmcp/Makefile b/biology/kmcp/Makefile index d52bac6491ea..2936637408be 100644 --- a/biology/kmcp/Makefile +++ b/biology/kmcp/Makefile @@ -1,7 +1,7 @@ PORTNAME= kmcp DISTVERSIONPREFIX= v DISTVERSION= 0.9.4 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/lamarc/Makefile b/biology/lamarc/Makefile index 46f4e102635a..ad200a6ffe56 100644 --- a/biology/lamarc/Makefile +++ b/biology/lamarc/Makefile @@ -1,25 +1,25 @@ PORTNAME= lamarc PORTVERSION= 2.1.8 DISTVERSIONSUFFIX= -src -PORTREVISION= 1 +PORTREVISION= 2 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= http://evolution.genetics.washington.edu/lamarc/download/ -MAINTAINER= ports@FreeBSD.org +MAINTAINER= hayzam@alchemilla.io COMMENT= Package of programs for computing population parameters WWW= https://evolution.genetics.washington.edu/lamarc/ LICENSE= APACHE20 -BROKEN_FreeBSD_14= fails to compile: no matching function for call to 'make_pair' - USE_CXXSTD= c++98 GNU_CONFIGURE= yes WRKSRC= ${WRKDIR}/${DISTNAME:S,${DISTVERSIONSUFFIX},,} +CXXFLAGS+= -Wno-unused-parameter -Wno-mismatched-tags + PLIST_FILES= bin/${PORTNAME} PORTDOCS= * diff --git a/biology/lamarc/files/patch-src_control_chainmanager.cpp b/biology/lamarc/files/patch-src_control_chainmanager.cpp new file mode 100644 index 000000000000..bf21359154ab --- /dev/null +++ b/biology/lamarc/files/patch-src_control_chainmanager.cpp @@ -0,0 +1,11 @@ +--- src/control/chainmanager.cpp.orig 2025-05-18 23:57:13 UTC ++++ src/control/chainmanager.cpp +@@ -1631,7 +1631,7 @@ vector<pair<double, long int> > ChainManager::SortChai + unsigned long int i; + for (i = 0; i < temps.size(); ++i) + { +- orderedtemps.push_back(make_pair<double, long int>(temps[i].GetTemperature(), i)); ++ orderedtemps.push_back(make_pair(temps[i].GetTemperature(), i)); + } + std::sort(orderedtemps.begin(), orderedtemps.end()); + return orderedtemps; diff --git a/biology/lamarc/files/patch-src_tools_mathx.cpp b/biology/lamarc/files/patch-src_tools_mathx.cpp new file mode 100644 index 000000000000..527dfe4af344 --- /dev/null +++ b/biology/lamarc/files/patch-src_tools_mathx.cpp @@ -0,0 +1,11 @@ +--- src/tools/mathx.cpp.orig 2025-05-19 00:00:29 UTC ++++ src/tools/mathx.cpp +@@ -778,7 +778,7 @@ std::pair<DoubleVec1d, DoubleVec2d> EigenCalculator::E + { + eigvals[i] = a[i][i]; + } +- return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs); ++ return std::make_pair(eigvals, eigvecs); + } // Eigen + + //------------------------------------------------------------------------------------ diff --git a/biology/lamarc/files/patch-src_tools_stringx.h b/biology/lamarc/files/patch-src_tools_stringx.h index d1ded1a7d8da..04019393fbac 100644 --- a/biology/lamarc/files/patch-src_tools_stringx.h +++ b/biology/lamarc/files/patch-src_tools_stringx.h @@ -1,6 +1,6 @@ --- src/tools/stringx.h.orig 2011-04-23 02:02:49 UTC +++ src/tools/stringx.h -@@ -107,6 +107,26 @@ struct CIStringCompare : public std::bin +@@ -107,6 +107,26 @@ bool ciStringEqual(const std::string& s1, const std::s bool ciStringEqual(const std::string& s1, const std::string& s2); @@ -27,10 +27,11 @@ //------------------------------------------------------------------------------------ template <class T> -@@ -188,26 +208,6 @@ bool FromString(const std::string & in, +@@ -187,26 +207,6 @@ DoubleVec1d StringToDoubleVecOrBarf(const std::string& + bool FromString(const std::string & in, method_type& out); DoubleVec1d StringToDoubleVecOrBarf(const std::string& in); - +- -// functions for making xmltags and lines of xml -std::string MakeTag(const std::string& str); -std::string MakeCloseTag(const std::string& str); @@ -50,7 +51,6 @@ -std::string Pretty(long number, int width=DEFWIDTH); -std::string Pretty(unsigned long number, int width=DEFWIDTH); -std::string Pretty(std::string str, int width=DEFWIDTH); -- + bool StringCompare(const std::string&, const char*, long, long); bool StringCompare(const std::string&, const std::string&, long, long); - diff --git a/biology/lamarc/files/patch-src_tree_arrangervec.cpp b/biology/lamarc/files/patch-src_tree_arrangervec.cpp new file mode 100644 index 000000000000..ff3636f3a571 --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_arrangervec.cpp @@ -0,0 +1,11 @@ +--- src/tree/arrangervec.cpp.orig 2025-05-18 23:55:20 UTC ++++ src/tree/arrangervec.cpp +@@ -116,7 +116,7 @@ void ArrangerVec::CopyAllMembers(const ArrangerVec & c + for(it = cp.arrangers.begin(); it != cp.arrangers.end(); it++) + { + Arranger* arr = (*it).second->Clone(); +- arrangers.insert(std::make_pair<string, Arranger*>(arr->GetName(), arr)); ++ arrangers.insert(std::make_pair(arr->GetName(), arr)); + } + } + } diff --git a/biology/lamarc/files/patch-src_tree_collector.cpp b/biology/lamarc/files/patch-src_tree_collector.cpp new file mode 100644 index 000000000000..bff56a70b261 --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_collector.cpp @@ -0,0 +1,11 @@ +--- src/tree/collector.cpp.orig 2025-05-18 23:58:39 UTC ++++ src/tree/collector.cpp +@@ -204,7 +204,7 @@ void ParamCollector::AddParamSummary(ForceParameters f + + void ParamCollector::AddParamSummary(ForceParameters fp, long ncopy) + { +- m_paramsum.push_back(make_pair<ForceParameters, long>(fp, ncopy)); ++ m_paramsum.push_back(std::make_pair(fp, ncopy)); + } + + //------------------------------------------------------------------------------------ diff --git a/biology/lamarc/files/patch-src_tree_prior.cpp b/biology/lamarc/files/patch-src_tree_prior.cpp new file mode 100644 index 000000000000..a8dbf7ab04ed --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_prior.cpp @@ -0,0 +1,17 @@ +--- src/tree/prior.cpp.orig 2025-05-18 23:58:05 UTC ++++ src/tree/prior.cpp +@@ -85,12 +85,12 @@ std::pair<double, double> Prior::RandomDraw() const + case LINEAR: + newparam = rnd.Float() * (m_upperbound - m_lowerbound) + m_lowerbound; + newlnparam = log(newparam); +- return std::make_pair<double, double>(newparam, newlnparam); ++ return std::make_pair(newparam, newlnparam); + break; + case LOGARITHMIC: + newlnparam = rnd.Float() * (m_lnupper - m_lnlower) + m_lnlower; + newparam = exp(newlnparam); +- return std::make_pair<double, double>(newparam, newlnparam); ++ return std::make_pair(newparam, newlnparam); + break; + } + string e = "Unknown prior type " + ToString(m_priortype) + diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile index 383b06145b85..fec0997b39be 100644 --- a/biology/libsbml/Makefile +++ b/biology/libsbml/Makefile @@ -1,7 +1,6 @@ PORTNAME= libsbml -PORTVERSION= 5.20.4 +PORTVERSION= 5.20.5 DISTVERSIONPREFIX= v -PORTREVISION= 1 CATEGORIES= biology devel MAINTAINER= sunpoet@FreeBSD.org @@ -74,7 +73,6 @@ post-patch: @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/CMakeLists.txt post-install-EXAMPLES-on: - ${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR} - ${RMDIR} ${STAGEDIR}${DATADIR} + ${MV} ${STAGEDIR}${DATADIR}examples ${STAGEDIR}${EXAMPLESDIR} .include <bsd.port.mk> diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo index 7884ce4f4a5c..7908d7960b79 100644 --- a/biology/libsbml/distinfo +++ b/biology/libsbml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1725559551 -SHA256 (sbmlteam-libsbml-v5.20.4_GH0.tar.gz) = 02c225d3513e1f5d6e3c0168456f568e67f006eddaab82f09b4bdf0d53d2050e -SIZE (sbmlteam-libsbml-v5.20.4_GH0.tar.gz) = 28796139 +TIMESTAMP = 1747546406 +SHA256 (sbmlteam-libsbml-v5.20.5_GH0.tar.gz) = 21c88c753a4a031f157a033de3810488b86f003e684c6ca7aa3d6e26e7e0acfc +SIZE (sbmlteam-libsbml-v5.20.5_GH0.tar.gz) = 28852940 diff --git a/biology/libsbml/files/patch-CMakeLists.txt b/biology/libsbml/files/patch-CMakeLists.txt index 037277324c79..32366d12deb1 100644 --- a/biology/libsbml/files/patch-CMakeLists.txt +++ b/biology/libsbml/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2023-04-03 10:48:28 UTC +--- CMakeLists.txt.orig 2025-05-05 04:53:07 UTC +++ CMakeLists.txt -@@ -430,8 +430,6 @@ if(WITH_EXPAT) +@@ -445,8 +445,6 @@ if(WITH_EXPAT) set(LIBSBML_XML_LIBRARY_INCLUDE ${EXPAT_INCLUDE_DIR}) set(LIBSBML_XML_LIBRARY_LIBS ${EXPAT_LIBRARY}) @@ -9,7 +9,7 @@ endif(WITH_EXPAT) -@@ -452,8 +450,6 @@ if(WITH_LIBXML) +@@ -467,8 +465,6 @@ if(WITH_LIBXML) set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR}) set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY}) @@ -18,7 +18,7 @@ endif(WITH_LIBXML) -@@ -473,8 +469,6 @@ if(WITH_XERCES) +@@ -488,8 +484,6 @@ if(WITH_XERCES) set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR}) set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY}) @@ -27,7 +27,7 @@ endif(WITH_XERCES) ############################################################################### -@@ -498,7 +492,6 @@ if(WITH_BZIP2) +@@ -513,7 +507,6 @@ if(WITH_BZIP2) set(USE_BZ2 ON) add_definitions( -DUSE_BZ2 ) list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2) @@ -35,16 +35,16 @@ endif(WITH_BZIP2) -@@ -608,8 +601,6 @@ valid. It should contain the file zlib.h, but it does - INTERFACE_INCLUDE_DIRECTORIES "${LIBZ_INCLUDE_DIR}") - endif() - +@@ -550,8 +543,6 @@ if(WITH_ZLIB) + set(USE_ZLIB ON) + add_definitions( -DUSE_ZLIB ) + list(APPEND SWIG_EXTRA_ARGS -DUSE_ZLIB) - list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindZLIB.cmake") - endif(WITH_ZLIB) # install find scripts only for used dependencies -@@ -981,22 +972,6 @@ if(WITH_DOXYGEN) +@@ -923,20 +914,6 @@ endif() add_subdirectory(docs) endif() @@ -62,8 +62,6 @@ - README.md - VERSION.txt -) -- --install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX}) - ############################################################################### - # + install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX}) + diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist index 7a382979c5e4..df36c508c663 100644 --- a/biology/libsbml/pkg-plist +++ b/biology/libsbml/pkg-plist @@ -107,6 +107,31 @@ include/sbml/extension/SBaseExtensionPoint.h include/sbml/extension/SBasePlugin.h include/sbml/extension/SBasePluginCreator.h include/sbml/extension/SBasePluginCreatorBase.h +include/sbml/html2md/html2md.h +include/sbml/html2md/table.h +include/sbml/maddy/blockparser.h +include/sbml/maddy/breaklineparser.h +include/sbml/maddy/checklistparser.h +include/sbml/maddy/codeblockparser.h +include/sbml/maddy/emphasizedparser.h +include/sbml/maddy/headlineparser.h +include/sbml/maddy/horizontallineparser.h +include/sbml/maddy/htmlparser.h +include/sbml/maddy/imageparser.h +include/sbml/maddy/inlinecodeparser.h +include/sbml/maddy/italicparser.h +include/sbml/maddy/latexblockparser.h +include/sbml/maddy/lineparser.h +include/sbml/maddy/linkparser.h +include/sbml/maddy/orderedlistparser.h +include/sbml/maddy/paragraphparser.h +include/sbml/maddy/parser.h +include/sbml/maddy/parserconfig.h +include/sbml/maddy/quoteparser.h +include/sbml/maddy/strikethroughparser.h +include/sbml/maddy/strongparser.h +include/sbml/maddy/tableparser.h +include/sbml/maddy/unorderedlistparser.h include/sbml/math/ASTNode.h include/sbml/math/ASTNodeType.h include/sbml/math/DefinitionURLRegistry.h @@ -236,6 +261,7 @@ share/cmake/Modules/FindLIBSBML.cmake %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/getAllElementsWithNotes.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferReactions.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferUnits.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inlineFunctionDefintions.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index b87a9c2d6b60..31f6fb7db166 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncbi-blast+ DISTVERSION= 2.16.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology perl5 python MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile index 43ccbb2354ba..8e02ebac7423 100644 --- a/biology/ncbi-entrez-direct/Makefile +++ b/biology/ncbi-entrez-direct/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncbi-entrez-direct DISTVERSION= 14.9.20210423 -PORTREVISION= 26 +PORTREVISION= 27 CATEGORIES= biology perl5 MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/ DISTFILES= edirect.tar.gz 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/seqkit/Makefile b/biology/seqkit/Makefile index 2d1577a4a940..3cd8e1318a0e 100644 --- a/biology/seqkit/Makefile +++ b/biology/seqkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= seqkit DISTVERSIONPREFIX= v DISTVERSION= 2.10.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/taxonkit/Makefile b/biology/taxonkit/Makefile index dfe61730aaee..fe4b34852a71 100644 --- a/biology/taxonkit/Makefile +++ b/biology/taxonkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= taxonkit DISTVERSIONPREFIX= v DISTVERSION= 0.19.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/unikmer/Makefile b/biology/unikmer/Makefile index 364d635628d0..4d571776c94e 100644 --- a/biology/unikmer/Makefile +++ b/biology/unikmer/Makefile @@ -1,7 +1,7 @@ PORTNAME= unikmer DISTVERSIONPREFIX= v DISTVERSION= 0.20.0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/vcflib/files/patch-src-zig-samples.zig b/biology/vcflib/files/patch-src-zig-samples.zig new file mode 100644 index 000000000000..e69584b175e0 --- /dev/null +++ b/biology/vcflib/files/patch-src-zig-samples.zig @@ -0,0 +1,31 @@ +diff --git src/zig/samples.zig src/zig/samples.zig +index cb05a1f2..ccd5b149 100644 +--- src/zig/samples.zig ++++ src/zig/samples.zig +@@ -28,7 +28,11 @@ const GENOTYPE_MISSING = -256; + fn split_samples(str: []const u8) *ArrayList([] const u8) { + var list = ArrayList([] const u8).init(allocator); + defer list.deinit(); +- var splits = std.mem.split(u8, str, " "); ++ ++ var splits = if (@hasDecl(std.mem, "splitScalar")) ++ std.mem.splitScalar(u8, str, ' ') ++ else ++ std.mem.split(u8, str, ' '); + while (splits.next()) |chunk| { + list.append(chunk) catch |err| { + std.debug.print("out of memory {}\n", .{err}); +@@ -61,10 +65,10 @@ const Genotypes = struct { + fn to_num(str: []const u8) !ArrayList(i64) { + var list = ArrayList(i64).init(allocator); + +- var splits = if (is_phased(str)) +- std.mem.split(u8, str, "|") ++ var splits = if (@hasDecl(std.mem, "splitScalar")) ++ std.mem.splitScalar(u8, str, if (is_phased(str)) '|' else '/') + else +- std.mem.split(u8, str, "/"); ++ std.mem.split(u8, str, if (is_phased(str)) '|' else '/' ); + + while (splits.next()) |chunk| { + const i: i64 = 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 |