diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/bbmap/Makefile | 2 | ||||
| -rw-r--r-- | biology/bbmap/distinfo | 6 | ||||
| -rw-r--r-- | biology/bbmap/pkg-plist | 64 | ||||
| -rw-r--r-- | biology/gatk/Makefile | 10 | ||||
| -rw-r--r-- | biology/gatk/distinfo | 10 | ||||
| -rw-r--r-- | biology/gatk/files/gatk.sh.in | 4 | ||||
| -rw-r--r-- | biology/gkl/Makefile | 3 | ||||
| -rw-r--r-- | biology/gkl/distinfo | 6 | ||||
| -rw-r--r-- | biology/gkl/files/patch-CMakeLists.txt | 4 | ||||
| -rw-r--r-- | biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h | 11 | ||||
| -rw-r--r-- | biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc | 11 | ||||
| -rw-r--r-- | biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h | 4 | ||||
| -rw-r--r-- | biology/hyphy/files/patch-src_core_global__things.cpp | 20 | ||||
| -rw-r--r-- | biology/linux-foldingathome/Makefile | 17 | ||||
| -rw-r--r-- | biology/linux-foldingathome/distinfo | 14 | ||||
| -rw-r--r-- | biology/py-bx-python/Makefile | 16 | ||||
| -rw-r--r-- | biology/py-bx-python/distinfo | 6 | ||||
| -rw-r--r-- | biology/seqan3/Makefile | 17 | ||||
| -rw-r--r-- | biology/seqan3/distinfo | 12 | ||||
| -rw-r--r-- | biology/seqan3/files/patch-cmake_CPM.cmake | 11 | ||||
| -rw-r--r-- | biology/seqan3/pkg-plist | 132 |
21 files changed, 196 insertions, 184 deletions
diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile index f002e215a910..533216187a45 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -1,5 +1,5 @@ PORTNAME= bbmap -DISTVERSION= 39.33 +DISTVERSION= 39.34 CATEGORIES= biology java MASTER_SITES= SF/bbmap/ DISTNAME= BBMap_${PORTVERSION} diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo index c2fdad3c90f0..c65e1b09d3ef 100644 --- a/biology/bbmap/distinfo +++ b/biology/bbmap/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753598961 -SHA256 (BBMap_39.33.tar.gz) = b82d06579e118467b5f129f06c93991196d25cc7e43cd233aeb777f85507175e -SIZE (BBMap_39.33.tar.gz) = 13433045 +TIMESTAMP = 1755776772 +SHA256 (BBMap_39.34.tar.gz) = c9c096c6ce3cc87da5607b731532bb9ac0aaebea2bd8fbf0a56e235968c4fbf4 +SIZE (BBMap_39.34.tar.gz) = 13743574 diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist index 9a9e248eafa3..6dc7649290c2 100644 --- a/biology/bbmap/pkg-plist +++ b/biology/bbmap/pkg-plist @@ -378,6 +378,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/align2/QuadHeap.java %%JAVAJARDIR%%/bbmap/align2/QualityTools.class %%JAVAJARDIR%%/bbmap/align2/QualityTools.java +%%JAVAJARDIR%%/bbmap/align2/README.md %%JAVAJARDIR%%/bbmap/align2/RefToIndex.class %%JAVAJARDIR%%/bbmap/align2/RefToIndex.java %%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.class @@ -527,6 +528,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner4.java %%JAVAJARDIR%%/bbmap/aligner/Query.class %%JAVAJARDIR%%/bbmap/aligner/Query.java +%%JAVAJARDIR%%/bbmap/aligner/README.md %%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.class %%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.java %%JAVAJARDIR%%/bbmap/aligner/ScrabbleAligner.class @@ -605,6 +607,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.java %%JAVAJARDIR%%/bbmap/assemble/Postfilter.class %%JAVAJARDIR%%/bbmap/assemble/Postfilter.java +%%JAVAJARDIR%%/bbmap/assemble/README.md %%JAVAJARDIR%%/bbmap/assemble/Rollback.class %%JAVAJARDIR%%/bbmap/assemble/Rollback.java %%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class @@ -680,6 +683,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist$PopThread.class %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.class %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.java +%%JAVAJARDIR%%/bbmap/barcode/README.md %%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.class %%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.java %%JAVAJARDIR%%/bbmap/barcode/Transition.class @@ -692,6 +696,11 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.java %%JAVAJARDIR%%/bbmap/bbmin/Minimizer.class %%JAVAJARDIR%%/bbmap/bbmin/Minimizer.java +%%JAVAJARDIR%%/bbmap/bbmin/README.md +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EnsembleRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EvidenceRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$GraphRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$RefinerParams.class %%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.class %%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.java %%JAVAJARDIR%%/bbmap/bin/AdjustEntropy.class @@ -750,8 +759,19 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/bin/CrystalChamber$Centroid.class %%JAVAJARDIR%%/bbmap/bin/CrystalChamber.class %%JAVAJARDIR%%/bbmap/bin/CrystalChamber.java +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2$Centroid.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.java %%JAVAJARDIR%%/bbmap/bin/DataLoader.class %%JAVAJARDIR%%/bbmap/bin/DataLoader.java +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$ConsensusResult.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$RefinerResult.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.java +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$ContigStatus.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$DBSCANResult.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.java %%JAVAJARDIR%%/bbmap/bin/FileRenamer.class %%JAVAJARDIR%%/bbmap/bin/FileRenamer.java %%JAVAJARDIR%%/bbmap/bin/GTDBLine.class @@ -762,6 +782,10 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/bin/GradeBins$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/GradeBins.class %%JAVAJARDIR%%/bbmap/bin/GradeBins.java +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph$Edge.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.java %%JAVAJARDIR%%/bbmap/bin/IDComparator.class %%JAVAJARDIR%%/bbmap/bin/IDComparator.java %%JAVAJARDIR%%/bbmap/bin/Key.class @@ -775,6 +799,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/bin/QuickBin$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.java +%%JAVAJARDIR%%/bbmap/bin/README.md %%JAVAJARDIR%%/bbmap/bin/SamLoader$LoadThread.class %%JAVAJARDIR%%/bbmap/bin/SamLoader.class %%JAVAJARDIR%%/bbmap/bin/SamLoader.java @@ -851,6 +876,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/bloom/PolyFilter$ProcessThread.class %%JAVAJARDIR%%/bbmap/bloom/PolyFilter.class %%JAVAJARDIR%%/bbmap/bloom/PolyFilter.java +%%JAVAJARDIR%%/bbmap/bloom/README.md %%JAVAJARDIR%%/bbmap/bloom/ReadCounter$1.class %%JAVAJARDIR%%/bbmap/bloom/ReadCounter$CountThread.class %%JAVAJARDIR%%/bbmap/bloom/ReadCounter.class @@ -886,6 +912,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.java %%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.class %%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.java +%%JAVAJARDIR%%/bbmap/cardinality/README.md %%JAVAJARDIR%%/bbmap/clump/Clump.class %%JAVAJARDIR%%/bbmap/clump/Clump.java %%JAVAJARDIR%%/bbmap/clump/ClumpList$ClumpThread.class @@ -928,6 +955,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/clump/PivotSet$HashThread.class %%JAVAJARDIR%%/bbmap/clump/PivotSet.class %%JAVAJARDIR%%/bbmap/clump/PivotSet.java +%%JAVAJARDIR%%/bbmap/clump/README.md %%JAVAJARDIR%%/bbmap/clump/ReadKey.class %%JAVAJARDIR%%/bbmap/clump/ReadKey.java %%JAVAJARDIR%%/bbmap/clump/Splitter.class @@ -940,6 +968,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/cluster/ClusterTools.java %%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.class %%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.java +%%JAVAJARDIR%%/bbmap/cluster/README.md %%JAVAJARDIR%%/bbmap/cluster/ReadTag.class %%JAVAJARDIR%%/bbmap/cluster/ReadTag.java %%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer$ClusterThread.class @@ -965,6 +994,8 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/consensus/Lilypad$ProcessThread.class %%JAVAJARDIR%%/bbmap/consensus/Lilypad.class %%JAVAJARDIR%%/bbmap/consensus/Lilypad.java +%%JAVAJARDIR%%/bbmap/consensus/README.md +%%JAVAJARDIR%%/bbmap/covid/README.md %%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.class %%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.java %%JAVAJARDIR%%/bbmap/dna/AminoAcid.class @@ -997,6 +1028,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/dna/MotifProbsN.java %%JAVAJARDIR%%/bbmap/dna/MotifSimple.class %%JAVAJARDIR%%/bbmap/dna/MotifSimple.java +%%JAVAJARDIR%%/bbmap/dna/README.md %%JAVAJARDIR%%/bbmap/dna/ScafLoc.class %%JAVAJARDIR%%/bbmap/dna/ScafLoc.java %%JAVAJARDIR%%/bbmap/dna/Scaffold.class @@ -1088,6 +1120,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.java %%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.class %%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.java +%%JAVAJARDIR%%/bbmap/driver/README.md %%JAVAJARDIR%%/bbmap/driver/ReduceSilva.class %%JAVAJARDIR%%/bbmap/driver/ReduceSilva.java %%JAVAJARDIR%%/bbmap/driver/RenameAndMux$MuxThread.class @@ -1188,6 +1221,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/fileIO/PipeThread.java %%JAVAJARDIR%%/bbmap/fileIO/QuickFile.class %%JAVAJARDIR%%/bbmap/fileIO/QuickFile.java +%%JAVAJARDIR%%/bbmap/fileIO/README.md %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$1.class %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteObjectThread.class %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteStringThread.class @@ -1266,6 +1300,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/fun/ProbShared2.java %%JAVAJARDIR%%/bbmap/fun/ProbShared3.class %%JAVAJARDIR%%/bbmap/fun/ProbShared3.java +%%JAVAJARDIR%%/bbmap/fun/README.md %%JAVAJARDIR%%/bbmap/gff/CompareGff.class %%JAVAJARDIR%%/bbmap/gff/CompareGff.java %%JAVAJARDIR%%/bbmap/gff/CompareGff_old.class @@ -1287,6 +1322,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/gff/GtfLine.java %%JAVAJARDIR%%/bbmap/gff/ParseCrispr.class %%JAVAJARDIR%%/bbmap/gff/ParseCrispr.java +%%JAVAJARDIR%%/bbmap/gff/README.md %%JAVAJARDIR%%/bbmap/gff/VcfToGff$1.class %%JAVAJARDIR%%/bbmap/gff/VcfToGff.class %%JAVAJARDIR%%/bbmap/gff/VcfToGff.java @@ -1321,6 +1357,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/hiseq/PlotHist.java %%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.class %%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.java +%%JAVAJARDIR%%/bbmap/hiseq/README.md %%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.class %%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.java %%JAVAJARDIR%%/bbmap/hiseq/Tile.class @@ -1333,6 +1370,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.java %%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.class %%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.java +%%JAVAJARDIR%%/bbmap/hmm/README.md %%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.class %%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.java %%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.class @@ -1351,6 +1389,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/icecream/PBHeader.java %%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.class %%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.java +%%JAVAJARDIR%%/bbmap/icecream/README.md %%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.class %%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.java %%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio$ProcessThread.class @@ -1364,6 +1403,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java %%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class %%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java +%%JAVAJARDIR%%/bbmap/jasper/README.md %%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class %%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java %%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class @@ -1555,6 +1595,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/jgi/PickSubset$Node.class %%JAVAJARDIR%%/bbmap/jgi/PickSubset.class %%JAVAJARDIR%%/bbmap/jgi/PickSubset.java +%%JAVAJARDIR%%/bbmap/jgi/README.md %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java %%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class @@ -1635,6 +1676,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/json/JsonObject.java %%JAVAJARDIR%%/bbmap/json/JsonParser.class %%JAVAJARDIR%%/bbmap/json/JsonParser.java +%%JAVAJARDIR%%/bbmap/json/README.md %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable$AllocThread.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java @@ -1678,6 +1720,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.java %%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.class %%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java +%%JAVAJARDIR%%/bbmap/kmer/README.md %%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class %%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java %%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.class @@ -1726,6 +1769,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.java %%JAVAJARDIR%%/bbmap/ml/Profiler.class %%JAVAJARDIR%%/bbmap/ml/Profiler.java +%%JAVAJARDIR%%/bbmap/ml/README.md %%JAVAJARDIR%%/bbmap/ml/RSLog.class %%JAVAJARDIR%%/bbmap/ml/RSLog.java %%JAVAJARDIR%%/bbmap/ml/ReduceColumns.class @@ -1790,6 +1834,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Ssra.class %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.class %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.java +%%JAVAJARDIR%%/bbmap/pacbio/README.md %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$1.class %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$ProcessThread.class %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.class @@ -1852,6 +1897,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/prok/PGMTools.java %%JAVAJARDIR%%/bbmap/prok/ProkObject.class %%JAVAJARDIR%%/bbmap/prok/ProkObject.java +%%JAVAJARDIR%%/bbmap/prok/README.md %%JAVAJARDIR%%/bbmap/prok/RiboMaker$ProcessThread.class %%JAVAJARDIR%%/bbmap/prok/RiboMaker.class %%JAVAJARDIR%%/bbmap/prok/RiboMaker.java @@ -1879,6 +1925,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/repeat/RepeatSet.java %%JAVAJARDIR%%/bbmap/server/PercentEncoding.class %%JAVAJARDIR%%/bbmap/server/PercentEncoding.java +%%JAVAJARDIR%%/bbmap/server/README.md %%JAVAJARDIR%%/bbmap/server/ServerTools$1.class %%JAVAJARDIR%%/bbmap/server/ServerTools.class %%JAVAJARDIR%%/bbmap/server/ServerTools.java @@ -1936,6 +1983,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/shared/PreParser.java %%JAVAJARDIR%%/bbmap/shared/Primes.class %%JAVAJARDIR%%/bbmap/shared/Primes.java +%%JAVAJARDIR%%/bbmap/shared/README.md %%JAVAJARDIR%%/bbmap/shared/SIMD.class %%JAVAJARDIR%%/bbmap/shared/SIMD.java %%JAVAJARDIR%%/bbmap/shared/SIMDAlign.class @@ -2007,6 +2055,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/sketch/KmerLimit2.java %%JAVAJARDIR%%/bbmap/sketch/MergeSketch.class %%JAVAJARDIR%%/bbmap/sketch/MergeSketch.java +%%JAVAJARDIR%%/bbmap/sketch/README.md %%JAVAJARDIR%%/bbmap/sketch/Record.class %%JAVAJARDIR%%/bbmap/sketch/Record.java %%JAVAJARDIR%%/bbmap/sketch/RecordSet.class @@ -2056,6 +2105,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.java %%JAVAJARDIR%%/bbmap/sort/MergeSorted.class %%JAVAJARDIR%%/bbmap/sort/MergeSorted.java +%%JAVAJARDIR%%/bbmap/sort/README.md %%JAVAJARDIR%%/bbmap/sort/ReadComparator.class %%JAVAJARDIR%%/bbmap/sort/ReadComparator.java %%JAVAJARDIR%%/bbmap/sort/ReadComparatorClump.class @@ -2325,6 +2375,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/structures/Point.java %%JAVAJARDIR%%/bbmap/structures/Quantizer.class %%JAVAJARDIR%%/bbmap/structures/Quantizer.java +%%JAVAJARDIR%%/bbmap/structures/README.md %%JAVAJARDIR%%/bbmap/structures/Range.class %%JAVAJARDIR%%/bbmap/structures/Range.java %%JAVAJARDIR%%/bbmap/structures/RawBitSet.class @@ -2433,6 +2484,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.java %%JAVAJARDIR%%/bbmap/tax/Query.class %%JAVAJARDIR%%/bbmap/tax/Query.java +%%JAVAJARDIR%%/bbmap/tax/README.md %%JAVAJARDIR%%/bbmap/tax/RenameGiToTaxid.class %%JAVAJARDIR%%/bbmap/tax/RenameGiToTaxid.java %%JAVAJARDIR%%/bbmap/tax/RenameIMG.class @@ -2502,6 +2554,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/template/BBTool_ST.java %%JAVAJARDIR%%/bbmap/template/DoWorker.class %%JAVAJARDIR%%/bbmap/template/DoWorker.java +%%JAVAJARDIR%%/bbmap/template/README.md %%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.class %%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.java %%JAVAJARDIR%%/bbmap/template/ThreadWaiter.class @@ -2560,6 +2613,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU.java %%JAVAJARDIR%%/bbmap/ukmer/OwnershipThread.class %%JAVAJARDIR%%/bbmap/ukmer/OwnershipThread.java +%%JAVAJARDIR%%/bbmap/ukmer/README.md %%JAVAJARDIR%%/bbmap/ukmer/WalkerU.class %%JAVAJARDIR%%/bbmap/ukmer/WalkerU.java %%JAVAJARDIR%%/bbmap/var/ApplyVarsToReference$1.class @@ -2579,6 +2633,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3$ProcessThread.class %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3.class %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3.java +%%JAVAJARDIR%%/bbmap/var/README.md %%JAVAJARDIR%%/bbmap/var/StackVariations$1.class %%JAVAJARDIR%%/bbmap/var/StackVariations$SVThread.class %%JAVAJARDIR%%/bbmap/var/StackVariations.class @@ -2608,6 +2663,8 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/var2/CallVariants2.java %%JAVAJARDIR%%/bbmap/var2/CompareVCF.class %%JAVAJARDIR%%/bbmap/var2/CompareVCF.java +%%JAVAJARDIR%%/bbmap/var2/FeatureVectorMaker.class +%%JAVAJARDIR%%/bbmap/var2/FeatureVectorMaker.java %%JAVAJARDIR%%/bbmap/var2/FilterSam$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/FilterSam.class %%JAVAJARDIR%%/bbmap/var2/FilterSam.java @@ -2617,6 +2674,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/var2/MergeSamples$MergeThread.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.java +%%JAVAJARDIR%%/bbmap/var2/README.md %%JAVAJARDIR%%/bbmap/var2/Realign$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/Realign.class %%JAVAJARDIR%%/bbmap/var2/Realign.java @@ -2657,3 +2715,9 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/var2/VcfWriter$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/VcfWriter.class %%JAVAJARDIR%%/bbmap/var2/VcfWriter.java +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan$QuantileTransformer.class +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan.class +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan.java +%%JAVAJARDIR%%/bbmap/var2/VectorElba$ElbaMinMaxValues.class +%%JAVAJARDIR%%/bbmap/var2/VectorElba.class +%%JAVAJARDIR%%/bbmap/var2/VectorElba.java diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index 41df894298f4..49a990d3f216 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -1,6 +1,5 @@ PORTNAME= gatk -DISTVERSION= 4.6.1.0 -PORTREVISION= 1 +DISTVERSION= 4.6.2.0 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -31,7 +30,7 @@ NO_ARCH= yes DEPS_CACHE_DIR= ${WRKDIR} TEST_ENV= ${MAKE_ENV} \ - JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" \ + JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so -DLIBFML_PATH=${PREFIX}/lib/libfml.so" \ GATK_LOCAL_JAR=${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar PLIST_FILES= bin/${PORTNAME} \ @@ -117,9 +116,10 @@ do-install: do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space @cd ${WRKSRC} && \ - ${SETENV} ${TEST_ENV} gradle8 -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test + ${SETENV} ${TEST_ENV} gradle8 test -# tests results as of version 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 +# tests as of 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 +# tests as of 4.6.2.0: 288719 tests completed, 300 failed, 37 skipped # see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib .include <bsd.port.mk> diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo index 2494dc43dd72..42fbad5e8a91 100644 --- a/biology/gatk/distinfo +++ b/biology/gatk/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1730356703 -SHA256 (gatk-4.6.1.0-deps.tar.gz) = ea0205776f26bbe51bcdea6dd10df975a2e4861a772901523ff7ab123119b8ad -SIZE (gatk-4.6.1.0-deps.tar.gz) = 922113997 -SHA256 (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 6f840406ce226e202421464e2ae044f3c0bc63da63f245568f8ca1bc7769d378 -SIZE (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 4317548196 +TIMESTAMP = 1756227460 +SHA256 (gatk-4.6.2.0-deps.tar.gz) = c956ec3b6a209b4eaf9c20cb312635498b360aa372f824b33d392aa0ac594a77 +SIZE (gatk-4.6.2.0-deps.tar.gz) = 903933113 +SHA256 (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = c76b61a549f49004a54ae86e88cd8b7a180a3bd2e4a56b1c9185f30971c79866 +SIZE (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = 4318674606 diff --git a/biology/gatk/files/gatk.sh.in b/biology/gatk/files/gatk.sh.in index d3d5c0f7bf5a..20c6c16d5164 100644 --- a/biology/gatk/files/gatk.sh.in +++ b/biology/gatk/files/gatk.sh.in @@ -23,5 +23,5 @@ fi # execute the command # add the LIBBWA_PATH system parameter (not sure whether the env. var or argument alone are sufficient) -JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so" \ -%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" +JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so" \ +%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" diff --git a/biology/gkl/Makefile b/biology/gkl/Makefile index 7c4c025158c6..128a190d5839 100644 --- a/biology/gkl/Makefile +++ b/biology/gkl/Makefile @@ -1,6 +1,5 @@ PORTNAME= gkl -DISTVERSION= 0.8.11-9 -DISTVERSIONSUFFIX= -g25670d8 +DISTVERSION= 0.9.1 CATEGORIES= biology devel MAINTAINER= yuri@FreeBSD.org diff --git a/biology/gkl/distinfo b/biology/gkl/distinfo index 35c01c063547..d1758a9bcd7a 100644 --- a/biology/gkl/distinfo +++ b/biology/gkl/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1722788727 -SHA256 (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 743d1eb48c2629454a6dcb98d9adca3aaedfe9c658e6f89e890b03b6e029df61 -SIZE (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 5310668 +TIMESTAMP = 1755972512 +SHA256 (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 8e32bc3c63013ca6468c65fbbb6af80a433652b640be868d0cb82cb70a919799 +SIZE (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 5363673 diff --git a/biology/gkl/files/patch-CMakeLists.txt b/biology/gkl/files/patch-CMakeLists.txt index 2cda423767df..a05193ec57f9 100644 --- a/biology/gkl/files/patch-CMakeLists.txt +++ b/biology/gkl/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2024-08-04 17:44:32 UTC +--- CMakeLists.txt.orig 2025-07-07 07:42:12 UTC +++ CMakeLists.txt -@@ -24,6 +24,8 @@ set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native) +@@ -28,6 +28,8 @@ set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native) # add CMakeLists.txt in subdirectories set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native) diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h new file mode 100644 index 000000000000..b47595807911 --- /dev/null +++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h @@ -0,0 +1,11 @@ +--- src/main/native/pdhmm/pdhmm-implementation.h.orig 2025-08-23 18:25:35 UTC ++++ src/main/native/pdhmm/pdhmm-implementation.h +@@ -31,7 +31,7 @@ + #include "avx512_impl.h" + #endif + +-#if defined(__linux__) ++#if defined(__linux__) || defined(__FreeBSD__) + #include <omp.h> + #endif + diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc new file mode 100644 index 000000000000..ebe9e8d41887 --- /dev/null +++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc @@ -0,0 +1,11 @@ +--- src/main/native/pdhmm/pdhmm-serial.cc.orig 2025-08-23 18:12:32 UTC ++++ src/main/native/pdhmm/pdhmm-serial.cc +@@ -24,7 +24,7 @@ + #include "pdhmm-serial.h" + #include "MathUtils.h" + #include <cstdio> +-#if defined(__linux__) ++#if defined(__linux__) || defined(__FreeBSD__) + #include <omp.h> + #endif + diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h index 4896be46607f..b4afa8fb6791 100644 --- a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h +++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h @@ -1,4 +1,4 @@ ---- src/main/native/pdhmm/pdhmm.h.orig 2024-08-04 16:31:53 UTC +--- src/main/native/pdhmm/pdhmm.h.orig 2025-07-07 07:42:12 UTC +++ src/main/native/pdhmm/pdhmm.h @@ -27,6 +27,9 @@ #ifdef linux @@ -8,5 +8,5 @@ +#include <omp.h> +#endif - inline INT_TYPE roundDownToNearestMultipleOf(INT_TYPE val, INT_TYPE mul) { return (val / mul) * mul; } + inline INT_TYPE CONCAT(roundDownToNearestMultipleOf_, SIMD_ENGINE)(INT_TYPE val, INT_TYPE mul) { return (val / mul) * mul; } diff --git a/biology/hyphy/files/patch-src_core_global__things.cpp b/biology/hyphy/files/patch-src_core_global__things.cpp new file mode 100644 index 000000000000..397be8520ae5 --- /dev/null +++ b/biology/hyphy/files/patch-src_core_global__things.cpp @@ -0,0 +1,20 @@ +--- src/core/global_things.cpp.orig 2025-08-22 19:21:44 UTC ++++ src/core/global_things.cpp +@@ -173,7 +173,7 @@ hyPointer MemAllocate(size_t bytes, bool zero, size_t + result = (hyPointer)zero ? calloc(bytes, 1) : malloc(bytes); + + if (result == nil) { +- HandleApplicationError(_String("Failed to allocate '") & bytes & "' bytes'", ++ HandleApplicationError(_String("Failed to allocate '") & (unsigned long)bytes & "' bytes'", + true); + } + return result; +@@ -186,7 +186,7 @@ hyPointer MemReallocate(hyPointer old_pointer, size_t + + if (result == nil) { + HandleApplicationError( +- _String("Failed to resize memory to '") & new_size & "' bytes'", true); ++ _String("Failed to resize memory to '") & (unsigned long)new_size & "' bytes'", true); + } + + return result; diff --git a/biology/linux-foldingathome/Makefile b/biology/linux-foldingathome/Makefile index db870ea430ca..7df5db1a03c8 100644 --- a/biology/linux-foldingathome/Makefile +++ b/biology/linux-foldingathome/Makefile @@ -1,10 +1,9 @@ PORTNAME= foldingathome DISTVERSION= 8.4.9 CATEGORIES= biology linux -MASTER_SITES= ${_MASTER_SITES} +MASTER_SITES= https://download.foldingathome.org/releases/public/fah-client/ PKGNAMEPREFIX= linux- -DISTNAME= fah-client_${DISTVERSION}-64bit-release -DISTFILES= ${_DISTFILES} +DISTNAME= ${_DISTNAME_${ARCH}} MAINTAINER= 0mp@FreeBSD.org COMMENT= Folding@home Client @@ -47,14 +46,12 @@ _FAHCLIENT_CONFIG_XML= ${ETCDIR}/config.xml _FAHCLIENT_WORK_DIR= /var/db/fahclient _FAHCLIENT_PROGRAM= ${PREFIX}/bin/fah-client -_MASTER_SITES_amd64= https://download.foldingathome.org/releases/public/fah-client/debian-10-64bit/release/ -_MASTER_SITES_aarch64= https://download.foldingathome.org/releases/public/fah-client/debian-stable-arm64/release/ +# The base name of the distribution file is the same for all supported +# architectures, so we need to work around that in a creative way. +_DISTNAME_amd64= debian-10-64bit/release/fah-client_${DISTVERSION}-64bit-release +_DISTNAME_aarch64= debian-stable-arm64/release/fah-client_${DISTVERSION}-64bit-release .if make(makesum) -_MASTER_SITES= ${ONLY_FOR_ARCHS:@.ARCH.@${_MASTER_SITES_${.ARCH.}}@} -_DISTFILES= ${ONLY_FOR_ARCHS:@.ARCH.@${DISTNAME}${EXTRACT_SUFX}?a=${.ARCH.}@} -.else -_MASTER_SITES= ${_MASTER_SITES_${ARCH}} -_DISTFILES= ${DISTNAME}${EXTRACT_SUFX}?a=${ARCH} +DISTFILES= ${ONLY_FOR_ARCHS:@.ARCH.@${_DISTNAME_${.ARCH.}}${EXTRACT_SUFX}@} .endif do-install: diff --git a/biology/linux-foldingathome/distinfo b/biology/linux-foldingathome/distinfo index a66f1eafad98..8db90e6fd74a 100644 --- a/biology/linux-foldingathome/distinfo +++ b/biology/linux-foldingathome/distinfo @@ -1,9 +1,5 @@ -TIMESTAMP = 1755706532 -SHA256 (fah-client_8.4.9-64bit-release.tar.bz2?a=aarch64) = 14ea352a42be0d34a1a0e2a4b46139e03d619a56bdd4908faaa56dc2665fcf3b -SIZE (fah-client_8.4.9-64bit-release.tar.bz2?a=aarch64) = 3667080 -SHA256 (fah-client_8.4.9-64bit-release.tar.bz2?a=amd64) = 14ea352a42be0d34a1a0e2a4b46139e03d619a56bdd4908faaa56dc2665fcf3b -SIZE (fah-client_8.4.9-64bit-release.tar.bz2?a=amd64) = 3667080 -SHA256 (fah-client_8.4.9-64bit-release.tar.bz2?a=aarch64) = 14ea352a42be0d34a1a0e2a4b46139e03d619a56bdd4908faaa56dc2665fcf3b -SIZE (fah-client_8.4.9-64bit-release.tar.bz2?a=aarch64) = 3667080 -SHA256 (fah-client_8.4.9-64bit-release.tar.bz2?a=amd64) = 14ea352a42be0d34a1a0e2a4b46139e03d619a56bdd4908faaa56dc2665fcf3b -SIZE (fah-client_8.4.9-64bit-release.tar.bz2?a=amd64) = 3667080 +TIMESTAMP = 1755790886 +SHA256 (debian-stable-arm64/release/fah-client_8.4.9-64bit-release.tar.bz2) = 14ea352a42be0d34a1a0e2a4b46139e03d619a56bdd4908faaa56dc2665fcf3b +SIZE (debian-stable-arm64/release/fah-client_8.4.9-64bit-release.tar.bz2) = 3667080 +SHA256 (debian-10-64bit/release/fah-client_8.4.9-64bit-release.tar.bz2) = 2acccbeda05649f6f913d29f91a22308e88ec3e117499f636a18dc56244d6cf1 +SIZE (debian-10-64bit/release/fah-client_8.4.9-64bit-release.tar.bz2) = 3649371 diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile index 6b66a17d1250..309fa98df6ca 100644 --- a/biology/py-bx-python/Makefile +++ b/biology/py-bx-python/Makefile @@ -1,6 +1,5 @@ PORTNAME= bx-python -DISTVERSION= 0.13.0 -PORTREVISION= 1 +DISTVERSION= 0.14.0 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,11 +13,18 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} -BUILD_DEPENDS= ${PY_DEPENDS} -RUN_DEPENDS= ${PY_DEPENDS} +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PY_DEPENDS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PY_DEPENDS} \ + ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR} USES= compiler python -USE_PYTHON= autoplist cython3 distutils +USE_PYTHON= pep517 cython3 autoplist + +post-patch: + # force cythonization, compilation fails otherwise for some reason + @${TOUCH} `${FIND} ${WRKSRC} -name "*.pyx" -o -name "*.pxd"` post-install: @${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/bx -name "*.so" | ${XARGS} ${STRIP_CMD} diff --git a/biology/py-bx-python/distinfo b/biology/py-bx-python/distinfo index 56d00203a687..85e09edf789a 100644 --- a/biology/py-bx-python/distinfo +++ b/biology/py-bx-python/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1734273029 -SHA256 (bx_python-0.13.0.tar.gz) = ce04696543367efc6b7995d9463efeda691b9a58f6f55a7bd831e642159b0644 -SIZE (bx_python-0.13.0.tar.gz) = 1899129 +TIMESTAMP = 1756062999 +SHA256 (bx_python-0.14.0.tar.gz) = c46eef1006d6107e31d2ff42f1ca27c34ddb080151309a909b4d2e53ca812cc6 +SIZE (bx_python-0.14.0.tar.gz) = 2085934 diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile index 9c8fc69ba93e..c1675008fd19 100644 --- a/biology/seqan3/Makefile +++ b/biology/seqan3/Makefile @@ -1,10 +1,16 @@ PORTNAME= seqan3 -DISTVERSION= 3.3.0 +DISTVERSION= 3.4.0 CATEGORIES= biology devel math +MASTER_SITES= https://github.com/cpm-cmake/CPM.cmake/releases/download/v0.42.0/:cpm +DISTFILES= CPM.cmake:cpm +DIST_SUBDIR= ${PORTNAME}-${DISTVERSION} +EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} \ + xxsds-sdsl-lite-d54d389_GH0${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= C++ header-only library for biological sequence analysis -WWW= https://github.com/seqan/seqan3 +WWW= https://www.seqan.de/ \ + https://github.com/seqan/seqan3 LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.md @@ -15,14 +21,13 @@ BUILD_DEPENDS= ${HPP_DEPENDS} RUN_DEPENDS= ${HPP_DEPENDS} \ coin-or-lemon>0:math/lemon -USES= cmake localbase +USES= cmake compiler:c++23-lang localbase USE_GITHUB= yes GH_ACCOUNT= seqan GH_TUPLE= xxsds:sdsl-lite:d54d389:sdsl_lite/submodules/sdsl-lite -USE_GCC= yes # tests only pass with gcc, see https://github.com/seqan/seqan3/issues/2643, otherwise gcc isn't needed because this is a header-only library -# tests fail to compile, see https://github.com/seqan/seqan3/issues/3191 +CMAKE_ARGS= -DCPM_LOCATION=${DISTDIR}/${DIST_SUBDIR} TEST_WRKSRC= ${WRKSRC}/.test @@ -33,7 +38,7 @@ post-install: do-test: @${MKDIR} ${TEST_WRKSRC} && cd ${TEST_WRKSRC} && \ - ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} ${WRKSRC}/test/unit && \ + ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFETCHCONTENT_FULLY_DISCONNECTED=OFF ${WRKSRC}/test/unit && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ctest diff --git a/biology/seqan3/distinfo b/biology/seqan3/distinfo index 8fa5387420f9..9e9fe56de4ee 100644 --- a/biology/seqan3/distinfo +++ b/biology/seqan3/distinfo @@ -1,5 +1,7 @@ -TIMESTAMP = 1694368553 -SHA256 (seqan-seqan3-3.3.0_GH0.tar.gz) = 96975406445c8a5974803eefa146ee2f85206f6d2c2bccf45171ee0b1a653fb8 -SIZE (seqan-seqan3-3.3.0_GH0.tar.gz) = 1564852 -SHA256 (xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1 -SIZE (xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835 +TIMESTAMP = 1756395731 +SHA256 (seqan3-3.4.0/CPM.cmake) = 2020b4fc42dba44817983e06342e682ecfc3d2f484a581f11cc5731fbe4dce8a +SIZE (seqan3-3.4.0/CPM.cmake) = 44969 +SHA256 (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 8e000e6788f1e2ada071b36f64231d56f18e2d687ab4122d86cd3aefc6c87743 +SIZE (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 1749810 +SHA256 (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1 +SIZE (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835 diff --git a/biology/seqan3/files/patch-cmake_CPM.cmake b/biology/seqan3/files/patch-cmake_CPM.cmake new file mode 100644 index 000000000000..c288163d7312 --- /dev/null +++ b/biology/seqan3/files/patch-cmake_CPM.cmake @@ -0,0 +1,11 @@ +--- cmake/CPM.cmake.orig 2025-08-28 15:36:29 UTC ++++ cmake/CPM.cmake +@@ -16,7 +16,7 @@ get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DO + # Expand relative path. This is important if the provided path contains a tilde (~) + get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DOWNLOAD_LOCATION} ABSOLUTE) + +-file (DOWNLOAD https://github.com/cpm-cmake/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake ++file (DOWNLOAD file://${CPM_LOCATION}/CPM.cmake + ${CPM_DOWNLOAD_LOCATION} EXPECTED_HASH SHA256=${CPM_HASH_SUM}) + + include (${CPM_DOWNLOAD_LOCATION}) diff --git a/biology/seqan3/pkg-plist b/biology/seqan3/pkg-plist index 19d86e63d82e..e727ba232e45 100644 --- a/biology/seqan3/pkg-plist +++ b/biology/seqan3/pkg-plist @@ -91,6 +91,7 @@ include/seqan3/alignment/scoring/all.hpp include/seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp include/seqan3/alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp include/seqan3/alignment/scoring/detail/simd_matrix_scoring_scheme.hpp +include/seqan3/alignment/scoring/hamming_scoring_scheme.hpp include/seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp include/seqan3/alignment/scoring/scoring_scheme_base.hpp include/seqan3/alignment/scoring/scoring_scheme_concept.hpp @@ -191,11 +192,16 @@ include/seqan3/contrib/README.md include/seqan3/contrib/parallel/buffer_queue.hpp include/seqan3/contrib/parallel/serialised_resource_pool.hpp include/seqan3/contrib/parallel/suspendable_queue.hpp +include/seqan3/contrib/sdsl-lite.hpp include/seqan3/contrib/std/.clang-format include/seqan3/contrib/std/.gitignore -include/seqan3/contrib/std/LICENSE +include/seqan3/contrib/std/LICENSE.md +include/seqan3/contrib/std/LICENSES/BSD-3-Clause.txt +include/seqan3/contrib/std/LICENSES/CC-BY-4.0.txt +include/seqan3/contrib/std/LICENSES/CC0-1.0.txt include/seqan3/contrib/std/README.md include/seqan3/contrib/std/all_view.hpp +include/seqan3/contrib/std/chunk_by_view.hpp include/seqan3/contrib/std/chunk_view.hpp include/seqan3/contrib/std/concepts.hpp include/seqan3/contrib/std/detail/adaptor_base.hpp @@ -203,7 +209,9 @@ include/seqan3/contrib/std/detail/adaptor_for_view_without_args.hpp include/seqan3/contrib/std/detail/adaptor_from_functor.hpp include/seqan3/contrib/std/detail/compiler_definitions.hpp include/seqan3/contrib/std/detail/exposition_only.hpp +include/seqan3/contrib/std/detail/movable_box.hpp include/seqan3/contrib/std/detail/non_propagating_cache.hpp +include/seqan3/contrib/std/enumerate_view.hpp include/seqan3/contrib/std/join_with_view.hpp include/seqan3/contrib/std/pair.hpp include/seqan3/contrib/std/to.hpp @@ -239,14 +247,13 @@ include/seqan3/core/debug_stream.hpp include/seqan3/core/debug_stream/all.hpp include/seqan3/core/debug_stream/byte.hpp include/seqan3/core/debug_stream/debug_stream_type.hpp +include/seqan3/core/debug_stream/default_printer.hpp include/seqan3/core/debug_stream/detail/to_string.hpp include/seqan3/core/debug_stream/optional.hpp include/seqan3/core/debug_stream/range.hpp include/seqan3/core/debug_stream/tuple.hpp include/seqan3/core/debug_stream/variant.hpp include/seqan3/core/detail/all.hpp -include/seqan3/core/detail/all_view.hpp -include/seqan3/core/detail/copyable_wrapper.hpp include/seqan3/core/detail/customisation_point.hpp include/seqan3/core/detail/deferred_crtp_base.hpp include/seqan3/core/detail/empty_type.hpp @@ -364,127 +371,10 @@ include/seqan3/search/views/minimiser.hpp include/seqan3/search/views/minimiser_hash.hpp include/seqan3/std/charconv include/seqan3/std/new -include/seqan3/submodules/sdsl-lite/include/sdsl/.gitignore -include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vector_il.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vectors.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bits.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_g.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_gg.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cereal.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder_comma.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder_elias_delta.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder_elias_gamma.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/coder_fibonacci.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/config.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_bwt.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_config.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_isa.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_lcp.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_lcp_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_sa.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/construct_sa_se.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_bitcompressed.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/csa_wt.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cst_fully.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cst_iterators.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cst_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/cst_sct3.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/dac_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/divsufsort.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/enc_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/fast_cache.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/hyb_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_buffer.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_mapper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/inv_perm_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/io.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/iterators.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_tree.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/k2_tree_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_byte.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_dac.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_tree.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_tree2.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_vlc.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_wt.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/louds_tree.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/memory_management.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/memory_tracking.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/platform.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/qsufsort.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/ram_filebuf.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/ram_fs.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int_scan.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int_v.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_scan.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_v.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_v5.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_vector_15.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sd_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sdsl_concepts.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/select_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/select_support_mcl.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/select_support_scan.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sfstream.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_int_stack.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_stack_support.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/structure_tree.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_array_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_arrays.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_tree_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_trees.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/uint128_t.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/uint256_t.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/uintx_t.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/util.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/vectors.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/vlc_vector.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wavelet_trees.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wm_int.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_algorithm.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_ap.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_blcd.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_epr.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_gmr.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_helper.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_huff.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_hutu.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_int.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_pc.hpp -include/seqan3/submodules/sdsl-lite/include/sdsl/wt_rlmn.hpp include/seqan3/utility/all.hpp include/seqan3/utility/bloom_filter/all.hpp include/seqan3/utility/bloom_filter/bloom_filter.hpp +include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp include/seqan3/utility/char_operations/all.hpp include/seqan3/utility/char_operations/predicate.hpp include/seqan3/utility/char_operations/predicate_detail.hpp |