[med-svn] [Git][med-team/mmseqs2][master] 8 commits: Fix build with CMake 4
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Oct 19 20:33:59 BST 2025
Andreas Tille pushed to branch master at Debian Med / mmseqs2
Commits:
1085e4ac by Andreas Tille at 2025-10-19T20:50:47+02:00
Fix build with CMake 4
Closes: #1113291
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63710852 by Andreas Tille at 2025-10-19T21:03:19+02:00
d/watch: version=5
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5717b94c by Andreas Tille at 2025-10-19T21:04:08+02:00
New upstream version 18-8cc5c+ds
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24a7bbfc by Andreas Tille at 2025-10-19T21:04:08+02:00
New upstream version
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025caa42 by Andreas Tille at 2025-10-19T21:04:20+02:00
Update upstream source from tag 'upstream/18-8cc5c+ds'
Update to upstream version '18-8cc5c+ds'
with Debian dir 216372b0ea944ec11b0aeb5569c485870c6710be
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bf8127c7 by Andreas Tille at 2025-10-19T21:04:20+02:00
Standards-Version: 4.7.2 (routine-update)
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236e2291 by Andreas Tille at 2025-10-19T21:11:05+02:00
debputy lint --auto-fix (routine-update)
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b420bca4 by Andreas Tille at 2025-10-19T21:27:23+02:00
Refresh patches
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330 changed files:
- .cirrus.yml
- + .github/workflows/Dockerfile.GPU-buster-cross-sbsa
- + .github/workflows/Dockerfile.GPU-manylinux2014
- .github/workflows/docker.yml
- .github/workflows/mac-arm64.yml
- + .github/workflows/test-gpu.yml
- .gitignore
- CMakeLists.txt
- Dockerfile
- LICENSE.md
- README.md
- azure-pipelines.yml
- cmake/FindAtomic.cmake
- cmake/MMseqsSetupDerivedTarget.cmake
- cmake/xxdi.pl
- data/PAM10.out
- data/PAM100.out
- data/PAM110.out
- data/PAM120.out
- data/PAM130.out
- data/PAM140.out
- data/PAM160.out
- data/PAM170.out
- data/PAM180.out
- data/PAM190.out
- data/PAM20.out
- data/PAM40.out
- data/PAM50.out
- data/PAM60.out
- data/PAM70.out
- data/PAM80.out
- data/PAM90.out
- + data/VTML200.out
- data/blosum100.out
- data/blosum30.out
- data/blosum35.out
- data/blosum40.out
- data/blosum45.out
- data/blosum50.out
- data/blosum55.out
- data/blosum60.out
- data/blosum65.out
- data/blosum70.out
- data/blosum75.out
- data/blosum80.out
- data/blosum85.out
- data/blosum90.out
- data/blosum95.out
- data/workflow/CMakeLists.txt
- data/workflow/blastp.sh
- data/workflow/cascaded_clustering.sh
- data/workflow/createindex.sh
- data/workflow/createtaxdb.sh
- data/workflow/databases.sh
- data/workflow/easyrbh.sh
- data/workflow/easysearch.sh
- data/workflow/nucleotide_clustering.sh
- + data/workflow/pickconsensusrep.sh
- data/workflow/searchslicedtargetprofile.sh
- data/workflow/taxpercontig.sh
- data/workflow/translated_search.sh
- data/workflow/tsv2exprofiledb.sh
- data/workflow/update_clustering.sh
- debian/changelog
- debian/control
- debian/patches/use_system_gzstream.patch
- debian/rules
- debian/watch
- − lib/cacode/CMakeLists.txt
- − lib/cacode/LICENSE.LAST
- − lib/cacode/LICENSE.NCBI
- − lib/cacode/README
- − lib/cacode/lambda_calculator.cpp
- − lib/cacode/lambda_calculator.h
- − lib/cacode/lubksb.cpp
- − lib/cacode/ludcmp.cpp
- − lib/cacode/nrutil.cpp
- − lib/cacode/nrutil.h
- + lib/fast_float/VERSION
- + lib/fast_float/fast_float.h
- + lib/fmt/LICENSE
- + lib/fmt/README.md
- + lib/fmt/VERSION
- + lib/fmt/fmt/args.h
- + lib/fmt/fmt/base.h
- + lib/fmt/fmt/chrono.h
- + lib/fmt/fmt/color.h
- + lib/fmt/fmt/compile.h
- + lib/fmt/fmt/core.h
- + lib/fmt/fmt/format-inl.h
- + lib/fmt/fmt/format.h
- + lib/fmt/fmt/os.h
- + lib/fmt/fmt/ostream.h
- + lib/fmt/fmt/printf.h
- + lib/fmt/fmt/ranges.h
- + lib/fmt/fmt/std.h
- + lib/fmt/fmt/xchar.h
- + lib/libmarv/.gitignore
- + lib/libmarv/LICENSE
- + lib/libmarv/Makefile
- + lib/libmarv/Readme.md
- + lib/libmarv/allqueries.fasta
- + lib/libmarv/src/CMakeLists.txt
- + lib/libmarv/src/base64.h
- + lib/libmarv/src/benchmarking.cuh
- + lib/libmarv/src/blosum.cu
- + lib/libmarv/src/blosum.hpp
- + lib/libmarv/src/config.hpp
- + lib/libmarv/src/convert.cuh
- + lib/libmarv/src/cudasw4.cuh
- + lib/libmarv/src/dbbatching.cuh
- + lib/libmarv/src/dbdata.cpp
- + lib/libmarv/src/dbdata.hpp
- + lib/libmarv/src/gapless_kernel_config.cuh
- + lib/libmarv/src/gpudatabaseallocation.cuh
- + lib/libmarv/src/hpc_helpers/all_helpers.cuh
- + lib/libmarv/src/hpc_helpers/coop_group_helpers.cuh
- + lib/libmarv/src/hpc_helpers/cuda_helpers.cuh
- + lib/libmarv/src/hpc_helpers/cuda_raiiwrappers.cuh
- + lib/libmarv/src/hpc_helpers/custom_thrust_allocators.cuh
- + lib/libmarv/src/hpc_helpers/hashers.cuh
- + lib/libmarv/src/hpc_helpers/hpc_helpers.h
- + lib/libmarv/src/hpc_helpers/io_helpers.h
- + lib/libmarv/src/hpc_helpers/nvtx_markers.cuh
- + lib/libmarv/src/hpc_helpers/packed_types.cuh
- + lib/libmarv/src/hpc_helpers/peer_access.cuh
- + lib/libmarv/src/hpc_helpers/simple_allocation.cuh
- + lib/libmarv/src/hpc_helpers/timers.cuh
- + lib/libmarv/src/hpc_helpers/type_helpers.h
- + lib/libmarv/src/hpc_helpers/utility_kernels.cuh
- + lib/libmarv/src/kernelhelpers.cuh
- + lib/libmarv/src/kernels.cuh
- + lib/libmarv/src/kseqpp/filereader.hpp
- + lib/libmarv/src/kseqpp/gziphelpers.hpp
- + lib/libmarv/src/kseqpp/kseqpp.hpp
- + lib/libmarv/src/length_partitions.hpp
- + lib/libmarv/src/main.cu
- + lib/libmarv/src/makedb.cpp
- + lib/libmarv/src/mapped_file.hpp
- + lib/libmarv/src/marv.cu
- + lib/libmarv/src/marv.h
- + lib/libmarv/src/mathops.cuh
- + lib/libmarv/src/mmapbuffer.hpp
- + lib/libmarv/src/options.cpp
- + lib/libmarv/src/options.hpp
- + lib/libmarv/src/pssm.cuh
- + lib/libmarv/src/pssmkernels_gapless.cuh
- + lib/libmarv/src/pssmkernels_gapless_instantiation_dpx.cu
- + lib/libmarv/src/pssmkernels_gapless_instantiation_dpx_kernelparamzero.cu
- + lib/libmarv/src/pssmkernels_gapless_instantiation_half2.cu
- + lib/libmarv/src/pssmkernels_gapless_instantiation_half2_kernelparamzero.cu
- + lib/libmarv/src/pssmkernels_smithwaterman.cuh
- + lib/libmarv/src/pssmkernels_smithwaterman_instantiation_dpx.cu
- + lib/libmarv/src/pssmkernels_smithwaterman_instantiation_float.cu
- + lib/libmarv/src/sequence_io.cpp
- + lib/libmarv/src/sequence_io.h
- + lib/libmarv/src/smithwaterman_kernel_config.cuh
- + lib/libmarv/src/target_subject_ids.cuh
- + lib/libmarv/src/tileconfigsearch.cu
- + lib/libmarv/src/types.hpp
- + lib/libmarv/src/util.cuh
- + lib/libmarv/tuningconfigs/A100/gapless.txt
- + lib/libmarv/tuningconfigs/A100/swendpos.txt
- + lib/libmarv/tuningconfigs/GraceHopper/gapless.txt
- + lib/libmarv/tuningconfigs/GraceHopper/swendpos.txt
- + lib/libmarv/tuningconfigs/H100/gapless.txt
- + lib/libmarv/tuningconfigs/H100/swendpos.txt
- + lib/libmarv/tuningconfigs/L4/gapless.txt
- + lib/libmarv/tuningconfigs/L4/swendpos.txt
- + lib/libmarv/tuningconfigs/L40S/gapless.txt
- + lib/libmarv/tuningconfigs/L40S/swendpos.txt
- + lib/libmarv/tuningconfigs/RTX4090/gapless.txt
- + lib/libmarv/tuningconfigs/RTX4090/swendpos.txt
- + lib/libmarv/tuningconfigs/T4/gapless.txt
- + lib/libmarv/tuningconfigs/T4/swendpos.txt
- − lib/omptl/Example.cpp
- − lib/omptl/License.txt
- − lib/omptl/algorithm
- − lib/omptl/numeric
- − lib/omptl/omptl
- − lib/omptl/omptl_algorithm
- − lib/omptl/omptl_algorithm_par.h
- − lib/omptl/omptl_algorithm_ser.h
- − lib/omptl/omptl_numeric
- − lib/omptl/omptl_numeric_extensions.h
- − lib/omptl/omptl_numeric_extensions_par.h
- − lib/omptl/omptl_numeric_extensions_ser.h
- − lib/omptl/omptl_numeric_par.h
- − lib/omptl/omptl_numeric_ser.h
- − lib/omptl/omptl_tools.h
- lib/simd/simd.h
- + lib/tantan/CMakeLists.txt
- + lib/tantan/mcf_simd.h
- + lib/tantan/tantan.cpp
- src/commons/tantan.h → lib/tantan/tantan.h
- lib/tinyexpr/CMakeLists.txt
- src/CMakeLists.txt
- src/CommandDeclarations.h
- src/MMseqsBase.cpp
- src/alignment/Alignment.cpp
- src/alignment/CMakeLists.txt
- src/alignment/CompressedA3M.cpp
- + src/alignment/Fwbw.cpp
- + src/alignment/Fwbw.h
- src/alignment/Matcher.cpp
- src/alignment/PSSMCalculator.cpp
- src/alignment/PSSMCalculator.h
- − src/alignment/PSSMMasker.h
- src/alignment/StripedSmithWaterman.cpp
- src/commons/Application.cpp
- src/commons/BaseMatrix.h
- src/commons/CMakeLists.txt
- src/commons/Command.cpp
- src/commons/Command.h
- src/commons/DBReader.cpp
- src/commons/DBReader.h
- src/commons/DBWriter.cpp
- src/commons/DBWriter.h
- src/commons/Debug.h
- src/commons/FastSort.h
- + src/commons/GpuUtil.cpp
- + src/commons/GpuUtil.h
- + src/commons/GzReader.h
- + src/commons/LambdaCalculation.cpp
- + src/commons/LambdaCalculation.h
- + src/commons/Masker.cpp
- + src/commons/Masker.h
- src/commons/MathUtil.h
- src/commons/MemoryMapped.cpp
- src/commons/MultiParam.h
- src/commons/Parameters.cpp
- src/commons/Parameters.h
- src/commons/Sequence.cpp
- src/commons/SubstitutionMatrix.cpp
- src/commons/SubstitutionMatrix.h
- src/commons/Util.cpp
- src/commons/Util.h
- − src/commons/tantan.cpp
- src/linclust/kmermatcher.cpp
- src/mmseqs.cpp
- src/multihit/MultiHitDb.cpp
- src/multihit/MultiHitSearch.cpp
- src/prefiltering/CacheFriendlyOperations.cpp
- src/prefiltering/CacheFriendlyOperations.h
- src/prefiltering/IndexBuilder.cpp
- src/prefiltering/IndexBuilder.h
- src/prefiltering/IndexTable.h
- src/prefiltering/Prefiltering.cpp
- src/prefiltering/Prefiltering.h
- src/prefiltering/PrefilteringIndexReader.cpp
- src/prefiltering/PrefilteringIndexReader.h
- src/prefiltering/QueryMatcher.cpp
- src/prefiltering/QueryMatcher.h
- src/prefiltering/QueryMatcherTaxonomyHook.h
- src/prefiltering/UngappedAlignment.cpp
- src/prefiltering/UngappedAlignment.h
- src/prefiltering/ungappedprefilter.cpp
- src/taxonomy/NcbiTaxonomy.cpp
- src/taxonomy/NcbiTaxonomy.h
- src/taxonomy/createbintaxonomy.cpp
- src/taxonomy/taxonomyreport.cpp
- src/test/CMakeLists.txt
- src/test/TestAlignment.cpp
- src/test/TestAlignmentPerformance.cpp
- src/test/TestAlignmentTraceback.cpp
- src/test/TestAlp.cpp
- src/test/TestBacktraceTranslator.cpp
- src/test/TestBestAlphabet.cpp
- src/test/TestCompositionBias.cpp
- src/test/TestDiagonalScoring.cpp
- src/test/TestDiagonalScoringPerformance.cpp
- src/test/TestKmerGenerator.cpp
- src/test/TestKmerNucl.cpp
- src/test/TestKmerScore.cpp
- src/test/TestKwayMerge.cpp
- src/test/TestMultipleAlignment.cpp
- src/test/TestPSSM.cpp
- src/test/TestPSSMPrune.cpp
- src/test/TestProfileAlignment.cpp
- src/test/TestReduceMatrix.cpp
- src/test/TestScoreMatrixSerialization.cpp
- src/test/TestSequenceIndex.cpp
- src/test/TestTanTan.cpp
- + src/test/TestUngappedCpuPerf.cpp
- src/util/CMakeLists.txt
- src/util/apply.cpp
- + src/util/calculatelambda.cpp
- src/util/convertalignments.cpp
- src/util/convertkb.cpp
- src/util/convertmsa.cpp
- src/util/createclusterdb.cpp
- src/util/createdb.cpp
- src/util/createtsv.cpp
- src/util/diskspaceavail.cpp
- src/util/expandaln.cpp
- src/util/extractframes.cpp
- src/util/filterdb.cpp
- + src/util/gpuserver.cpp
- src/util/indexdb.cpp
- + src/util/makepaddedseqdb.cpp
- src/util/masksequence.cpp
- src/util/msa2profile.cpp
- src/util/msa2result.cpp
- src/util/nrtotaxmapping.cpp
- src/util/pairaln.cpp
- + src/util/recoverlongestorf.cpp
- src/util/result2msa.cpp
- src/util/result2profile.cpp
- src/util/sequence2profile.cpp
- src/util/subtractdbs.cpp
- src/util/summarizeresult.cpp
- src/util/tsv2exprofiledb.cpp
- src/util/unpackdb.cpp
- src/workflow/CMakeLists.txt
- src/workflow/ClusterUpdate.cpp
- src/workflow/CreateIndex.cpp
- src/workflow/EasyCluster.cpp
- src/workflow/EasyLinclust.cpp
- src/workflow/EasyRbh.cpp
- src/workflow/EasySearch.cpp
- src/workflow/EasyTaxonomy.cpp
- src/workflow/Linsearch.cpp
- src/workflow/Map.cpp
- + src/workflow/PickConsensusRep.cpp
- src/workflow/Rbh.cpp
- src/workflow/Search.cpp
- src/workflow/Taxonomy.cpp
- util/build_osx.sh
- util/mmseqs_wrapper.bat
- + util/update_libmarv.sh
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/207f3e436197228330537294084277969bc72527...b420bca43574c0b7337dbd70bbf73dffc711fcee
--
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/207f3e436197228330537294084277969bc72527...b420bca43574c0b7337dbd70bbf73dffc711fcee
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