[med-svn] [Git][med-team/sortmerna][master] 20 commits: Packaging update (routine-update)

Andreas Tille (@tille) gitlab at salsa.debian.org
Mon Oct 19 13:54:34 BST 2026 


Andreas Tille pushed to branch master at Debian Med / sortmerna


Commits:
8e2d2be0 by Andreas Tille at 2026-09-17T08:15:25+02:00
Packaging update (routine-update)

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f0b14b22 by Andreas Tille at 2026-09-17T08:15:39+02:00
New upstream version

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dd6a730d by Andreas Tille at 2026-09-17T08:15:40+02:00
New upstream version 7.0.0
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979d0e80 by Andreas Tille at 2026-09-17T08:18:53+02:00
Update upstream source from tag 'upstream/7.0.0'

Update to upstream version '7.0.0'
with Debian dir afcd61568b698906d7f1b38e92659affc184a4f9
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5588c23f by Andreas Tille at 2026-09-17T08:18:54+02:00
Standards-Version: 4.7.4 (routine-update)

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14780dad by Andreas Tille at 2026-09-17T08:38:46+02:00
Changes made by cme

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d9792016 by Andreas Tille at 2026-09-17T07:38:58+01:00
Set upstream metadata fields: Bug-Database, Repository-Browse.

Changes-By: lintian-brush

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7cabc1d6 by Andreas Tille at 2026-09-17T08:39:00+02:00
debputy lint --auto-fix (routine-update)

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6f0f4013 by Andreas Tille at 2026-09-17T08:40:28+02:00
Drop sse2-support dependency Closes: #1144278

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c311ed3a by Andreas Tille at 2026-09-17T08:44:09+02:00
Most patches can be droped in new upstream version

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abecaebc by Andreas Tille at 2026-10-19T14:40:30+02:00
New upstream version

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5f682603 by Andreas Tille at 2026-10-19T14:40:31+02:00
New upstream version 7.1.0
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8331d3b9 by Andreas Tille at 2026-10-19T14:44:12+02:00
Update upstream source from tag 'upstream/7.1.0'

Update to upstream version '7.1.0'
with Debian dir 4f8495dabeeb913d48543b2979e4b80d95f3619a
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aa8ae9a1 by Andreas Tille at 2026-10-19T14:44:15+02:00
Changes made by cme

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1ca53b9d by Andreas Tille at 2026-10-19T13:44:26+01:00
Remove duplicate line from changelog.

Changes-By: lintian-brush

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057a381e by Andreas Tille at 2026-10-19T13:44:29+01:00
Set upstream metadata fields: Bug-Submit, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: source: upstream-metadata-missing-bug-tracking [debian/upstream/metadata]
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html

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e92befb4 by Andreas Tille at 2026-10-19T14:49:21+02:00
d/control:

   - add build-deps librapidarchive-dev, libparasail-dev, libbbhash-dev and
     zlib1g-dev
   - drop rapidjson-dev and libconcurrentqueue-dev.

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579b90bc by Andreas Tille at 2026-10-19T14:51:00+02:00
add rapidarchive.patch: use system librapidarchive

* add smr-api-disable.patch: skip the self-contained static bundle,
    which needs static parasail/rocksdb not available in Debian

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3fe4add2 by Andreas Tille at 2026-10-19T14:51:37+02:00
d/copyright: drop the ssw.c stanza, SSW was removed upstream

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f1b0fe14 by Andreas Tille at 2026-10-19T14:54:12+02:00
d/man/sortmerna.1: update for the 7.1.0 command line

- - - - -


271 changed files:

- .github/workflows/build_linux.yml
- + .github/workflows/build_linux_arm64.yml
- .github/workflows/build_multi_platform.yml
- .github/workflows/build_osx.yml
- − .github/workflows/build_windows.yml
- + .github/workflows/release.yml
- .gitignore
- 3rdparty.jinja
- 3rdparty/alp/CMakeLists.txt
- − 3rdparty/cmph/CMakeLists.txt
- − 3rdparty/cmph/bdz.c
- − 3rdparty/cmph/bdz.h
- − 3rdparty/cmph/bdz_ph.c
- − 3rdparty/cmph/bdz_ph.h
- − 3rdparty/cmph/bdz_structs.h
- − 3rdparty/cmph/bdz_structs_ph.h
- − 3rdparty/cmph/bitbool.h
- − 3rdparty/cmph/bmz.c
- − 3rdparty/cmph/bmz.h
- − 3rdparty/cmph/bmz8.c
- − 3rdparty/cmph/bmz8.h
- − 3rdparty/cmph/bmz8_structs.h
- − 3rdparty/cmph/bmz_structs.h
- − 3rdparty/cmph/brz.c
- − 3rdparty/cmph/brz.h
- − 3rdparty/cmph/brz_structs.h
- − 3rdparty/cmph/buffer_entry.c
- − 3rdparty/cmph/buffer_entry.h
- − 3rdparty/cmph/buffer_manager.c
- − 3rdparty/cmph/buffer_manager.h
- − 3rdparty/cmph/chd.c
- − 3rdparty/cmph/chd.h
- − 3rdparty/cmph/chd_ph.c
- − 3rdparty/cmph/chd_ph.h
- − 3rdparty/cmph/chd_structs.h
- − 3rdparty/cmph/chd_structs_ph.h
- − 3rdparty/cmph/chm.c
- − 3rdparty/cmph/chm.h
- − 3rdparty/cmph/chm_structs.h
- − 3rdparty/cmph/cmph.c
- − 3rdparty/cmph/cmph.h
- − 3rdparty/cmph/cmph_structs.c
- − 3rdparty/cmph/cmph_structs.h
- − 3rdparty/cmph/cmph_time.h
- − 3rdparty/cmph/cmph_types.h
- − 3rdparty/cmph/compressed_rank.c
- − 3rdparty/cmph/compressed_rank.h
- − 3rdparty/cmph/compressed_seq.c
- − 3rdparty/cmph/compressed_seq.h
- − 3rdparty/cmph/debug.h
- − 3rdparty/cmph/fch.c
- − 3rdparty/cmph/fch.h
- − 3rdparty/cmph/fch_buckets.c
- − 3rdparty/cmph/fch_buckets.h
- − 3rdparty/cmph/fch_structs.h
- − 3rdparty/cmph/graph.c
- − 3rdparty/cmph/graph.h
- − 3rdparty/cmph/hash.c
- − 3rdparty/cmph/hash.h
- − 3rdparty/cmph/hash_state.h
- − 3rdparty/cmph/jenkins_hash.c
- − 3rdparty/cmph/jenkins_hash.h
- − 3rdparty/cmph/miller_rabin.c
- − 3rdparty/cmph/miller_rabin.h
- − 3rdparty/cmph/select.c
- − 3rdparty/cmph/select.h
- − 3rdparty/cmph/select_lookup_tables.h
- − 3rdparty/cmph/vqueue.c
- − 3rdparty/cmph/vqueue.h
- − 3rdparty/cmph/vstack.c
- − 3rdparty/cmph/vstack.h
- CMakeLists.txt
- CMakePresets.json
- Dockerfile
- README.md
- + cmake/bundle_static_libs.cmake
- + cmake/conda_tc.cmake
- cmake/presets/CMakePresets_rocksdb.json
- − cmake/sortmernaConfig.cmake.in
- + conda_build_env.yaml
- + conda_run_env.yaml
- + copyright.tmpl
- debian/changelog
- debian/control
- debian/copyright
- debian/man/sortmerna.1
- − debian/patches/c23.patch
- − debian/patches/concurrentqueue.h.patch
- debian/patches/gcc-13.patch
- − debian/patches/pyhon3.12-syntax.patch
- + debian/patches/rapidarchive.patch
- debian/patches/series
- + debian/patches/smr-api-disable.patch
- debian/upstream/metadata
- debian/watch
- + docs/c_api.rst
- docs/index.rst
- include/ThreadPool.hpp
- include/alignment.hpp
- include/baserec.hpp
- include/bitvector.hpp
- include/build_version.h
- include/cmd.hpp
- include/common.hpp
- include/config.h
- include/index.hpp
- include/indexdb.hpp
- include/izlib.hpp
- include/kseq_load.hpp
- include/kvdb.hpp
- include/loadgenome.hpp
- include/minoccur.hpp
- include/options.hpp
- include/otumap.h
- include/output.hpp
- include/paralleltraversal.hpp
- include/processor.hpp
- include/read.hpp
- include/readfeed.hpp
- include/readfile.h
- − include/readsqueue.hpp
- include/readstate.h
- include/readstats.hpp
- include/references.hpp
- include/refstats.hpp
- include/report.h
- include/report_biom.h
- include/report_blast.h
- include/report_denovo.h
- include/report_fastx.h
- include/report_fx_base.h
- include/report_fx_other.h
- include/report_sam.h
- + include/restart.hpp
- + include/smr_api.h
- − include/ssw.h
- include/ssw.hpp
- include/summary.hpp
- + include/thread_errors.hpp
- include/traverse_bursttrie.hpp
- include/triestats.hpp
- include/version.h
- − include/writer.hpp
- scripts/env.jinja
- + scripts/presets.tmpl.yaml
- scripts/run.py
- + scripts/t18.jinja
- + scripts/t18_1.jinja
- + scripts/t18_6.jinja
- + scripts/t19.jinja
- + scripts/t19_1.jinja
- + scripts/t19_3.jinja
- + scripts/t19_5.jinja
- + scripts/t19_6.jinja
- + scripts/t19_7.jinja
- + scripts/t2.jinja
- + scripts/t20.jinja
- + scripts/t20_1.jinja
- + scripts/t20_5.jinja
- + scripts/t20_6.jinja
- + scripts/t2_1.jinja
- + scripts/t3.jinja
- + scripts/t38.jinja
- + scripts/t39.jinja
- + scripts/t3_1.jinja
- + scripts/t41.jinja
- + scripts/t43.jinja
- + scripts/t46.jinja
- + scripts/t52.jinja
- + scripts/t53.jinja
- + scripts/t54.jinja
- + scripts/t54_1.jinja
- + scripts/t55.jinja
- + scripts/t55_1.jinja
- + scripts/t56.jinja
- + scripts/t57.jinja
- scripts/test.jinja
- + scripts/update_copyright_header.py
- setup.py
- + src/smr_api/CMakeLists.txt
- + src/smr_api/smr_api.cpp
- src/sortmerna/CMakeLists.txt
- src/sortmerna/alignment.cpp
- src/sortmerna/bitvector.cpp
- src/sortmerna/cmd.cpp
- src/sortmerna/index.cpp
- src/sortmerna/indexdb.cpp
- src/sortmerna/izlib.cpp
- src/sortmerna/kseq_load.cpp
- src/sortmerna/kvdb.cpp
- src/sortmerna/main.cpp
- src/sortmerna/minoccur.cpp
- src/sortmerna/options.cpp
- src/sortmerna/otumap.cpp
- src/sortmerna/output.cpp
- src/sortmerna/paralleltraversal.cpp
- src/sortmerna/processor.cpp
- src/sortmerna/read.cpp
- − src/sortmerna/read_control.cpp
- src/sortmerna/readfeed.cpp
- src/sortmerna/readstats.cpp
- src/sortmerna/references.cpp
- src/sortmerna/refstats.cpp
- src/sortmerna/report.cpp
- src/sortmerna/report_biom.cpp
- src/sortmerna/report_blast.cpp
- src/sortmerna/report_denovo.cpp
- src/sortmerna/report_fastx.cpp
- src/sortmerna/report_fx_base.cpp
- src/sortmerna/report_fx_other.cpp
- src/sortmerna/report_sam.cpp
- + src/sortmerna/restart.cpp
- + src/sortmerna/smr_log.cpp
- − src/sortmerna/ssw.c
- src/sortmerna/summary.cpp
- src/sortmerna/traverse_bursttrie.cpp
- src/sortmerna/util.cpp
- − src/sortmerna/writer.cpp
- src/util/build_version.cpp.in
- − src/winapi/CMakeLists.txt
- − src/winapi/include/sys/time.h
- − src/winapi/include/unistd.h
- − src/winapi/unistd.cpp
- − src/winapi/wintime.cpp
- data/empty_file.fasta → test_data/empty_file.fasta
- data/gg_13_8_ref_set.fasta → test_data/gg_13_8_ref_set.fasta
- data/illumina_GQ099317.fasta → test_data/illumina_GQ099317.fasta
- data/ref_GQ099317_forward_and_rc.fasta → test_data/ref_GQ099317_forward_and_rc.fasta
- data/ref_short_seqs.fasta → test_data/ref_short_seqs.fasta
- data/rRNA_databases/README.txt → test_data/refs/README.txt
- data/rRNA_databases/rfam-5.8s-database-id98.fasta → test_data/refs/rfam-5.8s-database-id98.fasta
- data/rRNA_databases/rfam-5s-database-id98.fasta → test_data/refs/rfam-5s-database-id98.fasta
- data/rRNA_databases/scripts/edit_U_to_T_rna.py → test_data/refs/scripts/edit_U_to_T_rna.py
- data/rRNA_databases/scripts/generate_databases.sh → test_data/refs/scripts/generate_databases.sh
- data/rRNA_databases/scripts/hmmer_clean.sh → test_data/refs/scripts/hmmer_clean.sh
- data/rRNA_databases/silva-arc-16s-id95.fasta → test_data/refs/silva-arc-16s-id95.fasta
- data/rRNA_databases/silva-arc-23s-id98.fasta → test_data/refs/silva-arc-23s-id98.fasta
- data/rRNA_databases/silva-bac-16s-id90.fasta → test_data/refs/silva-bac-16s-id90.fasta
- data/rRNA_databases/silva-bac-23s-id98.fasta → test_data/refs/silva-bac-23s-id98.fasta
- data/rRNA_databases/silva-euk-18s-id95.fasta → test_data/refs/silva-euk-18s-id95.fasta
- data/rRNA_databases/silva-euk-28s-id98.fasta → test_data/refs/silva-euk-28s-id98.fasta
- data/rRNA_databases/silva_ids_acc_tax.tar.gz → test_data/refs/silva_ids_acc_tax.tar.gz
- data/set2_environmental_study_550_amplicon.fasta → test_data/set2_environmental_study_550_amplicon.fasta
- data/set2_environmental_study_550_amplicon.fasta.gz → test_data/set2_environmental_study_550_amplicon.fasta.gz
- data/set4_mate_pairs_metatranscriptomics.fastq → test_data/set4_mate_pairs_metatranscriptomics.fastq
- data/set4_mate_pairs_metatranscriptomics_1.fastq → test_data/set4_mate_pairs_metatranscriptomics_1.fastq
- data/set4_mate_pairs_metatranscriptomics_1.fastq.gz → test_data/set4_mate_pairs_metatranscriptomics_1.fastq.gz
- data/set4_mate_pairs_metatranscriptomics_2.fastq → test_data/set4_mate_pairs_metatranscriptomics_2.fastq
- data/set4_mate_pairs_metatranscriptomics_2.fastq.gz → test_data/set4_mate_pairs_metatranscriptomics_2.fastq.gz
- data/set5_simulated_amplicon_silva_bac_16s.fasta → test_data/set5_simulated_amplicon_silva_bac_16s.fasta
- data/set7_arc_bac_16S_database_match.fasta → test_data/set7_arc_bac_16S_database_match.fasta
- data/silva-arc-16s-database-id95.fasta → test_data/silva-arc-16s-database-id95.fasta
- + test_data/silva-arc-16s-database-id95_part.fasta
- data/silva-bac-16s-database-id85.fasta → test_data/silva-bac-16s-database-id85.fasta
- data/t0_expected_alignment.blast → test_data/t0_expected_alignment.blast
- data/test_read.fasta → test_data/test_read.fasta
- data/test_ref.fasta → test_data/test_ref.fasta
- + tests/golden/small/aligned.blast
- + tests/golden/small/aligned.fa
- + tests/golden/small/aligned.sam
- + tests/golden/small/other.fa
- + tests/golden/tiny/aligned.blast
- + tests/golden/tiny/aligned.fa
- + tests/golden/tiny/aligned.sam
- + tests/smr_api/CMakeLists.txt
- + tests/smr_api/test_harness.h
- + tests/smr_api/test_link.c
- + tests/smr_api/test_smoke.c
- tests/sortmerna/CMakeLists.txt
- tests/sortmerna/kvdb.cpp
- tests/sortmerna/main.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/f804d7fe9a72fd25835b7a80e5fa32947a9bc8e1...f1b0fe148d94cd5525131d63c1a79803592e0518

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View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/f804d7fe9a72fd25835b7a80e5fa32947a9bc8e1...f1b0fe148d94cd5525131d63c1a79803592e0518
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