[med-svn] [Git][med-team/ncbi-vdb][master] 15 commits: New upstream version 3.4.1+dfsg

Aaron M. Ucko (@ucko) gitlab at salsa.debian.org
Mon Sep 28 02:11:09 BST 2026 


Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb


Commits:
4dfcc5f6 by Aaron M. Ucko at 2026-08-29T21:51:46-04:00
New upstream version 3.4.1+dfsg
- - - - -
8a0a61fe by Aaron M. Ucko at 2026-08-29T21:53:28-04:00
Merge tag upstream/3.4.1+dfsg.

Upstream version 3.4.1(+dfsg).

- - - - -
731274a6 by Aaron M. Ucko at 2026-08-29T22:29:15-04:00
debian/patches: Update accordingly.

* Consolidate fix_cmake.patch, zstd.patch, and new #include fixups as
  system_compression.patch.
* Formally update remaining patches as needed.

- - - - -
fc78212a by Aaron M. Ucko at 2026-09-06T11:57:55-04:00
debian/rules: Update libncbi-vdb-dev d-shlibmove invocation.

libvdbapp.a has replaced all of libkapp.a but the main() wrapper,
which kept the kapp name and moved to libngs-c++-dev from sra-sdk, and
libkapp-norsrc.a is gone.

- - - - -
59f29d0f by Aaron M. Ucko at 2026-09-06T11:59:12-04:00
d/rules: Install kapp/version-hash.h from libs for sra-sdk's sake.

Hold off for now on splitting off a private-headers package, which
would be tiny.

- - - - -
59d436d3 by Aaron M. Ucko at 2026-09-06T22:41:01-04:00
debian/rules: Stop passing NO_VDB3 to dh_auto_install

... to accommodate cmake --install (already effectively in play), which
doesn't support that syntax (no longer needed anyway).

- - - - -
c62f5e76 by Aaron M. Ucko at 2026-09-06T22:42:05-04:00
d/rules: Set the new DYNAMIC_LINK option to ON for futureproofing.

The variables it affects don't actually come into play, at least so far.

- - - - -
61f20fc0 by Aaron M. Ucko at 2026-09-06T22:42:09-04:00
Standards-Version: 4.7.4 (routine-update)

- - - - -
75f92738 by Aaron M. Ucko at 2026-09-06T22:42:09-04:00
Changes made by cme

- - - - -
7b399945 by Aaron M. Ucko at 2026-09-06T22:42:09-04:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)

- - - - -
b6659d1c by Aaron M. Ucko at 2026-09-06T22:42:09-04:00
Remove unused entry from debian/source/include-binaries.

Changes-By: lintian-brush
Fixes: lintian: source: unused-entry-in-debian-source-include-binaries debian/sra-tools.gpg [debian/source/include-binaries:1]
See-also: https://lintian.debian.org/tags/unused-entry-in-debian-source-include-binaries.html

- - - - -
5e8ba01e by Aaron M. Ucko at 2026-09-06T22:42:09-04:00
Reformat the Last-Update date as ISO YYYY-MM-DD.

Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/spelling.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/system_compression.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/libsam-extract_shared.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html

- - - - -
4c7b6919 by Aaron M. Ucko at 2026-09-06T22:42:09-04:00
Avoid explicitly specifying -Wl,--as-needed linker flag.

Changes-By: lintian-brush
Fixes: lintian: source: debian-rules-uses-as-needed-linker-flag [debian/rules]
See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html

- - - - -
a9c33c16 by Aaron M. Ucko at 2026-09-06T22:42:09-04:00
debian/copyright: Note Bison-2.2 exception

... for files otherwise under GPL-3+, per lrc (licenserecon).

- - - - -
bbd0293d by Aaron M. Ucko at 2026-09-27T21:07:34-04:00
Finalize ncbi-vdb 3.4.1+dfsg-1 for unstable.

- - - - -


406 changed files:

- CHANGES.md
- LICENSE
- Makefile
- build/.gitignore
- build/Makefile.env
- build/Makefile.vers
- build/common.cmake
- build/env.cmake
- build/install-root.sh
- + build/san_test.cpp
- + build/test.cpp
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/detect_BITS.patch
- − debian/patches/fix_cmake.patch
- debian/patches/fix_x32.patch
- debian/patches/libsam-extract_shared.patch
- debian/patches/series
- debian/patches/soversion.patch
- debian/patches/spelling.patch
- + debian/patches/system_compression.patch
- debian/patches/system_mbedtls_3.patch
- − debian/patches/zstd.patch
- debian/rules
- debian/source/include-binaries
- − interfaces/cc/clang/arm64/atomic.h
- interfaces/cc/clang/x86_64/atomic.h → interfaces/cc/clang/atomic.h
- interfaces/cc/clang/arm64/atomic32.h → interfaces/cc/clang/atomic32.h
- interfaces/cc/clang/arm64/atomic64.h → interfaces/cc/clang/atomic64.h
- − interfaces/cc/clang/x86_64/atomic32.h
- − interfaces/cc/clang/x86_64/atomic64.h
- interfaces/cc/gcc/x86_64/arch-impl.h
- interfaces/insdc/sra.h
- interfaces/insdc/sra.vschema
- interfaces/kapp/args.h
- interfaces/kapp/main.h → interfaces/kapp/vdbapp.h
- interfaces/kfg/config.h
- interfaces/kfg/kart-priv.h
- interfaces/kfg/kfg-priv.h
- interfaces/kfs/file-impl.h
- interfaces/kfs/file-v1.h
- interfaces/kfs/md5.h
- interfaces/klib/klib-priv.h
- interfaces/klib/vdb_release_version.h
- interfaces/kns/impl.h
- interfaces/kns/stream.h
- interfaces/ktst/unit_test.hpp
- interfaces/ktst/unit_test_suite.hpp
- interfaces/sra/454.vschema
- interfaces/vfs/resolver.h
- libs/align/align-access.c
- libs/align/bam.c
- libs/align/samextract-lib.cpp
- libs/align/samextract-pool.c
- libs/align/samextract.h
- libs/align/writer-cmn.c
- libs/align/writer-reference.c
- libs/axf/ref-preserve_qual.c
- libs/axf/refseq.c
- libs/axf/refseq.h
- libs/axf/wgs.c
- libs/blast/blast-mgr.c
- libs/blast/reader.c
- libs/cipher/.gitignore → libs/cipher/cipher-1.7/.gitignore
- libs/kapp/CMakeLists.txt
- libs/kapp/args.c
- libs/kapp/linux/ram.c
- libs/kapp/log-xml.c
- libs/kapp/tokenizer.c
- libs/kapp/unix/sysmain.c → libs/kapp/unix/sysapp.c
- libs/kapp/main-priv.h → libs/kapp/vdbapp-priv.h
- libs/kapp/main.c → libs/kapp/vdbapp.c
- interfaces/kfs/teefile.h → libs/kapp/vdbapp.cpp
- test/kapp/report-kns-agent.c → libs/kapp/version-hash.h
- libs/kdb/libkdb.vers.h
- libs/kdb/page-map.c
- libs/kdb/rdbmgr.c
- libs/kdb/wdatabase.c
- libs/kdb/wmeta.c
- libs/kdb/wmetadatanode.c
- libs/kdb/wtrieidx-v2.c
- libs/kfg/config.c
- libs/kfg/default_kfg.h
- libs/kfg/kart.c
- libs/kfs/CMakeLists.txt
- libs/kfs/arc.c
- libs/kfs/bzip.c
- libs/kfs/cacheteefile3.c
- libs/kfs/file.c
- libs/kfs/gzip.c
- libs/kfs/md5.c
- − libs/kfs/teefile.c
- libs/klib/btree.c
- libs/klib/hashfile.c
- libs/klib/judy/CMakeLists.txt
- libs/klib/pbstree-impl.c
- libs/klib/printf.c
- libs/klib/report-klib.c
- libs/klib/singletons.h
- libs/klib/status-rc.c
- libs/klib/trie.c
- libs/kns/CMakeLists.txt
- libs/kns/http-file.c
- libs/kns/http-request.c
- libs/kns/manager.c
- libs/kns/stream-from-buffer.c
- libs/kns/stream.c
- libs/kns/linux/sysendpoint.c → libs/kns/unix/sysendpoint.c
- libs/kns/unix/sysstream.c
- libs/ktst/CMakeLists.txt
- + libs/ktst/branch-engineering.c
- libs/ktst/testenv.cpp
- libs/ktst/testrunner.cpp
- libs/ncbi-vdb/CMakeLists.txt
- libs/ncbi-vdb/libncbi-vdb.vers
- libs/schema/ASTBuilder-func.cpp
- libs/schema/ASTBuilder.cpp
- libs/schema/AST_Expr.cpp
- libs/sra/sramgr-cmn.c
- libs/sraxf/format-spot-name.c
- libs/sraxf/fpcodec.c
- libs/sraxf/index_lookup.c
- libs/sraxf/rewrite-spot-name.c
- libs/sraxf/spot-filter.c
- libs/sraxf/v0-decompress-local.h
- libs/vdb/CMakeLists.txt
- libs/vdb/cursor-cmn.c
- libs/vdb/database-cmn.c
- libs/vdb/database-depend.c
- libs/vdb/libvdb.vers.h
- libs/vdb/phys-load.c
- libs/vdb/prod-cmn.c
- libs/vdb/report-vdb.c
- libs/vdb/schema-dump.c
- libs/vdb/schema-expr.c
- libs/vdb/wphys.c
- libs/vfs/SraDesc.c
- libs/vfs/manager-priv.h
- libs/vfs/manager.c
- libs/vfs/path.c
- libs/vfs/remote-services.c
- libs/vfs/resolver-cgi.h
- libs/vfs/resolver-priv.h
- libs/vfs/resolver.c
- libs/vfs/services-priv.h
- libs/vfs/services.c
- libs/vxf/bunzip.c
- libs/vxf/bzip.c
- libs/vxf/funzip.c
- libs/vxf/fzip.c
- libs/vxf/irzip.c
- libs/vxf/iunzip.c
- libs/vxf/izip.c
- libs/vxf/simple-sub-select.c
- libs/vxf/unzip.c
- libs/vxf/zip.c
- test/CMakeLists.txt
- test/align/CMakeLists.txt
- + test/align/db/VDB-5931.config
- + test/align/db/VDB-5931.fasta
- + test/align/db/VDB-5931.references
- test/align/test-config.cpp
- test/axf/test-RestoreRead.cpp
- test/cc/CMakeLists.txt
- test/cc/asm-test.cpp
- test/cc/test-int128.cpp
- test/cipher/CMakeLists.txt
- test/cipher/test.sh
- test/cloud/CMakeLists.txt
- test/cloud/test-aws.cpp
- test/cloud/test-cloud.cpp
- test/cloud/test-gcp.cpp
- test/judy_test/judytest.c
- + test/kapp/.gitignore
- test/kapp/CMakeLists.txt
- − test/kapp/append-arg-test.c
- − test/kapp/env-test-tool.c
- − test/kapp/kapp-test.cpp
- + test/kapp/options.txt
- test/kapp/run-sig-core.sh
- test/kapp/rc-mod-exitcode.c → test/kapp/sig-core-vdbapp.c
- − test/kapp/sig-core.c
- + test/kapp/vdbapp-test.cpp
- test/kdb/CMakeLists.txt
- test/kdb/VDB-4705.cpp
- test/kdb/VDB-4706.cpp
- test/kdb/VDB-5323.cpp
- test/kdb/kdbtest.cpp
- test/kdb/makedb.cpp
- test/kdb/rowsettest.cpp
- test/kdb/test-pagemap.cpp
- test/kdb/test-rblob.cpp
- test/kdb/test-rcolumn.cpp
- test/kdb/test-rdatabase.cpp
- test/kdb/test-rindex.cpp
- test/kdb/test-rmanager.cpp
- test/kdb/test-rmetadata.cpp
- test/kdb/test-rmetanode.cpp
- test/kdb/test-rtable.cpp
- test/kdb/test-wblob.cpp
- test/kdb/test-wcolumn.cpp
- test/kdb/test-wdatabase.cpp
- test/kdb/test-windex.cpp
- test/kdb/test-wmanager.cpp
- test/kdb/test-wmetadata.cpp
- test/kdb/test-wmetanode.cpp
- test/kdb/test-wtable.cpp
- test/kdb/wkdbtest.cpp
- test/kdbtext/CMakeLists.txt
- test/kdbtext/test-blob.cpp
- test/kdbtext/test-column.cpp
- test/kdbtext/test-database.cpp
- test/kdbtext/test-index.cpp
- test/kdbtext/test-manager.cpp
- test/kdbtext/test-metadata.cpp
- test/kdbtext/test-metanode.cpp
- test/kdbtext/test-path.cpp
- test/kdbtext/test-table.cpp
- test/kfc/test-except.c
- test/kfg/CMakeLists.txt
- test/kfg/fuzz-seeds/default.kfg
- test/kfg/fuzz-seeds/incomplete.kfg
- test/kfg/fuzz-seeds/local.kfg
- test/kfg/fuzz-seeds/only-remote-repository.kfg
- test/kfg/fuzz-seeds/resolver.kfg
- test/kfg/keystoretest.cpp
- test/kfg/kfgtest.cpp
- test/kfg/ncbi-home-from-env.cpp
- test/kfg/propertiestest.cpp
- test/kfg/repositorytest.cpp
- test/kfg/wb-test-kfg.cpp
- test/kfs/CMakeLists.txt
- test/kfs/appendfiletest.cpp
- test/kfs/cachetee-out-of-space.cpp
- test/kfs/cachetee2test.cpp
- test/kfs/cachetee3test.cpp
- test/kfs/cacheteetest.cpp
- test/kfs/kdf.cpp
- test/kfs/kfstest.cpp
- test/kfs/lru_cache_test.cpp
- test/kfs/md5test.cpp
- test/kfs/ramfiletest.cpp
- test/kfs/resolvetest.cpp
- test/kfs/simple_q_test.cpp
- + test/kfs/test-empty-file_file_observer.cpp
- test/kfs/test-gzip.cpp
- test/kfs/test-link.cpp
- + test/kfs/test-read_observer-bz2.cpp
- + test/kfs/test-read_observer-gz.cpp
- + test/kfs/test-read_observer.cpp
- test/klib/CMakeLists.txt
- test/klib/asm-test.c
- test/klib/md5appendtest.c
- test/klib/printf-test.c
- test/klib/test-KOutMsgOverflow.cpp
- test/klib/test-SraReleaseVersion.cpp
- test/klib/test-base64.cpp
- test/klib/test-btree.cpp
- test/klib/test-data-buffer-print.c
- test/klib/test-guid.cpp
- test/klib/test-hashfile.cpp
- test/klib/test-hashtable.cpp
- test/klib/test-json-parser.cpp
- test/klib/test-json.cpp
- test/klib/test-klib.cpp
- test/klib/test-log.cpp
- test/klib/test-out.cpp
- test/klib/test-pack.cpp
- test/klib/test-progress.cpp
- test/klib/test-rcenum.cpp
- test/klib/test-report.cpp
- test/klib/test-sha-32bit.cpp
- test/klib/test-symtab.cpp
- test/klib/test-time.cpp
- test/klib/test-vnamelist.cpp
- test/kns/CMakeLists.txt
- test/kns/KNSManagerSingletonTest.cpp
- + test/kns/ObserverTest.hpp
- test/kns/TestProxy.hpp
- test/kns/http-test.c
- test/kns/http_dropconnection_test.cpp
- test/kns/httptest.cpp
- test/kns/knstest.cpp
- test/kns/test-aws-proxy.cpp
- test/kns/test-connect.cpp
- + test/kns/test-empty-file_stream_observer.cpp
- + test/kns/test-empty-file_stream_observer.hpp
- + test/kns/test-empty-stdin_observer.cpp
- test/kns/test-google-proxy.cpp
- test/kns/test-http-request.cpp
- test/kns/test-ipc.cpp
- test/kns/test-mutual-authentication.cpp
- test/kns/test-opt-bitmap.cpp
- test/kns/test-proxy-with-env.cpp
- test/kns/test-proxy-with-scheme.cpp
- test/kns/test-proxy-with-scheme_failure.cpp
- test/kns/test-proxy.cpp
- test/kns/test-refresh-expired-url.cpp
- + test/kns/test-stdin_observer.cpp
- + test/kns/test-stream_observer.cpp
- + test/kns/test-stream_observer.hpp
- test/kns/test-timeouts.cpp
- test/kns/test200for-whole-file.cpp
- test/kns/test_allow_all_certificates.cpp
- test/kns/test_dis_allow_all_certificates.cpp
- test/kproc/kproctest.cpp
- test/krypto/CMakeLists.txt
- test/krypto/test-aes-ciphers.c
- test/krypto/test-cipher-speed.c
- test/krypto/test-csprng.c
- test/krypto/test-encdec.cpp
- test/krypto/test-hash-in-pwd.cpp
- − test/krypto/test-krypto-slow.cpp
- test/krypto/test-modes.c
- test/krypto/test-reenc.cpp
- test/krypto/test-rsa-aes-hmac.cpp
- test/ktst/ktsttest.cpp
- test/ncbi-vdb/CMakeLists.txt
- test/ncbi-vdb/so_check.sh
- test/ncbi-vdb/test-link.cpp
- test/ncbi-vdb/test-wlink.cpp
- test/only-remote-repository.kfg
- test/schema/AST_Fixture.cpp
- test/schema/AST_Fixture.hpp
- test/schema/CMakeLists.txt
- test/schema/local.kfg
- test/schema/test-schema-diff.cpp
- test/schema/test-schema-parse.cpp
- test/schema/test-schema-scan.cpp
- test/schema/wb-test-schema-ast.cpp
- test/schema/wb-test-schema-db.cpp
- test/schema/wb-test-schema-func.cpp
- test/schema/wb-test-schema-lex.cpp
- test/schema/wb-test-schema-parser.cpp
- test/schema/wb-test-schema-table.cpp
- test/schema/wb-test-schema-view.cpp
- test/sraxf/CMakeLists.txt
- test/sraxf/fix_read_seg-test.cpp
- test/sraxf/test-format_spot_name.cpp
- test/sraxf/test_spot-check.c
- test/sraxf/test_syn_quality.cpp
- test/vdb/CMakeLists.txt
- test/vdb/Test-VDB_schema_priv.cpp
- test/vdb/Test_VDB_dependencies_404first.cpp
- test/vdb/Test_VDB_dependencies_wgs.cpp
- test/vdb/WVDB_Fixture.hpp
- test/vdb/check-user-agent-header-in-thread.cpp
- test/vdb/kfg/linux/test-dependencies.kfg
- + test/vdb/rowwritetest.c
- test/vdb/test-VDB-3060.cpp
- test/vdb/test-VDB-3061.cpp
- test/vdb/test-VDB-3305.cpp
- test/vdb/test-VDB-3418.cpp
- test/vdb/test-VDB-4156.cpp
- + test/vdb/test-VDB-NodeDrop.cpp
- + test/vdb/test-VDB-TooBigMeta.cpp
- test/vdb/test-VDBManagerGetObjVersion.cpp
- test/vdb/test-blob-val.cpp
- test/vdb/test-bytecode.cpp
- test/vdb/test-database-cmn.cpp
- test/vdb/test-dependencies_dflt.cpp
- test/vdb/test-link.c
- test/vdb/test-linker.cpp
- test/vdb/test-sparse-col.cpp
- test/vdb/test-tablecursor.cpp
- test/vdb/test-textvdb.cpp
- test/vdb/test-vdb-meta-cmp-copy.cpp
- test/vdb/test-vdb-slow.cpp
- test/vdb/test-vdb.cpp
- test/vdb/test-view-cursor.cpp
- test/vdb/test-view-vt.cpp
- test/vdb/test-view.cpp
- test/vdb/test-wtablecursor.cpp
- test/vdb/test-wvdb-slow.cpp
- test/vdb/test-wvdb.cpp
- test/vfs/CMakeLists.txt
- test/vfs/Test_VFS_no-nm-cgi.cpp
- test/vfs/Test_VFS_resolver_dflt.cpp
- + test/vfs/file-observer-test.hpp
- test/vfs/managertest.cpp
- test/vfs/path-test.c
- test/vfs/pathtest.cpp
- − test/vfs/redirect-rejected-names-cgi-http-to-https.cpp
- − test/vfs/resolver-cgi.h
- test/vfs/test-SraDesc.cpp
- test/vfs/test-attached-vdbcache.cpp
- test/vfs/test-caching-test.cpp
- test/vfs/test-caching.cpp
- + test/vfs/test-file_observer.cpp
- test/vfs/test-json-response.cpp
- test/vfs/test-log-names-error.cpp
- − test/vfs/test-names-30.cpp
- test/vfs/test-perm.cpp
- test/vfs/test-resolve-qual.cpp
- test/vfs/test-resolve.cpp
- test/vfs/test-resolver-with-log.cpp
- test/vfs/test-resolver4.cpp
- test/vfs/test-sdl-response.cpp
- test/vfs/test-services.cpp
- test/vfs/test-vfs-resolve.cpp
- test/vfs/test-vpath-open.hpp
- test/vfs/test_VFS_cache_sdl.cpp
- test/vxf/VDB-2915.cpp
- test/vxf/local_config/local.kfg
- test/vxf/wb-test-vxf.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/b505155e2b0cd9c052b6e669d2e1894bb17b8186...bbd0293dc328406cb34632bd55b5259674f40e3c

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View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/b505155e2b0cd9c052b6e669d2e1894bb17b8186...bbd0293dc328406cb34632bd55b5259674f40e3c
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