-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 20 Jan 2023 17:57:36 -0500 Source: sra-sdk Architecture: source Version: 3.0.3+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Changed-By: Aaron M. Ucko <ucko@debian.org> Closes: 1024155 1025278 Changes: sra-sdk (3.0.3+dfsg-2) unstable; urgency=medium . * Upload to unstable. * .gitignore: Update patterns corresponding to test output. * debian/control: - Drop vestigial versioned dependency on libncbi-wvdb2. - Limit architecture-dependent packages to amd64 and arm64. The only other architecture ncbi-vdb supports is x32, but these tools require a 64-bit address space. * debian/not-installed: Refresh. - Correct location of explicitly tagged lib*-static.a. - Drop spurious entries (with hardcoded amd64 paths, no less). * debian/patches/fix_ngs-c++-underlinkage.patch (new): Link libngs-c++ against all internal dependencies. Hold off for now on linking against libncbi-vdb, though anyone looking to substitute libncbi-wvdb would need to contrive to supply a suitable definition of KDBManagerMakeRead. * debian/patches/label_online_tests.patch: Extend as needed. All existing labels confirmed to remain appropriate. * debian/patches/link_vdb_dynamically.patch: Extend prior to building tests again. To wit, additionally cover makeinputs, from tools/loaders/general-loader/test. (All other tests were already OK at this point.) * debian/patches/prefer_dynamic_libraries.patch: Comment out upstream logic that favored static linkage. * debian/rules: - Skip rpaths, not needed even for libhdf5. - Explicitly enable tests, disabled by default these days. - Update test cleanup logic to allow for build area reuse. * debian/salsa-ci.yml: Retire remaining customizations. . sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium . [ Andreas Tille ] * Breaks+Replaces: libncbi-vdb-dev (<< 3), libngs-sdk-dev (<< 3) Closes: #1024155 . [ Aaron M. Ucko ] * New upstream version. * .gitignore: - Unhardcode architecture name in build tree (obj-*). - Ignore build results under ngs/ngs-python (dist, ngs.egg-info). * debian/{control,salsa-ci.yml}: Build against libncbi-vdb-dev 3.0.1+. * debian/copyright: Account for layout changes as of 3.0.1 and drop references to content removed upstream, both in Files-Excluded and in special cases. * debian/patches: Update for 3.0.1+; in particular, account for layout changes and better support for using system libraries. * debian/rules: - Correctly accommodate multiple supported Python versions. (I'd insufficiently adapted ncbi-ngs's relevant logic.) - Account for layout changes and CMAKE_INSTALL_LIBDIR support (with the latter yielding multiarch paths). - Clean up newly generated files under ngs/ngs-python. * debian/{rules,sra-toolkit.install}: Move sratools and *-orig to a new /usr/lib/sra-toolkit directory; repoint symlinks accordingly. (Closes: #1025278.) * Standards-Version: 4.6.2 (routine-update) . sra-sdk (3.0.0+dfsg-1) experimental; urgency=medium . [ Andreas Tille ] * New upstream version * Standards-Version: 4.6.1 (routine-update) * Build-Depends: default-jdk, flex, bison . [ Aaron M. Ucko ] * debian/control: - Account for consolidation of ngs-sdk (albeit with some intervening changes, notably library restructuring); take the opportunity to add a -java-doc package.0 - Let python3-ngs bypass libncbi-ngs-dev and use libncbi-ngs3 directly. - Drop build dependency on libvdb-sqlite-dev, now internal to sra-sdk. * debian/libngs-java-doc.javadoc: Enable javadoc installation. * debian/{libngs-java.{jlibs,poms},ngs-java.pom(.asc)}: Adopt (and adapt) from ngs-sdk. * debian/*ngs*.examples (new): Install upstream NGS examples. * debian/not-installed: Ignore usr/jar/*.jar (installed elsewhere, via jh_installlibs), usr/lib64/lib*-static.a, usr/share/examples* (installed elsewhere, via dh_installexamples), and usr/share/javadoc/ngs-doc (installed elsewhere, via jh_installjavadoc). * debian/patches/use_debian_packaged_re2.patch: Comment out an inappropriate add_dependencies call in test/sharq/CMakeLists.txt. * Add more patches for remaining build issues: fix_javadoc_build.patch, link_magic_dynamically.patch, link_vdb_dynamically.patch, and use_debian_packaged_compression_libs.patch. * debian/patches/use_soversions.patch (new): Give shared libraries proper versioned SONAMEs; use them from the Python bindings. * debian/rules: - Adopt (and adapt) assorted build logic from ngs-sdk. - Pass VDB header path via -DVDB_INCDIR rather than via general compilation flags. - Install configuration files explicitly; the CMake setup insists on putting them in the wrong place for us. - Extend bin deversioning to *+ (i.e., kar+). * debian/salsa-ci.yml: Use ncbi-vdb's aptly repo to get 3.x for now. . [ Pierre Gruet ] * debian/control: - Add missing build dependencies on liblzma-dev and libsam-extract-dev. - Mark libngs-java as Architecture: all; loosen its dependencies on libncbi-ngs-dev slightly to account for possible binNMUs. - Introduce a libngs-jni package, on which libngs-java can and will depend in lieu of libncbi-ngs-dev (or patching source to support using libncbi-ngs3 directly). * debian/libngs-java-doc.lintian-overrides: Override complaints about javadoc-embedded jQuery per the discussion starting at https://lists.debian.org/debian-java/2018/06/msg00020.html. * debian/libngs-jni.links.in: Provide a general formula for libngs-jni's central symlink. * debian/rules: Add logic to fill in the specifics. . [ Aaron M. Ucko ] * (debian/).gitignore (new): Ignore build and (offline) test results. * debian/control: - Make python3-ngs (safely!) Architecture: all too. - Attempt Architecture: any for sra-toolkit (modulo B-D availability). This setting matches architecture-dependent NGS packages'; if it doesn't work out, we'll want to rein them all in for simplicity. - Honor ${misc:Depends} for libngs-java per Lintian. * debian/copyright: Reflect a full inventory, including convenience copies of several third-party libraries for which it would be good to substitute existing packages at some point. * debian/patches/label_online_tests (new): Label tests that involve data retrieval as "online". * debian/patches/reflect_code_donations.patch (new): Clean up stray licenseless copyright statements per consultation with upstream (as quoted in the patch's header). * debian/patches/use_stock_magic.patch (new): Let copycat use the stock magic-number database in /usr/share/misc. * debian/rules: - Skip tests labeled "online" to avoid breaking on autobuilders, which require builds to work fully offline. - Refrain from shipping .gitignore files alongside examples. - Clean up after tests (offline ones, anyway). * Remove trailing whitespace in debian/changelog (routine-update) Checksums-Sha1: 4692e4cc7fb1812e45f4032d0acaddd7a99124bf 2881 sra-sdk_3.0.3+dfsg-2.dsc 1a3d280ed4c4626160619f48492f11b59508896d 3783724 sra-sdk_3.0.3+dfsg-2.debian.tar.xz 44a6aa7c6a48fd7d0c20c6fee39fde7272f8e8b8 16848 sra-sdk_3.0.3+dfsg-2_source.buildinfo Checksums-Sha256: ebd78238e0ec430cbdafd2a29bedebe0028d65071c3170fbe050b01a150bd3e1 2881 sra-sdk_3.0.3+dfsg-2.dsc 0e8da13007ea9657e42da735aca0d3343e741038faa45a3f6cad7797efa8c341 3783724 sra-sdk_3.0.3+dfsg-2.debian.tar.xz c457c4614d0172b0d6a172fa8054f14f3b32f90692c05ef3c7fe42f744fd79f1 16848 sra-sdk_3.0.3+dfsg-2_source.buildinfo Files: 492e61d6f3067942e0df938a5e7d797e 2881 science optional sra-sdk_3.0.3+dfsg-2.dsc 6688552cac2fd15a2b2d996ba2a946bc 3783724 science optional sra-sdk_3.0.3+dfsg-2.debian.tar.xz c9ced9174cfa81894e3cd2fe97ef5274 16848 science optional sra-sdk_3.0.3+dfsg-2_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmPLHPsACgkQHnCRsfFK ZKJRfg//cPwDCgxt5tBcXCL2jmdbYmNZZWSMCSJ9O2XTMW05qHSS+169JWgFziaM x/et6XkUMVYqFEeMvGQs4FVI+uOcs89jsing9/jkizrrf2OiCF3Q7/Nm76U4uVIn fOBu4XUrtBNFMeJ5XsDIYw8lhpadUnmy6kOgp9C6D6XIqHJ7OjpX2mxlhioaKFz3 FXlpsGDsU0LvC0f+som9Zoxu7N7gOuQ4Kf32BpiFeCIIHeh8/iR7eZlly4Fo3lcu j2A5wrgD8Gx35JKiKc/7ioPtojrAhKOcl3NoO1CKmvLdpVNHMNILTGTaVSQ+yfrv fwqCXOMT+V95kF8zrHqA/xgazSVy29nNoY3G3mxvIlW17+ocyo52jWCN/prGeIoU m/zlpsSTKNNsPyP3sRy49IfDhagsYYLoXIY3VYaJwPufOqA3jdYMy1NEWa4zq2jH SUKZu3cRD6Aez821fiPSDZ8JDXNfe0kVv89Wvu6uIBemMMboIoKiCmgh/qTFslL7 faUTavNQ42HjCgPRJSJjw4dbtWscQ8VgQeNK534p9m8/97hxIGaRTLF37aCmO/o2 pAIpod4Lzl/b4/8CZYijxG+m6FzehcVhdYUJMotXag7bOBSNcS/TEpsHmkto5RVz diWDa/exgjbh1UEY4oEfcnYgL23LpTfi5ZHhUmeaZyxduMtw8+g= =yhNh -----END PGP SIGNATURE-----