-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sun, 27 Sep 2026 21:07:56 -0400 Source: sra-sdk Architecture: source Version: 3.4.1+dfsg-1 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: 1144917 Changes: sra-sdk (3.4.1+dfsg-1) unstable; urgency=medium . * New upstream release. - test-sra no longer crashes under glibc 2.43. (Closes: #1144917.) * debian/control: - Bump libngs-c++-dev Breaks/Replaces on libncbi-vdb-dev to (<< 3.4) per libkapp.a takeover. (NB: sra-sdk took over the name and the main() wrapper, but ncbi-vdb retained the remaining content under the name libvdbapp.a.) - Bump B-D on libncbi-vdb-dev to (>= 3.4.1+dfsg~) and add one on python3-setuptools-whl to support Test_NGS_Python_install's patch. * debian/copyright: Revisit per licenserecon (lrc). - Add stanzas for bxzstr, rwqueue, SparkKMer.java, sse2neon.h, taskflow (complete with internal special cases), and tsl. - Wildcard (N. Lohmann's) json.hpp. - Extend BitMagic (libs/inc/bm) date range. - Formally rename BSD-3-clause-CLI11 to BSD-3-clause, uncontended. * debian/not-installed: Broaden lib*ngs*-static.a to lib*-static.a. * debian/patches: Update existing patches for new release. Notably: - bypass-libxml2-ATTRIBUTE_UNUSED.patch, fix_bm_for_gcc15.patch: Disable (fully superseded). - include_cstdint_for_gcc15.patch: Drop superseded portion. - label_online_tests.patch: Resync; leave out Test_NGS_Python_install. - link_vdb_dynamically.patch, prefer_dynamic_libraries.patch: Drop build/env.cmake changes; we can now set DYNAMIC_LINK=ON instead. - setuptools.patch: Repurpose somewhat. (setup.py has already migrated to setuptools, but the new accompanying test-install.sh [Test_NGS_Python_install] uses pip and needs patching to take infrastructure wheels from the local filesystem rather than PyPI.) - support_libre2-11.patch, use_debian_packaged_*.patch: Resync. * debian/patches/not_just_ubuntu.patch (new): Don't use a build-wide Python virtual env. under Debian (or any other derivative) either. * debian/patches/public_version-hash.patch (new): In tools/loaders/sharq/version.h, #include <kapp/version-hash.h> without a leading ../libs/, which works only when building against uninstalled VDB. (As of 3.4.1, Debian's installation makes the header public.) * debian/patches/tiny_csra_shell.patch (new): Run test/external/fasterq-dump/tiny_csra.sh under bash per its use of [[. (As is, it could never officially fail. No further changes needed, though.) * debian/rules: - Don't clean "expected" (golden) *.orig files. To that end, move custom cleanup logic to override_dh_clean (vs. _autoclean). - override_dh_auto_install: Add libkapp.a* to libngs-c++-dev. - execute_after_dh_auto_build (new): Take over javadoc invocation from the upstream build system, which no longer ever runs javadoc itself. - override_dh_auto_configure: Set the new DYNAMIC_LINK option to ON, thereby linking dynamically against dependencies in most cases. (Some portions of the tree still need patching to do so.) * debian/tests/run-unit-test: Stop testing cache-mgr, retired upstream. * Standards-Version: 4.7.4 (routine-update) * Reflow Uploaders field (cme) * Remove Priority field (cme) * Drop 'Rules-Requires-Root: no' from d/control (routine-update) * Reformat the Last-Update date as ISO YYYY-MM-DD. * No tab in license text (routine-update) . sra-sdk (3.2.1+dfsg-7) UNRELEASED; urgency=medium . * Fix watch file Checksums-Sha1: 3bcf9527c866c4ff58447fec76ce5ae0c0b2f812 3036 sra-sdk_3.4.1+dfsg-1.dsc 15a020e8c65d4115f28d85703c3d531045161446 50290644 sra-sdk_3.4.1+dfsg.orig.tar.xz 4e010bfd54e18c033616a64a60acde4f55db9bbb 3798672 sra-sdk_3.4.1+dfsg-1.debian.tar.xz Checksums-Sha256: e9ebcf5412fc1b8bc3f95a9a2a3ab136ff3bc69cd9de12f35d522d2d62872b39 3036 sra-sdk_3.4.1+dfsg-1.dsc 658663be972005fbae4d6b53963fb1aff069a1d4c4c2a81c320910f40701f66c 50290644 sra-sdk_3.4.1+dfsg.orig.tar.xz 5015efbb2fd710377d940d614816a1c9010461c5cabc9bba73e9f6d728a74d86 3798672 sra-sdk_3.4.1+dfsg-1.debian.tar.xz Files: 8df5493df73a2dea7728f5219363f60d 3036 science optional sra-sdk_3.4.1+dfsg-1.dsc 37f30ef5d9a181d2881a833416a3036e 50290644 science optional sra-sdk_3.4.1+dfsg.orig.tar.xz 1981d0b2c494ba60b5d8d0c7e5342505 3798672 science optional sra-sdk_3.4.1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmq5vnUACgkQHnCRsfFK ZKIwmxAAlEOCoGhnItVBW1hnf1vED/GxA9BNqzPPiWG5dxO+QTed824CfJ3j2OBS f0JTr6m+zPAXtbFMjd6330be9Cnwzy6Po2YCNEOmXuCG3EdO7CzElqRHbTDg5z0A mA/nYn2FG7AbwGQ0VL/TY9T2HKi7V3n476HuRgBmwe6huWmNHJzpX00YPtQCZu1Z Z7yGYRKgOpkXS3KKqfP2nxabdahNPMJZ1D+9/+pyWldSl1pO57p/TLcQUxHNUOdF uDwluvG4XFq4SkCmsjTAIYJSwEqkgosxO3w3jG9gZyserguRm3OvhVFl2ZNmIP/2 aBRz6LoBB0NlWVp758YWZj4e1pxx33omR4Zn8cW5Rrfu72YIy9kaziDpUZncTb84 Xusy0p4B2RaeCOfXl/QYLsUuqrPadpIg/0LGUuIdU7MizKJ9djHj29E4vZnM1fBD twxKwAIXyuvolxzubTV/W3S6w4IyV44YDsjVPbrmIVV0TpcPqkuPNHiSbU041cRv RnxFr0Ja6Nt3xyXnoOvRdZ3padmxmi1+rr+qmL4IDh21ky6kb+K1S02PcyIttCCA xy8V2lRjdUcpGqtYA+73kW7bapzbvVxRMWhyuyK1o/vHHKVgO0R2h+Mc/PeXOob/ uUNZgA45XZ1qMHr+1Huhy6Ieo3bRK1hsHtm/611PJgL8R6mFkwM= =p8N0 -----END PGP SIGNATURE-----
