Your message dated Mon, 28 Sep 2026 01:34:14 +0000
with message-id <[email protected]>
and subject line Bug#1144917: fixed in sra-sdk 3.4.1+dfsg-1
has caused the Debian Bug report #1144917,
regarding sra-sdk: autopkgtest regression: Segmentation fault
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1144917: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1144917
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: sra-sdk
Version: 3.2.1+dfsg-6
Severity: serious
X-Debbugs-CC: [email protected] [email protected]
Control: affects -1 src:glibc
Hi,
While checking the glibc transition (bug 1141940), I noticed that your
autopkgtest fails with the new glibc and it failing with a Segmentation
fault. To be open about it, we'll not be holding back the glibc
transition for this package, please have a look at it.
Paul
https://ci.debian.net/packages/s/sra-sdk/unstable/amd64/74480346/
60s autopkgtest [12:02:15]: test run-unit-test: [-----------------------
60s >>>>>Decompressing test-data archive...
60s dbGaP-0/
60s dbGaP-0/SRR2042184.fasta
60s meta/
60s meta/prj_phs710EA_test.ngc
60s meta/SRR6650398_experiment.xml
60s meta/SRR6650398.bam
60s meta/SRR2042184_run.xml
60s meta/SRR2042184_experiment.xml
60s meta/SRR6650398_illumina_run.xml
60s meta/SRR7032226_run.xml
60s meta/SRR7032226_experiment.xml
60s meta/reference.fna
60s meta/SRR6650398_fastq_run.xml
60s public/
60s public/nannot/
60s public/wgs/
60s public/refseq/
60s public/refseq/NC_000962.3
60s public/sra/
60s public/sra/SRR7032226.sra
60s public/sra/SRR6650398.sra
60s public/sra/SRR2042184.sra
60s public/files/
60s >>>>>Running test-sra...
63s 2026-08-20T12:02:18 test-sra.3.2.1 fatal: SIGNAL - Segmentation fault
64s autopkgtest [12:02:19]: test run-unit-test: -----------------------]
OpenPGP_signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: sra-sdk
Source-Version: 3.4.1+dfsg-1
Done: Aaron M. Ucko <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sra-sdk, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <[email protected]> (supplier of updated sra-sdk package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----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
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
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-----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=p8N0
-----END PGP SIGNATURE-----
pgpAmwOaoIIvQ.pgp
Description: PGP signature
--- End Message ---
