Your message dated Thu, 24 Sep 2026 08:50:29 +0000
with message-id <[email protected]>
and subject line Bug#1144002: fixed in uncalled 2.3+ds-4
has caused the Debian Bug report #1144002,
regarding uncalled: FTBFS: /usr/bin/x86_64-linux-gnu-ld.bfd: cannot find
-lhdf5: No such file or directory
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.
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--
1144002: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1144002
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: uncalled
Version: 2.3+ds-3
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the past)
X-Debbugs-Cc: [email protected]
Dear maintainer,
uncalled FTBFS:
x86_64-linux-gnu-g++ -g -O2
-ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-DH5_USE_110_API -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial
-I/usr/include/fast5/ -I/usr/include/
-I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.14 -c
src/self_align_ref.cpp -o
build/temp.linux-x86_64-cpython-314/src/self_align_ref.o -std=c++11 -O3
x86_64-linux-gnu-g++ -g -O2
-ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-DH5_USE_110_API -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g
-fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2
-ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-DH5_USE_110_API build/temp.linux-x86_64-cpython-314/src/chunk.o
build/temp.linux-x86_64-cpython-314/src/client_sim.o
build/temp.linux-x86_64-cpython-314/src/event_detector.o
build/temp.linux-x86_64-cpython-314/src/event_profiler.o
build/temp.linux-x86_64-cpython-314/src/fast5_reader.o
build/temp.linux-x86_64-cpython-314/src/map_pool.o
build/temp.linux-x86_64-cpython-314/src/mapper.o
build/temp.linux-x86_64-cpython-314/src/normalizer.o
build/temp.linux-x86_64-cpython-314/src/pybinder.o
build/temp.linux-x86_64-cpython-314/src/range.o
build/temp.linux-x86_64-cpython-314/src/read_buffer.o
build/temp.linux-x86_64-cpython-314/src/realtime_pool.o
build/temp.linux-x86_64-cpython-314/src/seed_tracker.o
build/temp.linux-x86_64-cpython-314/src/self_align_ref.o -L
-L/usr/lib/x86_64-linux-gnu -lbwa -lhdf5 -lz -ldl -lm -o
/build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.14_uncalled/build/_uncalled.cpython-314-x86_64-linux-gnu.so
/usr/bin/x86_64-linux-gnu-ld.bfd: cannot find -lhdf5: No such file or directory
collect2: error: ld returned 1 exit status
error: command '/usr/bin/x86_64-linux-gnu-g++' failed with exit code 1
E: pybuild pybuild:485: build: plugin distutils failed with: exit code=1:
/usr/bin/python3 setup.py build
See
https://buildd.debian.org/status/fetch.php?pkg=uncalled&arch=amd64&ver=2.3%2Bds-3%2Bb5&stamp=1786284410&raw=0
for details.
Cheers
--
Sebastian Ramacher
--- End Message ---
--- Begin Message ---
Source: uncalled
Source-Version: 2.3+ds-4
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
uncalled, 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.
Andreas Tille <[email protected]> (supplier of updated uncalled 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: Thu, 24 Sep 2026 10:21:30 +0200
Source: uncalled
Architecture: source
Version: 2.3+ds-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1144002
Changes:
uncalled (2.3+ds-4) unstable; urgency=medium
.
* Team upload.
* d/watch: version=5
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Replace pkg-config with pkgconf in Build-Depends
* debian_hdf5: link against the hdf5 library name reported by
pkg-config instead of hardcoding -lhdf5, which fails to link
against current libhdf5-dev. (Closes: #1144002)
* tests: tolerate the 'uncalled map' fast5-read failure caused by the
libhdf5 2.2.0 legacy-chunk regression (CVE-2025-44904 fix) so the
autopkgtest passes until HDF5 can read such files again.
Checksums-Sha1:
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3e78059161116cd2e16d5165edf6d6680d6fc5fc 6624 uncalled_2.3+ds-4.debian.tar.xz
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uncalled_2.3+ds-4_amd64.buildinfo
Files:
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f65b7749ed41c379c9b7f3909090eade 6624 science optional
uncalled_2.3+ds-4.debian.tar.xz
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uncalled_2.3+ds-4_amd64.buildinfo
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