Your message dated Thu, 24 Sep 2026 13:19:34 +0000
with message-id <[email protected]>
and subject line Bug#1097784: fixed in relion 5.1.0+dfsg-1
has caused the Debian Bug report #1097784,
regarding relion: ftbfs with GCC-15
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
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--
1097784: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097784
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:relion
Version: 3.1.3-4
Severity: important
Tags: sid forky
User: [email protected]
Usertags: ftbfs-gcc-15
[This bug is NOT targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.
The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/relion_3.1.3-4_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other Common build failures are new warnings resulting in build failures
with -Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-15/porting_to.html
[...]
from
/build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.h:24,
from
/build/reproducible-path/relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:23:
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h: In member function ‘int
Image<T>::readTIFF(TIFF*, long int, bool, bool, const FileName&)’:
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:16: warning: ‘uint32’ is
deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~
In file included from /usr/include/x86_64-linux-gnu/tiffio.h:31,
from /build/reproducible-path/relion-3.1.3/src/image.h:57:
/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:43:23: warning: ‘uint32’ is
deprecated [-Wdeprecated-declarations]
43 | uint32 width, length; // apparent dimensions in the file
| ^~~~~~
/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:16: warning: ‘uint16’ is
deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:30: warning: ‘uint16’ is
deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:44:45: warning: ‘uint16’ is
deprecated [-Wdeprecated-declarations]
44 | uint16 sampleFormat, bitsPerSample, resolutionUnit;
| ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:32: warning: ‘uint32’ is
deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~
/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:185:43: warning: ‘uint32’ is
deprecated [-Wdeprecated-declarations]
185 | uint32 cur_width, cur_length;
| ^~~~~~~~~~
/usr/include/x86_64-linux-gnu/tiff.h:86:38: note: declared here
86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED;
| ^~~~~~
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:32: warning: ‘uint16’ is
deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
/build/reproducible-path/relion-3.1.3/src/rwTIFF.h:186:50: warning: ‘uint16’ is
deprecated [-Wdeprecated-declarations]
186 | uint16 cur_sampleFormat, cur_bitsPerSample;
| ^~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/tiff.h:83:38: note: declared here
83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED;
| ^~~~~~
make[4]: *** [src/apps/CMakeFiles/relion_lib.dir/build.make:1790:
src/apps/CMakeFiles/relion_lib.dir/__/jaz/img_proc/filter_helper.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/build/reproducible-path/relion-3.1.3/build'
make[3]: *** [CMakeFiles/Makefile2:321: src/apps/CMakeFiles/relion_lib.dir/all]
Error 2
make[3]: Leaving directory '/build/reproducible-path/relion-3.1.3/build'
make[2]: *** [Makefile:139: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/relion-3.1.3/build'
make[1]: *** [debian/rules:41: override_dh_auto_build] Error 2
make[1]: Leaving directory '/build/reproducible-path/relion-3.1.3'
make: *** [debian/rules:33: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: relion
Source-Version: 5.1.0+dfsg-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
relion, 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 relion 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 14:27:25 +0200
Source: relion
Architecture: source
Version: 5.1.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1097784 1113466
Changes:
relion (5.1.0+dfsg-1) unstable; urgency=medium
.
[ Pierre Gruet ]
* New upstream version 5.0.1+dfsg:
- Repacking without embedded copy of Eigen
* Adding B-D on libtorch-dev
* Raising Standards version to 4.7.3:
- Removing Priority: optional, which is default
.
[ Yavor Doganov ]
* New upstream release:
+ Fixes FTBFS with GCC 15 (Closes: #1097784).
* debian/patches/0001-Repair-wrong-comment-sign...patch: Delete; was
cherry-picked from upstream.
* debian/patches/typos.patch: Remove hunks applied upstream; fix more
spelling errors.
* debian/patches/format-security.patch: New; fix FTBFS
with -Werror=format-security.
* debian/patches/python3.patch: New; migrate the relion_it script from
Python 2 to 3 as it's the core of on-the-fly processing.
* debian/patches/system-eigen.patch: New; use the system Eigen library.
* Run wrap-and-sort -ast.
* debian/control
- (Build-Depends): Remove fluid (unnecessary). Add libpng-dev,
dh-sequence-python3, python3 and libeigen3-dev.
- (relion) <Depends>: Add ctffind (<< 5). <Recommends>: Add ghostscript
(for generating PDF files), pbzip2, xz-utils and zstd (for reading
compressed MRC movies).
- (relion-gui) <Depends>: Add ${python3:Depends} and python3-tk.
(Breaks, Replaces): Remove; obsolete.
(Rules-Requires-Root): Remove; it's the default.
* debian/rules: Enable full hardening.
(CONFIGURE_COMMON): Remove redundant flags that are already set by
debhelper's cmake build system. Fix FTBFS with CMake 4 by adding
-DCMAKE_POLICY_VERSION_MINIMUM=3.5 (Closes: #1113466).
Add -DPYTHON_EXE_PATH=/usr/bin/python3 to override upstream's test
which relies on a Conda environment.
(NUMJOBS, MAKE_-J): Remove; gymnastics no longer necessary.
(override_dh_auto_configure): Run dh_auto_configure.
(override_dh_auto_build): Remove; redundant.
(override_dh_auto_clean): Likewise.
(override_dh_auto_install): Run dh_auto_install --destdir. Rename
scripts with .py extension to fix W: script-with-language-extension.
Delete Python/Bash scripts which will fail due to missing modules.
* debian/relion-gui.install: Install schemes in /usr/share/relion.
* debian/README.Debian: New file; document missing functionality.
* debian/watch: Upgrade to version 5.
* debian/salsa-ci.yml: Use the default recipe.
* debian/copyright: Update copyright years, fix superfluous patterns,
add EPL and MPL-2 licenses.
.
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.7.4 (routine-update)
* Build-Depends: pybuild-plugin-pyproject (routine-update)
* Add missing build-dependency on python3-setuptools.
* debputy lint --auto-fix (routine-update)
* d/copyright:
- Drop unused licenses
- Do not mention removed src/Eigen
- Use link to /usr/share/common-licenses/MPL-2.0 instead of full text
* Fix FTBFS with Eigen 5
* debian/rules: relion_schemegui is installed without a .py suffix
since upstream 5.1.0; adjust the script renaming in
override_dh_auto_install.
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Files:
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