Your message dated Thu, 24 Sep 2026 13:19:34 +0000
with message-id <[email protected]>
and subject line Bug#1113466: fixed in relion 5.1.0+dfsg-1
has caused the Debian Bug report #1113466,
regarding relion: FTBFS with CMake 4
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.)
--
1113466: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113466
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: relion
Version: 3.1.3-4
Severity: serious
User: [email protected]
Usertags: cmake-4
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for CMake 4, relion failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
+------------------------------------------------------------------------------+
| Build Sat, 30 Aug 2025 16:57:46 +0000 |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: relion
Binary: relion, relion-gui
Architecture: any
Version: 3.1.3-4
Maintainer: Debian Med Packaging Team
<[email protected]>
Uploaders: Roland Fehrenbacher <[email protected]>, Andreas Tille
<[email protected]>,
Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/relion
Vcs-Git: https://salsa.debian.org/med-team/relion.git
Testsuite: autopkgtest
Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev,
mpi-default-dev, libtiff-dev, fluid
Package-List:
relion deb science optional arch=any
relion-gui deb science optional arch=any
Checksums-Sha1:
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cbd977bd73a6270bab2fc9aca5779296c528315b 12056 relion_3.1.3-4.debian.tar.xz
Checksums-Sha256:
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relion_3.1.3.orig.tar.gz
5dfd505bf26bb03602300ad0b21ed1e6459f97491725abdb5dfa79427972a46a 12056
relion_3.1.3-4.debian.tar.xz
Files:
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dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-4.dsc:
no acceptable signature found
dpkg-source: info: extracting relion in /build/reproducible-path/relion-3.1.3
dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz
dpkg-source: info: unpacking relion_3.1.3-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying
0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
dpkg-source: info: applying typos.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=sbuild
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=sbuild
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -b
dpkg-buildpackage: info: source package relion
dpkg-buildpackage: info: source version 3.1.3-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <[email protected]>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/relion-3.1.3'
dh_clean
rm -rf build
make[1]: Leaving directory '/build/reproducible-path/relion-3.1.3'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/relion-3.1.3'
mkdir /build/reproducible-path/relion-3.1.3/build
cd /build/reproducible-path/relion-3.1.3/build; \
CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles"
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON
-DGUI=ON -DCUDA=OFF /build/reproducible-path/relion-3.1.3
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 has been removed from CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
Or, add -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to try configuring anyway.
-- Configuring incomplete, errors occurred!
make[1]: *** [debian/rules:37: override_dh_auto_configure] Error 1
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
--------------------------------------------------------------------------------
Build finished at 2025-08-30T16:57:57Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/2410094/
The most likely cause of build failures is the removed backwards compatibility
for
CMake versions earlier than 3.5. You can find additional information in my
debian-devel announcement:
https://lists.debian.org/debian-devel/2025/04/msg00310.html
About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.
You can find the build task here:
https://debusine.debian.net/work-request/154727/
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks,
Timo
--- 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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