Your message dated Thu, 24 Sep 2026 20:22:47 +0000
with message-id <[email protected]>
and subject line Bug#1040128: fixed in relion-cuda 5.1.0+dfsg-1
has caused the Debian Bug report #1040128,
regarding relion-cuda: FTBFS with cub 2.0.1: error: function "cub::Debug" has
already been defined
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.)
--
1040128: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1040128
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: relion-cuda
Version: 3.1.3-2
Severity: serious
Tags: ftbfs sid trixie
Justification: fails to build from source
Hi,
relion-cuda FTBFS in the combination of CUDA 11.8 and CUB 2.0.1:
...
nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37'
architectures are deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
/usr/include/cub/util_debug.cuh(184): error: function "cub::Debug" has already
been defined
/usr/include/cub/util_debug.cuh(184): error: function "cub::Debug" has already
been defined
/usr/include/cub/util_debug.cuh(184): error: function "cub::Debug" has already
been defined
Generated
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_backprojector.cu.o
successfully.
Generated
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o
successfully.
/usr/include/cub/util_debug.cuh(184): error: function "cub::Debug" has already
been defined
1 error detected in the compilation of
"/build/relion-cuda-3.1.3/src/acc/cuda/cuda_projector_plan.cu".
-- Removing
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o
/usr/bin/cmake -E rm -f
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o
CMake Error at
relion_gpu_util_generated_cuda_projector_plan.cu.o.Release.cmake:280 (message):
Error generating file
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o
make[4]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/build.make:129:
src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o]
Error 1
make[4]: *** Waiting for unfinished jobs....
Generated
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_benchmark_utils.cu.o
successfully.
1 error detected in the compilation of
"/build/relion-cuda-3.1.3/src/acc/cuda/cuda_autopicker.cu".
1 error detected in the compilation of
"/build/relion-cuda-3.1.3/src/acc/cuda/cuda_helper_functions.cu".
-- Removing
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_autopicker.cu.o
-- Removing
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o
/usr/bin/cmake -E rm -f
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_autopicker.cu.o
/usr/bin/cmake -E rm -f
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o
CMake Error at relion_gpu_util_generated_cuda_autopicker.cu.o.Release.cmake:280
(message):
Error generating file
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_autopicker.cu.o
make[4]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/build.make:80:
src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o]
Error 1
CMake Error at
relion_gpu_util_generated_cuda_helper_functions.cu.o.Release.cmake:280
(message):
Error generating file
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o
make[4]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/build.make:101:
src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o]
Error 1
1 error detected in the compilation of
"/build/relion-cuda-3.1.3/src/acc/cuda/cuda_ml_optimiser.cu".
-- Removing
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o
/usr/bin/cmake -E rm -f
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o
CMake Error at
relion_gpu_util_generated_cuda_ml_optimiser.cu.o.Release.cmake:280 (message):
Error generating file
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o
make[4]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/build.make:115:
src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_ml_optimiser.cu.o]
Error 1
Generated
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/./relion_gpu_util_generated_helper.cu.o
successfully.
make[4]: Leaving directory '/build/relion-cuda-3.1.3/build'
make[3]: *** [CMakeFiles/Makefile2:300:
src/apps/CMakeFiles/relion_gpu_util.dir/all] Error 2
make[3]: Leaving directory '/build/relion-cuda-3.1.3/build'
make[2]: *** [Makefile:139: all] Error 2
make[2]: Leaving directory '/build/relion-cuda-3.1.3/build'
make[1]: *** [debian/rules:41: override_dh_auto_build] Error 2
make[1]: Leaving directory '/build/relion-cuda-3.1.3'
make: *** [debian/rules:33: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
Andreas
relion-cuda.sid.build.gz
Description: application/gzip
--- End Message ---
--- Begin Message ---
Source: relion-cuda
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-cuda, 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-cuda 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 20:56:51 +0200
Source: relion-cuda
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: 1036681 1040128 1147432
Changes:
relion-cuda (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.
* 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-cuda) <Depends>: Add ctffind (<< 5). <Recommends>: Add
ghostscript (for generating PDF files), pbzip2, xz-utils and zstd
(for reading compressed MRC movies).
- (relion-gui-cuda) <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.
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 with CUDA=ON and
CMAKE_CUDA_HOST_COMPILER=/usr/bin/cuda-gcc.
(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-cuda.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.
* New upstream release fixes relion-cuda FTBFS with CUDA 12 (nvcc no
longer supports sm_35) and with cub 2.0.1.
(Closes: #1036681, #1040128, #1147432)
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