[Debian-med-packaging] Bug#1097784: relion: ftbfs with GCC-15
Matthias Klose
doko at debian.org
Mon Feb 17 17:50:17 GMT 2025
Package: src:relion
Version: 3.1.3-4
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
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
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