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#1110702 promod3 ftbfs with GCC 15 #1110702

Package:: src:promod3
Source:: src:promod3
Submitter:: Matthias Klose
Date:: 2025-09-04 18:00:28 UTC
Severity:: normal
Tags:
#1110702#5
Date:: 2025-08-10 08:55:29 UTC
From:
To:
this looks related to GCC 15:

[...]
[ 92%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat
[ 92%] Generating
../../stage/share/promod3/loop_data/torsion_sampler_extended.dat
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data && sh -c
PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\
/usr/bin/python3\ '/<<PKGBUILDDIR>>/loop/data/convert_binaries.py'\
'/<<PKGBUILDDIR>>/loop/data/portable_torsion_sampler.dat'\
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\
TorsionSampler
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data && sh -c
PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\
/usr/bin/python3\ '/<<PKGBUILDDIR>>/loop/data/convert_binaries.py'\
'/<<PKGBUILDDIR>>/loop/data/portable_torsion_sampler_extended.dat'\
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\
TorsionSampler
[ 92%] Generating
../../stage/share/promod3/loop_data/torsion_sampler_coil.dat
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data && sh -c
PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\
/usr/bin/python3\ '/<<PKGBUILDDIR>>/loop/data/convert_binaries.py'\
'/<<PKGBUILDDIR>>/loop/data/portable_ff_lookup_charmm.dat'\
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\
ForcefieldLookup
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data && sh -c
PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\
/usr/bin/python3\ '/<<PKGBUILDDIR>>/loop/data/convert_binaries.py'\
'/<<PKGBUILDDIR>>/loop/data/portable_torsion_sampler_coil.dat'\
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\
TorsionSampler
Compound library not available. Some functionality may not work as expected.
Compound library not available. Some functionality may not work as expected.
Compound library not available. Some functionality may not work as expected.
Compound library not available. Some functionality may not work as expected.
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
   File "/<<PKGBUILDDIR>>/loop/data/convert_binaries.py", line 20, in
<module>
     from promod3 import loop
   File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py",
line 18, in <module>
     import promod3.sidechain
   File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/sidechain/__init__.py",
line 17, in <module>
     from ._sidechain import *
TypeError: No to_python (by-value) converter found for C++ type:
geom::Vec3List
   File "/<<PKGBUILDDIR>>/loop/data/convert_binaries.py", line 20, in
<module>
     from promod3 import loop
   File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py",
line 18, in <module>
     import promod3.sidechain
   File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/sidechain/__init__.py",
line 17, in <module>
     from ._sidechain import *
TypeError: No to_python (by-value) converter found for C++ type:
geom::Vec3List
   File "/<<PKGBUILDDIR>>/loop/data/convert_binaries.py", line 20, in
<module>
     from promod3 import loop
   File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py",
line 18, in <module>
     import promod3.sidechain
   File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/sidechain/__init__.py",
line 17, in <module>
     from ._sidechain import *
TypeError: No to_python (by-value) converter found for C++ type:
geom::Vec3List
   File "/<<PKGBUILDDIR>>/loop/data/convert_binaries.py", line 20, in
<module>
     from promod3 import loop
   File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py",
line 18, in <module>
     import promod3.sidechain
   File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/sidechain/__init__.py",
line 17, in <module>
     from ._sidechain import *
TypeError: No to_python (by-value) converter found for C++ type:
geom::Vec3List
make[3]: ***
[loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make:78:
stage/share/promod3/loop_data/torsion_sampler.dat] Error 1
make[3]: ***
[loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make:78:
stage/share/promod3/loop_data/torsion_sampler_extended.dat] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:2123:
loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/all]
Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: ***
[loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make:78:
stage/share/promod3/loop_data/torsion_sampler_coil.dat] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: ***
[loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make:78:
stage/share/promod3/loop_data/ff_lookup_charmm.dat] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:2051:
loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/all] Error 2
make[2]: *** [CMakeFiles/Makefile2:2267:
loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/all]
Error 2
make[2]: *** [CMakeFiles/Makefile2:2087:
loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/all]
Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:139: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4
"INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:4: binary] Error 25
#1110702 promod3 ftbfs with GCC 15 #1110702

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