Bug#1057951: marked as done (promod3: FTBFS: No such file or directory: 'model.pdb')

[Debian Bug Tracking System]

Your message dated Mon, 11 Dec 2023 14:51:36 +0000
with message-id <e1rchda-00go8f...@fasolo.debian.org>
and subject line Bug#1057951: fixed in promod3 3.3.1+ds-2
has caused the Debian Bug report #1057951,
regarding promod3: FTBFS: No such file or directory: 'model.pdb'
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 ow...@bugs.debian.org
immediately.)


-- 
1057951: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1057951
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Package: src:promod3
Version: 3.3.1+ds-1
Severity: serious
Tags: ftbfs

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
 debian/rules binary
dh binary --with python3
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
        -DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr 
-DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib
        cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake 
-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc 
-DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON 
-DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON 
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run 
-DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON 
-DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON 
-DOST_ROOT=/usr -DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib ..
-- The CXX compiler identification is GNU 13.2.0
-- The C compiler identification is GNU 13.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped

[... snipped ...]

make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make 
loop/pymod/CMakeFiles/loop_pymod.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/pymod/__init__.py 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/loop/__init__.py
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./backbone.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  0%] Built target loop_pymod
make  -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make 
scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/scoring/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color="
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./bb_trace_param.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make 
scoring/src/CMakeFiles/promod3_scoring_headers.dir/build
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./data_bag.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./backbone_score_base.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./backbone_overall_scorer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./dense_hash_table.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./scoring_object_loader.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./dense_map.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./dense_map.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./density_creator.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./forcefield_lookup.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./frag_db.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./cbeta_env_listener.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./fragger.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./hydrogen_constructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./cb_packing_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./hydrogen_rule_lookup.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./cbeta_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./idx_handler.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./reduced_env_listener.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./reduced_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./loop_object_loader.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./clash_env_listener.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./mm_system_creator.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./clash_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./psipred_prediction.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./density_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./stem_geom.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./hbond_env_listener.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./structure_db.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./hbond_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./torsion_sampler.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./ss_agreement_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./ushort_vec.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./ss_agreement_env_listener.hh 
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./sidechain_atom_rule_lookup.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./torsion_score.hh 
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./pairwise_scoring_function.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh
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/<<PKGBUILDDIR>>/loop/src/./sidechain_atom_constructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/sidechain/pymod /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color="
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./frame.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_graph.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make 
sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/pymod/__init__.py 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/sidechain/__init__.py
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./particle.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./particle_scoring_base.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh
[  0%] Built target sidechain_pymod
make  -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make 
modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/modelling/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color="
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./particle_scoring.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make 
modelling/src/CMakeFiles/promod3_modelling_headers.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./extension_scheme.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./scwrl4_particle_scoring.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./gap.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./scwrl3_particle_scoring.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./gap_extender.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./vina_particle_scoring.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./model.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./all_atom_relaxer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_cruncher.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./backbone_relaxer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_density.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./ccd.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_group.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_id.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./kic.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_lib.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./loop_candidate.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_lib_entry.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./monte_carlo.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_lib_reader.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./monte_carlo_closer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./monte_carlo_cooler.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./sidechain_connector.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./sidechain_object_loader.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./monte_carlo_sampler.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_constructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./monte_carlo_scorer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./rigid_blocks.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./rotamer_lookup.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./score_container.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./scwrl4_rotamer_constructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./scwrl3_rotamer_constructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./scoring_weights.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./vina_rotamer_constructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./sidechain_reconstructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./subrotamer_optimizer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./sidechain_env_listener.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./motif_finder.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh
[  0%] Built target promod3_sidechain_headers
make  -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make 
core/init/CMakeFiles/init___init__.py_pymod.dir/depend
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./robin_hood.h 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/core/init /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/init 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make 
core/init/CMakeFiles/init___init__.py_pymod.dir/build
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/src/./afdb.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: Nothing to be done for 
'core/init/CMakeFiles/init___init__.py_pymod.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  1%] Built target init___init__.py_pymod
make  -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make 
scoring/data/CMakeFiles/scoring_data_dir.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/scoring/data /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/data 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color="
[  1%] Built target promod3_modelling_headers
make  -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make 
sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/sidechain/data /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/data 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make 
scoring/data/CMakeFiles/scoring_data_dir.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make 
sidechain/data/CMakeFiles/sidechain_data_dir.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  1%] Built target scoring_data_dir
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make 
modelling/tests/CMakeFiles/test_data_modelling.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/modelling/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake "--color="
[  1%] Built target sidechain_data_dir
make  -f scripts/CMakeFiles/subst_pm.dir/build.make 
scripts/CMakeFiles/subst_pm.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/scripts /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scripts 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make 
modelling/tests/CMakeFiles/test_data_modelling.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f scripts/CMakeFiles/subst_pm.dir/build.make 
scripts/CMakeFiles/subst_pm.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake 
-DINPUT_FILE=/<<PKGBUILDDIR>>/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 
-DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.11/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages 
-DPython_EXECUTABLE=/usr/bin/python3 -P /<<PKGBUILDDIR>>/cmake_support/substitute.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1cjx-1.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta
[  1%] Built target subst_pm
make  -f actions/tests/CMakeFiles/test_data_actions.dir/build.make 
actions/tests/CMakeFiles/test_data_actions.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/actions/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake "--color="
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f actions/tests/CMakeFiles/test_data_actions.dir/build.make 
actions/tests/CMakeFiles/test_data_actions.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1cjx-1.pdb.gz 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/actions/tests/data/gly.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions/data/gly.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1crn.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/actions/tests/data/seq.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions/data/seq.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1CRN.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/actions/tests/data/seq_ins.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions/data/seq_ins.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1crn_build.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb
[  1%] Built target test_data_actions
make  -f core/src/CMakeFiles/promod3_core_headers.dir/build.make 
core/src/CMakeFiles/promod3_core_headers.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/core/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color="
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f core/src/CMakeFiles/promod3_core_headers.dir/build.make 
core/src/CMakeFiles/promod3_core_headers.dir/build
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1crn_cut.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./check_io.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./cluster.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1crn_final.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./dynamic_spatial_organizer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./export_helper.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./geom_base.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1crn_rec.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./geom_stems.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./message.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./portable_binary_data_sink.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1crn_sc.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./portable_binary_data_source.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1crn_sc_test.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./portable_binary_serializer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./runtime_profiling.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1CRNA.hhm 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./superpose.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./enumerator.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1eye.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./graph.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./tree.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./tetrahedral_polytope.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./graph_minimizer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1eye_rec.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/core/src/./eigen_types.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
[  1%] Built target promod3_core_headers
make  -f core/init/CMakeFiles/init_pymod.dir/build.make 
core/init/CMakeFiles/init_pymod.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/core/init /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/init 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color="
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1eye_sc_test.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f core/init/CMakeFiles/init_pymod.dir/build.make 
core/init/CMakeFiles/init_pymod.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  1%] Built target init_pymod
make  -f scripts/CMakeFiles/promod3_scripts.dir/build.make 
scripts/CMakeFiles/promod3_scripts.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/scripts /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scripts 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f scripts/CMakeFiles/promod3_scripts.dir/build.make 
scripts/CMakeFiles/promod3_scripts.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/bin/pm
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scripts/pm /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/bin/pm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  1%] Built target promod3_scripts
make  -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make 
actions/tests/CMakeFiles/test_action_build-model.py_run.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/actions/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-model.py_run.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make 
actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
[  1%] running checks test_action_build-model.py
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions && sh -c 
"PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/
  /usr/bin/python3 /<<PKGBUILDDIR>>/actions/tests/test_action_build-model.py"
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1ITX-A-11_sidechain.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1K5C-A-16_clash.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/1mcg.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/2aoh-1_cut.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb
Compound library not available. Some functionality may not work as expected.
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/2aoh-1_cut_A.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/2aoh-1_cut_B.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/2dbs.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/2jlp-1.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/2jlp-1.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/2xim-1.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/2xim-1.pdb.gz 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/3b08-3.pdb.gz 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/3b08-3.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/4nyk.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/4R6K-A-13_sidechain.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/4ksl-1.pdb.gz 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/4ksl-1.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/5d52-1.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/5d52-1_cut.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/5d52-1_cut_A.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/5d52-1_cut_B.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/CA-3cm91E.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/CA-3cm91E.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/cbeta.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/cbeta.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/compounds.chemlib 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/compounds.chemlib
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/del.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/ff_NAD.dat 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/gly.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/gly_on_top.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/gly_almost_on_top.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/gly_shifted_nter.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/hetero-punched.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/ins.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/modelCApartial-5tgl1A.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/neighbor-punched.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/neighbor-punched.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/port_frag_db.dat 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/port_frag_db.dat
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/port_str_db.dat 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/sep.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/sep.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/sep.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/seq.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/seq.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/smtl2bl4.1.pdb 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/smtl2bl4.1.pdb
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/ter.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/ter.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/terminal_deletion_aln.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/terminal_deletion_aln.fasta
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 
make_directory /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/modelling/tests/data/double_gap_aln.fasta 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/modelling/data/double_gap_aln.fasta
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  1%] Built target test_data_modelling
make  -f 
actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make 
actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/actions/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f 
actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make 
actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  1%] running checks test_action_build-rawmodel.py
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions && sh -c 
"PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/
  /usr/bin/python3 /<<PKGBUILDDIR>>/actions/tests/test_action_build-rawmodel.py"
Compound library not available. Some functionality may not work as expected.
.E..
----------------------------------------------------------------------
Ran 3 tests in 1.334s

OK
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  1%] Built target test_action_build-rawmodel.py_run
make  -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make 
actions/tests/CMakeFiles/test_action_help.py_run.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/actions/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_help.py_run.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make 
actions/tests/CMakeFiles/test_action_help.py_run.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  2%] running checks test_action_help.py
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions && sh -c 
"PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/
  /usr/bin/python3 /<<PKGBUILDDIR>>/actions/tests/test_action_help.py"
Compound library not available. Some functionality may not work as expected.
..
----------------------------------------------------------------------
Ran 2 tests in 0.026s

OK
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  2%] Built target test_action_help.py_run
make  -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make 
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/actions/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/actions/tests 
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  3%] running checks test_actions.py
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/actions && sh -c 
"PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/
  /usr/bin/python3 /<<PKGBUILDDIR>>/actions/tests/test_actions.py"
Compound library not available. Some functionality may not work as expected.
.
----------------------------------------------------------------------
Ran 1 test in 0.000s

OK
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  3%] Built target test_actions.py_run
make  -f core/src/CMakeFiles/promod3_core.dir/build.make 
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/core/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f core/src/CMakeFiles/promod3_core.dir/build.make 
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: Nothing to be done for 'core/src/CMakeFiles/promod3_core.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  6%] Built target promod3_core
make  -f core/tests/CMakeFiles/test_suite_core.dir/build.make 
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> 
/<<PKGBUILDDIR>>/core/tests /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/tests 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f core/tests/CMakeFiles/test_suite_core.dir/build.make 
core/tests/CMakeFiles/test_suite_core.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  6%] Building CXX object 
core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 
-DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include 
-I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection 
-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 
-fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o -MF 
CMakeFiles/test_suite_core.dir/test_check_io.cc.o.d -o CMakeFiles/test_suite_core.dir/test_check_io.cc.o -c 
/<<PKGBUILDDIR>>/core/tests/test_check_io.cc
..
======================================================================
ERROR: testExit0 (__main__.HelpActionTests.testExit0)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/actions/tests/test_action_build-model.py", line 48, in 
testExit0
    os.remove('model.pdb')
FileNotFoundError: [Errno 2] No such file or directory: 'model.pdb'

----------------------------------------------------------------------
Ran 3 tests in 5.583s

FAILED (errors=1)
make[4]: *** 
[actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make:74: 
actions/tests/CMakeFiles/test_action_build-model.py_run] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:3475: 
actions/tests/CMakeFiles/test_action_build-model.py_run.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[  7%] Building CXX object 
core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 
-DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include 
-I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection 
-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 
-fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -MF 
CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o.d -o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -c 
/<<PKGBUILDDIR>>/core/tests/test_portable_binary.cc
[  7%] Building CXX object 
core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 
-DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include 
-I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection 
-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 
-fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -MF 
CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o.d -o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -c 
/<<PKGBUILDDIR>>/core/tests/test_graph_minimizer.cc
[  8%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 
-DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include 
-I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection 
-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 
-fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o -MF CMakeFiles/test_suite_core.dir/tests.cc.o.d -o 
CMakeFiles/test_suite_core.dir/tests.cc.o -c /<<PKGBUILDDIR>>/core/tests/tests.cc
[  8%] Linking CXX executable ../../tests/core/test_suite_core
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E 
cmake_link_script CMakeFiles/test_suite_core.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 
-std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro 
CMakeFiles/test_suite_core.dir/test_check_io.cc.o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o 
CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o CMakeFiles/test_suite_core.dir/tests.cc.o -o 
../../tests/core/test_suite_core   -L/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64  
-Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64 
/usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.3.1 
/usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so 
/usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so 
/usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so 
/usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so 
/usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so 
/usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  8%] Built target test_suite_core
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:840: CMakeFiles/check.dir/rule] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:172: check] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j2 check ARGS\+=--verbose 
ARGS\+=-j2 returned exit code 2
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202312/

About the archive rebuild: The build was made using virtual machines
from AWS, with enough memory, enough disk, and either one or two
CPUs, using a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

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.

--- End Message ---

--- Begin Message ---

Source: promod3
Source-Version: 3.3.1+ds-2
Done: Andrius Merkys <mer...@debian.org>

We believe that the bug you reported is fixed in the latest version of
promod3, 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 1057...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated promod3 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 ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Mon, 11 Dec 2023 08:52:41 -0500
Source: promod3
Architecture: source
Version: 3.3.1+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1057951
Changes:
 promod3 (3.3.1+ds-2) unstable; urgency=medium
 .
   * Simplify debian/rules.
   * Execute tests sequentially to fix FTBFS due to dependency of test
     execution order (Closes: #1057951)
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promod3_3.3.1+ds-2.debian.tar.xz
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