Bug#1057951: promod3: FTBFS: No such file or directory: 'model.pdb'

[Santiago Vila]

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 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh
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 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh
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
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./sidechain_atom_constructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./pairwise_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/loop/src/./structure_db_custom_types.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./constraint_constructor.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh
make[4]: Leaving 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/./all_atom_score_base.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh
[  0%] Built target promod3_loop_headers
make  -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make 
scoring/pymod/CMakeFiles/scoring_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>>/scoring/pymod /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/pymod 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color="
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./all_atom_overall_scorer.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make 
scoring/pymod/CMakeFiles/scoring_pymod.dir/build
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./all_atom_interaction_env_listener.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/pymod/__init__.py 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/scoring/__init__.py
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./all_atom_interaction_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  0%] Built target scoring_pymod
make  -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make 
sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./all_atom_packing_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh
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/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color="
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./all_atom_clash_score.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make 
sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build
make[4]: Entering 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/./bb_dep_rotamer_lib.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/sidechain/src/./disulfid.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different 
/<<PKGBUILDDIR>>/scoring/src/./scwrl3_energy_functions.hh 
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[  0%] Built target promod3_scoring_headers
make  -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make 
sidechain/pymod/CMakeFiles/sidechain_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>>/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 
actions/tests/CMakeFiles/test_actions.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_actions.py_run.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make 
actions/tests/CMakeFiles/test_actions.py_run.dir/build
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 
core/src/CMakeFiles/promod3_core.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.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f core/src/CMakeFiles/promod3_core.dir/build.make 
core/src/CMakeFiles/promod3_core.dir/build
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 
core/tests/CMakeFiles/test_suite_core.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/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.