Package: src:promod3 Version: 3.6.0+ds-1 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202603/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot 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 add an affects on src:promod3, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --with python3 dh_clean 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 PKG_CONFIG=/usr/bin/pkg-config 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 15.2.0 -- The C compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info [... snipped ...] cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod && [too-long-redacted] ain/pymod/export_rotamer_lib.cc In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/eigen_types.hh:23, from /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/superpose.hh:24, from /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/loop/backbone.hh:33, from /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/modelling/kic.hh:21, from /<<PKGBUILDDIR>>/modelling/src/kic.cc:17: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function âstatic void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, 16, 16>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1, 1, 1, 16> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, 16, 16>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]â: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: âresultâ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | <Index,Mode, | ~~~~~~~~~~~~ 329 | LhsScalar, LhsBlasTraits::NeedToConjugate, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 | RhsScalar, RhsBlasTraits::NeedToConjugate, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 331 | RowMajor> | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 4 of type âconst double*â to âstatic void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]â declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod && [too-long-redacted] port_sidechain_object_loader.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod && [too-long-redacted] d/export_rotamer_constructor.cc [ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] modelling/src/loop_candidate.cc [ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] >>/modelling/src/monte_carlo.cc [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] lling/src/monte_carlo_closer.cc [ 74%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod && [too-long-redacted] /export_subrotamer_optimizer.cc [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] lling/src/monte_carlo_cooler.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] ling/src/monte_carlo_sampler.cc [ 77%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod && [too-long-redacted] dechain/pymod/wrap_sidechain.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] lling/src/monte_carlo_scorer.cc [ 77%] Linking CXX shared module ../../stage/lib/python3.13/site-packages/promod3/sidechain/_sidechain.so cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>> [too-long-redacted] ux-gnu/libboost_graph.so.1.90.0 make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 77%] Built target _sidechain [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] >/modelling/src/rigid_blocks.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] odelling/src/score_container.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] odelling/src/scoring_weights.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] /src/sidechain_reconstructor.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] g/src/sidechain_env_listener.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /u [too-long-redacted] >/modelling/src/motif_finder.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -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 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o -MF CMakeFiles/promod3_modelling.dir/afdb.cc.o.d -o CMakeFiles/promod3_modelling.dir/afdb.cc.o -c /<<PKGBUILDDIR>>/modelling/src/afdb.cc [ 81%] Linking CXX shared library ../../stage/lib/libpromod3_modelling.so cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>> [too-long-redacted] ux-gnu/libboost_regex.so.1.90.0 cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib/libpromod3_modelling.so.3.6.0 ../../stage/lib/libpromod3_modelling.so.3.6 ../../stage/lib/libpromod3_modelling.so make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 81%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[3]: 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/pymod /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" _modelling make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] ymod/export_extension_scheme.cc cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] >/modelling/pymod/export_gap.cc [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] ng/pymod/export_gap_extender.cc [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] /pymod/export_loop_candidate.cc [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] ng/pymod/export_loop_closure.cc [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] modelling/pymod/export_model.cc [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] ing/pymod/export_monte_carlo.cc [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] ng/pymod/export_rigid_blocks.cc [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] pymod/export_score_container.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/core/demangle.hpp:14, from /usr/include/boost/core/typeinfo.hpp:135, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/function_template.hpp:14, from /usr/include/boost/function/function0.hpp:10, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /<<PKGBUILDDIR>>/modelling/pymod/export_score_container.cc:17: In member function âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from âvoid promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]â at /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: â* [too-long-redacted] ialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /<<PKGBUILDDIR>>/modelling/pymod/export_score_container.cc:19: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function âvoid promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]â: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: â<anonymous>â declared here 83 | const K key = boost::python::extract<K>(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] pymod/export_scoring_weights.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/core/demangle.hpp:14, from /usr/include/boost/core/typeinfo.hpp:135, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/function_template.hpp:14, from /usr/include/boost/function/function0.hpp:10, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:17: In member function âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from âvoid promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]â at /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: â* [too-long-redacted] ialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:21: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function âvoid promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]â: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: â<anonymous>â declared here 83 | const K key = boost::python::extract<K>(keys[i]); | ^~~~~~~~~~~~~~~~~~~ In member function âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from âboost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)â at /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:112:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: â* [too-long-redacted] ialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc: In function âboost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)â: /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:112:39: note: â<anonymous>â declared here 112 | String seq = extract<String>(args[0]); | ^ In member function âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from âboost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)â at /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:179:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: â* [too-long-redacted] ialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc: In function âboost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)â: /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:179:39: note: â<anonymous>â declared here 179 | String seq = extract<String>(args[0]); | ^ In member function âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from âboost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)â at /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:47:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: â* [too-long-redacted] ialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc: In function âboost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)â: /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:47:39: note: â<anonymous>â declared here 47 | String seq = extract<String>(args[0]); | ^ In file included from /usr/include/c++/15/string:56, from /usr/include/boost/core/demangle.hpp:14, from /usr/include/boost/core/typeinfo.hpp:135, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/function_template.hpp:14, from /usr/include/boost/function/function0.hpp:10, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /<<PKGBUILDDIR>>/modelling/pymod/export_scoring_weights.cc:17: In member function âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from âstd::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]â at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from âvoid promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]â at /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: â* [too-long-redacted] ialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /<<PKGBUILDDIR>>/modelling/pymod/export_scoring_weights.cc:19: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function âvoid promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]â: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: â<anonymous>â declared here 83 | const K key = boost::python::extract<K>(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] port_sidechain_reconstructor.cc [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] ng/pymod/export_motif_finder.cc [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] /modelling/pymod/export_afdb.cc [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && [too-long-redacted] delling/pymod/wrap_modelling.cc [ 90%] Linking CXX shared module ../../stage/lib/python3.13/site-packages/promod3/modelling/_modelling.so cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>> [too-long-redacted] ux-gnu/libboost_graph.so.1.90.0 make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 90%] Built target _modelling make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[3]: 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.dir/DependInfo.cmake "--color=" _init make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 90%] Built target _init make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make[3]: 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>>/loop/data /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake "--color=" generate_loop_data_ff_lookup_charmm.dat make[3]: 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>>/loop/data /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake "--color=" generate_loop_data_torsion_sampler.dat make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat [ 91%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/<<PKGBUILDDIR>>/loop/data/convert_binaries.py'\ '/<<PKGBUILDDIR>>/loop/data/portable_ff_lookup_charmm.dat'\ '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/<<PKGBUILDDIR>>/loop/data/convert_binaries.py'\ '/<<PKGBUILDDIR>>/loop/data/portable_torsion_sampler.dat'\ '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Traceback (most recent call last): Traceback (most recent call last): File "/<<PKGBUILDDIR>>/loop/data/convert_binaries.py", line 20, in <module> from promod3 import loop File "/<<PKGBUILDDIR>>/loop/data/convert_binaries.py", line 20, in <module> from promod3 import loop File "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/promod3/__init__.py", line 18, in <module> import promod3.sidechain File "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/promod3/sidechain/__init__.py", line 17, in <module> from ._sidechain import * TypeError: No to_python (by-value) converter found for C++ type: geom::Vec3 File "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/promod3/__init__.py", line 18, in <module> import promod3.sidechain File "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/promod3/sidechain/__init__.py", line 17, in <module> from ._sidechain import * TypeError: No to_python (by-value) converter found for C++ type: geom::Vec3 make[3]: *** [loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make:78: stage/share/promod3/loop_data/torsion_sampler.dat] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:2051: loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/all] Error 2 make[2]: *** Waiting for unfinished jobs.... make[3]: *** [loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make:78: stage/share/promod3/loop_data/ff_lookup_charmm.dat] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:2267: loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[1]: *** [Makefile:139: all] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2 make: *** [debian/rules:4: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
