[Debichem-devel] Bug#1129830: promod3: FTBFS with boost 1.90
Santiago Vila
sanvila at debian.org
Thu Mar 5 23:21:29 GMT 2026
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 ‘static 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]’:
/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ 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 ‘const double*’ to ‘static 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]’ 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 ‘std::__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>]’,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:1176:20,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:617:20,
inlined from ‘void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]’ 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: ‘* [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 ‘void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]’:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: ‘<anonymous>’ 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 ‘std::__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>]’,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:1176:20,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:617:20,
inlined from ‘void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]’ 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: ‘* [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 ‘void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]’:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: ‘<anonymous>’ declared here
83 | const K key = boost::python::extract<K>(keys[i]);
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::__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>]’,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:1176:20,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:617:20,
inlined from ‘boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)’ at /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:112:39:
/usr/include/c++/15/bits/basic_string.h:1165:19: warning: ‘* [too-long-redacted] ialized [-Wmaybe-uninitialized]
1165 | size_type __sz = _M_string_length;
| ^~~~
/<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc: In function ‘boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)’:
/<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:112:39: note: ‘<anonymous>’ declared here
112 | String seq = extract<String>(args[0]);
| ^
In member function ‘std::__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>]’,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:1176:20,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:617:20,
inlined from ‘boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)’ at /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:179:39:
/usr/include/c++/15/bits/basic_string.h:1165:19: warning: ‘* [too-long-redacted] ialized [-Wmaybe-uninitialized]
1165 | size_type __sz = _M_string_length;
| ^~~~
/<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc: In function ‘boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)’:
/<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:179:39: note: ‘<anonymous>’ declared here
179 | String seq = extract<String>(args[0]);
| ^
In member function ‘std::__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>]’,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:1176:20,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:617:20,
inlined from ‘boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)’ at /<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:47:39:
/usr/include/c++/15/bits/basic_string.h:1165:19: warning: ‘* [too-long-redacted] ialized [-Wmaybe-uninitialized]
1165 | size_type __sz = _M_string_length;
| ^~~~
/<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc: In function ‘boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)’:
/<<PKGBUILDDIR>>/modelling/pymod/export_monte_carlo.cc:47:39: note: ‘<anonymous>’ 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 ‘std::__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>]’,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:1176:20,
inlined from ‘std::__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>]’ at /usr/include/c++/15/bits/basic_string.h:617:20,
inlined from ‘void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]’ 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: ‘* [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 ‘void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map<K, V>&) [with K = std::__cxx11::basic_string<char>; V = float]’:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: ‘<anonymous>’ 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
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