[Debichem-devel] Bug#1124176: macromoleculebuilder: FTBFS: /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1: undefined reference to `gemmi::populate_structure_from_block(gemmi::cif::Block const&, gemmi::Structure&)'
Santiago Vila
sanvila at debian.org
Sun Dec 28 18:26:01 GMT 2025
Package: src:macromoleculebuilder
Version: 4.2+dfsg-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/202512/
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:macromoleculebuilder, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
-DCMAKE_BUILD_TYPE=Release \
-DENABLE_LEPTON=OFF \
-DGEMMI_DIR=/usr \
-DOpenMM_INCLUDE_DIR=/usr/include \
-DSimTKmolmodel=/usr \
[... snipped ...]
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59: required from here
22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59: required from here
25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
| ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
from /<<PKGBUILDDIR>>/include/CifOutput.h:5,
from /<<PKGBUILDDIR>>/src/CifOutput.cpp:1:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
282 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
284 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
378 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/PeriodicPdbAndEnergyWriter.h:13,
from /<<PKGBUILDDIR>>/include/CifOutput.h:12:
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59: required from here
22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59: required from here
25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
| ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
262 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
261 | const char* spaces = " \t";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
262 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
261 | const char* spaces = " \t";
| ^~~~~~
[ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -MF CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -c /<<PKGBUILDDIR>>/src/ProgressWriter.cpp
[ 84%] Building CXX object CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -MF CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o.d -o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -c /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp
In file included from /<<PKGBUILDDIR>>/include/NtC_Class_Container.h:14,
from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:16:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
282 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
284 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
378 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/NTC_FORCE_CLASS.h:4,
from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:17:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
[ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -MF CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -c /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
262 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
261 | const char* spaces = " \t";
| ^~~~~~
[ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCForces.cpp.o -MF CMakeFiles/MMB.dir/src/NtCForces.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCForces.cpp.o -c /<<PKGBUILDDIR>>/src/NtCForces.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
from /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp:13:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
282 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
284 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
378 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
262 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
261 | const char* spaces = " \t";
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/NtCForces.h:13,
from /<<PKGBUILDDIR>>/src/NtCForces.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
282 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
284 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
378 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59: required from here
22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59: required from here
25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
| ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
262 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
261 | const char* spaces = " \t";
| ^~~~~~
[ 93%] Linking CXX shared library libMMB.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -ffile-p [too-long-redacted] pack.so -lpthread -lrt -ldl -lm
/usr/bin/cmake -E cmake_symlink_library libMMB.so.4.1 libMMB.so.4.1 libMMB.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.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>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/MMB_EXEC.dir/DependInfo.cmake "--color="
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 96%] Building CXX object CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -MD -MT CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -MF CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o.d -o CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -c /<<PKGBUILDDIR>>/src/RNABuilder.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/src/RNABuilder.cpp:22:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
282 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
284 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
378 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59: required from here
22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59: required from here
25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
| ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
262 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
261 | const char* spaces = " \t";
| ^~~~~~
[100%] Linking CXX executable MMB
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB_EXEC.dir/link.txt --verbose=1
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1: undefined reference to `gemmi::populate_structure_from_block(gemmi::cif::Block const&, gemmi::Structure&)'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1: undefined reference to `gemmi::populate_structure_from_pdb_stream(gemmi::AnyStream&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, gemmi::Structure&, gemmi::PdbReadOptions)'
collect2: error: ld returned 1 exit status
/usr/bin/c++ -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro -fcf-protection -Wl,--dependency-file=CMakeFiles/MMB_EXEC.dir/link.d CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -o MMB -L/<<PKGBUILDDIR>>/SYSTEM -Wl,-rpath,/<<PKGBUILDDIR>>/SYSTEM:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libMMB.so.4.1 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm
make[3]: *** [CMakeFiles/MMB_EXEC.dir/build.make:114: MMB] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:125: CMakeFiles/MMB_EXEC.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:9: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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