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 âvoid ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]â: /<<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: âintâ and âstd::vector<DensityStretch, std::allocator<DensityStretch> >::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 61 | for (int i = 0 ; i <residueStretchVector.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of âvoid ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]â: /<<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: âintâ and âstd::vector<DensityStretch, std::allocator<DensityStretch> >::size_typeâ {aka âlong unsigned intâ} [-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 âvirtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this âifâ 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 âifâ 284 | return 0; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h: In member function âconst SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: âstd::__cxx11::basic_string<char>::size_typeâ {aka âlong unsigned intâ} and âintâ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function âvoid BiopolymerClass::printAtomInfoVector()â: /<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<MMBAtomInfo>::size_typeâ {aka âlong unsigned intâ} [-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 âbool ThreadingStruct::hasResidue(ResidueID, int)â: /<<PKGBUILDDIR>>/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ResidueID>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/Threading.h: In member function âvoid ThreadingStruct::supplementIncludedResidues(int, int)â: /<<PKGBUILDDIR>>/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ResidueID>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function âvoid AtomSpringContainer::printAllAlignmentStats()â: /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ThreadingStruct>::size_typeâ {aka âlong unsigned intâ} [-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 âvoid ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]â: /<<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: âintâ and âstd::vector<DensityStretch, std::allocator<DensityStretch> >::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 61 | for (int i = 0 ; i <residueStretchVector.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of âvoid ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]â: /<<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: âintâ and âstd::vector<DensityStretch, std::allocator<DensityStretch> >::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/Utils.h: At global scope: /<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: â{anonymous}::digitsâ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: â{anonymous}::spacesâ 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: â{anonymous}::digitsâ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: â{anonymous}::spacesâ 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 âvirtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this âifâ 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 âifâ 284 | return 0; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h: In member function âconst SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: âstd::__cxx11::basic_string<char>::size_typeâ {aka âlong unsigned intâ} and âintâ [-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 âvoid BiopolymerClass::printAtomInfoVector()â: /<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<MMBAtomInfo>::size_typeâ {aka âlong unsigned intâ} [-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: â{anonymous}::digitsâ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: â{anonymous}::spacesâ 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 âvirtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this âifâ 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 âifâ 284 | return 0; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h: In member function âconst SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: âstd::__cxx11::basic_string<char>::size_typeâ {aka âlong unsigned intâ} and âintâ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function âvoid BiopolymerClass::printAtomInfoVector()â: /<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<MMBAtomInfo>::size_typeâ {aka âlong unsigned intâ} [-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: â{anonymous}::digitsâ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: â{anonymous}::spacesâ 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 âvirtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this âifâ 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 âifâ 284 | return 0; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h: In member function âconst SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: âstd::__cxx11::basic_string<char>::size_typeâ {aka âlong unsigned intâ} and âintâ [-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 âvoid BiopolymerClass::printAtomInfoVector()â: /<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<MMBAtomInfo>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/Threading.h: In member function âbool ThreadingStruct::hasResidue(ResidueID, int)â: /<<PKGBUILDDIR>>/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ResidueID>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/Threading.h: In member function âvoid ThreadingStruct::supplementIncludedResidues(int, int)â: /<<PKGBUILDDIR>>/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ResidueID>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function âvoid AtomSpringContainer::printAllAlignmentStats()â: /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ThreadingStruct>::size_typeâ {aka âlong unsigned intâ} [-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 âvoid ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]â: /<<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: âintâ and âstd::vector<DensityStretch, std::allocator<DensityStretch> >::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 61 | for (int i = 0 ; i <residueStretchVector.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of âvoid ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]â: /<<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: âintâ and âstd::vector<DensityStretch, std::allocator<DensityStretch> >::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/Utils.h: At global scope: /<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: â{anonymous}::digitsâ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: â{anonymous}::spacesâ 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' [ 93%] Built target MMB 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=" make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/build 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 âvirtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:282:10: warning: this âifâ 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 âifâ 284 | return 0; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h: In member function âconst SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) constâ: /<<PKGBUILDDIR>>/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: âstd::__cxx11::basic_string<char>::size_typeâ {aka âlong unsigned intâ} and âintâ [-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 âvoid BiopolymerClass::printAtomInfoVector()â: /<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<MMBAtomInfo>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/Threading.h: In member function âbool ThreadingStruct::hasResidue(ResidueID, int)â: /<<PKGBUILDDIR>>/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ResidueID>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/Threading.h: In member function âvoid ThreadingStruct::supplementIncludedResidues(int, int)â: /<<PKGBUILDDIR>>/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ResidueID>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function âvoid AtomSpringContainer::printAllAlignmentStats()â: /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ThreadingStruct>::size_typeâ {aka âlong unsigned intâ} [-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 âvoid ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]â: /<<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: âintâ and âstd::vector<DensityStretch, std::allocator<DensityStretch> >::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 61 | for (int i = 0 ; i <residueStretchVector.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of âvoid ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]â: /<<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: âintâ and âstd::vector<DensityStretch, std::allocator<DensityStretch> >::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/include/Utils.h: At global scope: /<<PKGBUILDDIR>>/include/Utils.h:262:17: warning: â{anonymous}::digitsâ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /<<PKGBUILDDIR>>/include/Utils.h:261:17: warning: â{anonymous}::spacesâ 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 --------------------------------------------------------------------------------
