[Debichem-devel] Bug#1027828: macromoleculebuilder: FTBFS in bullseye (a2x: ERROR: "xsltproc" [...] returned non-zero exit status 5)
Santiago Vila
sanvila at debian.org
Tue Jan 3 20:35:12 GMT 2023
Package: src:macromoleculebuilder
Version: 3.2+dfsg-2
Severity: serious
Tags: ftbfs
Control: fixed -1 4.0.0+dfsg-2
Dear maintainer:
During a rebuild of all packages in bullseye, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary-indep
dh binary-indep
dh_update_autotools_config -i
dh_autoreconf -i
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf parameterization/build
dh_auto_configure -- \
-DOpenMM_INCLUDE_DIR=/usr/include \
-DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0"
cd obj-x86_64-linux-gnu && 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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DOpenMM_INCLUDE_DIR=/usr/include "-DCMAKE_CXX_FLAGS=-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0" ..
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -i
cd obj-x86_64-linux-gnu && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.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/MMBlib.dir/DependInfo.cmake --color=
Dependee "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/DependInfo.cmake" is newer than depender "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/depend.internal".
Dependee "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/depend.internal".
Scanning dependencies of target MMBlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 3%] Building CXX object CMakeFiles/MMBlib.dir/src/Utils.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Utils.cpp.o -c /<<PKGBUILDDIR>>/src/Utils.cpp
In file included from /<<PKGBUILDDIR>>/src/Utils.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/Utils.cpp: In function ‘int ValidateNonNegativeInt(int)’:
/<<PKGBUILDDIR>>/src/Utils.cpp:526:1: warning: control reaches end of non-void function [-Wreturn-type]
526 | }
| ^
[ 6%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o -c /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:18,
from /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:13:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘bool BiopolymerClass::setRenumberPdbResidues(bool)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1067:5: warning: no return statement in function returning non-void [-Wreturn-type]
1067 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘bool BiopolymerClassContainer::setRenumberPdbResidues(bool)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4725:1: warning: no return statement in function returning non-void [-Wreturn-type]
4725 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::validateBiopolymerType() const’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:356:1: warning: control reaches end of non-void function [-Wreturn-type]
356 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘SimTK::String BiopolymerClass::getBiopolymerTypeAsString()’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1062:1: warning: control reaches end of non-void function [-Wreturn-type]
1062 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::validateAtomPathName(SimTK::Compound::AtomPathName)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1133:1: warning: control reaches end of non-void function [-Wreturn-type]
1133 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘const SimTK::ResidueInfo::Index BiopolymerClass::getResidueIndex(ResidueID)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1529:1: warning: control reaches end of non-void function [-Wreturn-type]
1529 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘SimTK::String BiopolymerClass::getRepresentativeAtomName()’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1552:1: warning: control reaches end of non-void function [-Wreturn-type]
1552 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘double BiopolymerClass::getRepresentativeAtomMassThreshold()’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1569:1: warning: control reaches end of non-void function [-Wreturn-type]
1569 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClassContainer::initializeBiopolymer(SimTK::String, SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, double, std::vector<Displacement>, double, double, std::vector<SecondaryStructureStretch>)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2749:1: warning: control reaches end of non-void function [-Wreturn-type]
2749 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClassContainer::getBiopolymerClassIndex(SimTK::String)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2850:1: warning: control reaches end of non-void function [-Wreturn-type]
2850 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘BiopolymerClass& BiopolymerClassContainer::updBiopolymerClass(int)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2867:1: warning: control reaches end of non-void function [-Wreturn-type]
2867 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClassContainer::validateChainID(SimTK::String)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:3038:1: warning: control reaches end of non-void function [-Wreturn-type]
3038 | }
| ^
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘ResidueID BiopolymerClassContainer::residueID(std::map<const SimTK::String, double>, const char*, SimTK::String)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4174:1: warning: control reaches end of non-void function [-Wreturn-type]
4174 | }
| ^
[ 10%] Building CXX object CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o -c /<<PKGBUILDDIR>>/src/UnitCellParameters.cpp
/<<PKGBUILDDIR>>/src/UnitCellParameters.cpp: In member function ‘const double UnitCellParameters::angleInRange(double)’:
/<<PKGBUILDDIR>>/src/UnitCellParameters.cpp:165:2: warning: control reaches end of non-void function [-Wreturn-type]
165 | }
| ^
/<<PKGBUILDDIR>>/src/UnitCellParameters.cpp: In member function ‘const bool UnitCellParameters::exitIfNotValid() const’:
/<<PKGBUILDDIR>>/src/UnitCellParameters.cpp:270:1: warning: control reaches end of non-void function [-Wreturn-type]
270 | }
| ^
[ 13%] Building CXX object CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o -c /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 17%] Building CXX object CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o -c /<<PKGBUILDDIR>>/src/DisplacementContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:18,
from /<<PKGBUILDDIR>>/include/DisplacementContainer.h:14,
from /<<PKGBUILDDIR>>/src/DisplacementContainer.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/DisplacementContainer.cpp: In member function ‘Displacement& DisplacementContainer::updDisplacement(SimTK::String)’:
/<<PKGBUILDDIR>>/src/DisplacementContainer.cpp:41:1: warning: control reaches end of non-void function [-Wreturn-type]
41 | };
| ^
[ 20%] Building CXX object CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o -c /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 24%] Building CXX object CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o -c /<<PKGBUILDDIR>>/src/MoleculeContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/ConstraintContainer.h:14,
from /<<PKGBUILDDIR>>/include/MoleculeContainer.h:9,
from /<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:3:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp: In member function ‘SimTK::Compound CompoundObjectMapContainer::fetchCompound(SimTK::String)’:
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:73:1: warning: control reaches end of non-void function [-Wreturn-type]
73 | }
| ^
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp: In member function ‘SimTK::Biotype CompoundObjectMapContainer::fetchBiotype(SimTK::String)’:
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:92:1: warning: control reaches end of non-void function [-Wreturn-type]
92 | }
| ^
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp: In member function ‘const SimTK::Element CompoundObjectMapContainer::fetchElement(SimTK::String)’:
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:220:1: warning: control reaches end of non-void function [-Wreturn-type]
220 | }
| ^
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp: In member function ‘SimTK::Compound::SingleAtom CompoundObjectMapContainer::fetchSingleAtom(SimTK::String, SimTK::Compound::AtomName&, SimTK::String, SimTK::Angle)’:
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:244:1: warning: control reaches end of non-void function [-Wreturn-type]
244 | }
| ^
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp: In member function ‘bool MoleculeClassContainer::hasChainID(SimTK::String)’:
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:722:1: warning: control reaches end of non-void function [-Wreturn-type]
722 | }
| ^
[ 27%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o -c /<<PKGBUILDDIR>>/src/DensityContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:18,
from /<<PKGBUILDDIR>>/include/DensityContainer.h:14,
from /<<PKGBUILDDIR>>/src/DensityContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 31%] Building CXX object CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o -c /<<PKGBUILDDIR>>/src/BasePairContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:18,
from /<<PKGBUILDDIR>>/include/BasePairContainer.h:14,
from /<<PKGBUILDDIR>>/src/BasePairContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp: In member function ‘bool BasePairContainer::hasWatsonCrickCisPair(SimTK::String, ResidueID)’:
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp:184:1: warning: control reaches end of non-void function [-Wreturn-type]
184 | }
| ^
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp: In member function ‘const BaseInteraction BasePairContainer::getWatsonCrickCisPair(SimTK::String, ResidueID)’:
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp:206:1: warning: control reaches end of non-void function [-Wreturn-type]
206 | } // of method
| ^
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp: In member function ‘const ResidueID BasePairContainer::getWatsonCrickCisPairingResidue(SimTK::String, ResidueID)’:
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp:223:1: warning: control reaches end of non-void function [-Wreturn-type]
223 | }
| ^
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp: In member function ‘const SimTK::String BasePairContainer::getWatsonCrickCisPairingChain(SimTK::String, ResidueID)’:
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp:237:1: warning: control reaches end of non-void function [-Wreturn-type]
237 | }
| ^
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp: In member function ‘const ResidueID BasePairContainer::getLastWatsonCrickCisPairingResidueOfRun(SimTK::String, ResidueID, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp:289:1: warning: control reaches end of non-void function [-Wreturn-type]
289 | } // of getLastWatsonCrickCisPairingResidueOfRun
| ^
[ 34%] Building CXX object CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o -c /<<PKGBUILDDIR>>/src/ContactContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/ContactContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 37%] Building CXX object CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o -c /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/ConstraintContainer.h:14,
from /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:10:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 41%] Building CXX object CMakeFiles/MMBlib.dir/src/Repel.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Repel.cpp.o -c /<<PKGBUILDDIR>>/src/Repel.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/PeriodicScrubber.h:16,
from /<<PKGBUILDDIR>>/include/Repel.h:21,
from /<<PKGBUILDDIR>>/src/Repel.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)’:
/<<PKGBUILDDIR>>/src/Repel.cpp:127:49: note: ‘#pragma message: USE_OPENMM is defined’
127 | #pragma message ("USE_OPENMM is defined")
| ^
[ 44%] Building CXX object CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o -c /<<PKGBUILDDIR>>/src/MonoAtoms.cpp
In file included from /<<PKGBUILDDIR>>/src/MonoAtoms.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/MonoAtoms.cpp: In member function ‘const int MonoAtoms::getResidueIndex(ResidueID)’:
/<<PKGBUILDDIR>>/src/MonoAtoms.cpp:153:1: warning: control reaches end of non-void function [-Wreturn-type]
153 | }
| ^
/<<PKGBUILDDIR>>/src/MonoAtoms.cpp: In member function ‘MonoAtoms MonoAtomsContainer::getMonoAtoms(SimTK::String)’:
/<<PKGBUILDDIR>>/src/MonoAtoms.cpp:277:1: warning: control reaches end of non-void function [-Wreturn-type]
277 | }
| ^
[ 48%] Building CXX object CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o -c /<<PKGBUILDDIR>>/src/ParameterReader.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/src/ParameterReader.cpp:17:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 51%] Building CXX object CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o -c /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp
In file included from /<<PKGBUILDDIR>>/include/BaseInteractionParameterReader.h:22,
from /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp:16:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 55%] Building CXX object CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o -c /<<PKGBUILDDIR>>/src/TetherForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/TetherForce.h:20,
from /<<PKGBUILDDIR>>/src/TetherForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 58%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/BiopolymerClassTwoTransformForces.h:18,
from /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:10:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 62%] Building CXX object CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o -c /<<PKGBUILDDIR>>/src/WaterDroplet.cpp
In file included from /<<PKGBUILDDIR>>/include/WaterDroplet.h:16,
from /<<PKGBUILDDIR>>/src/WaterDroplet.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/WaterDroplet.cpp: In member function ‘WaterDroplet WaterDropletContainer::getWaterDroplet(std::string)’:
/<<PKGBUILDDIR>>/src/WaterDroplet.cpp:108:1: warning: control reaches end of non-void function [-Wreturn-type]
108 | }
| ^
/<<PKGBUILDDIR>>/src/WaterDroplet.cpp: In member function ‘WaterDroplet& WaterDropletContainer::updWaterDroplet(std::string)’:
/<<PKGBUILDDIR>>/src/WaterDroplet.cpp:120:1: warning: control reaches end of non-void function [-Wreturn-type]
120 | }
| ^
[ 65%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o -c /<<PKGBUILDDIR>>/src/DensityMap.cpp
In file included from /<<PKGBUILDDIR>>/src/DensityMap.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘GridPoint& DensityMap::updGridPoint(GridIndices)’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:127:5: warning: control reaches end of non-void function [-Wreturn-type]
127 | }
| ^
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘SimTK::Vec3 DensityMap::calcInterpolatedFirstQuadrantGradient(GridPoint&, SimTK::Vec3) const’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:1448:1: warning: control reaches end of non-void function [-Wreturn-type]
1448 | }
| ^
[ 68%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o -c /<<PKGBUILDDIR>>/src/DensityForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/DensityForce.h:20,
from /<<PKGBUILDDIR>>/src/DensityForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 72%] Building CXX object CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /<<PKGBUILDDIR>>/src/ElectrostaticPotentialGridForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/ElectrostaticPotentialGridForce.h:20,
from /<<PKGBUILDDIR>>/src/ElectrostaticPotentialGridForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 75%] Building CXX object CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o -c /<<PKGBUILDDIR>>/src/ErrorManager.cpp
/<<PKGBUILDDIR>>/src/ErrorManager.cpp: In member function ‘ErrorManager& ErrorManager::operator=(const ErrorManager&)’:
/<<PKGBUILDDIR>>/src/ErrorManager.cpp:25:1: warning: no return statement in function returning non-void [-Wreturn-type]
24 | _buffer << em._buffer.rdbuf();
+++ |+ return *this;
25 | }
| ^
[ 79%] Building CXX object CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/PeriodicPdbAndEnergyWriter.h:13,
from /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:15:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 82%] Building CXX object CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o -c /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:18,
from /<<PKGBUILDDIR>>/include/NtC_Class_Container.h:14,
from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:16:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 86%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o -c /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:18,
from /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 89%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o
/usr/bin/c++ -DMMBlib_EXPORTS -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o -c /<<PKGBUILDDIR>>/src/NtCForces.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
from /<<PKGBUILDDIR>>/include/NtCForces.h:19,
from /<<PKGBUILDDIR>>/src/NtCForces.cpp:10:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[ 93%] Linking CXX shared library libMMBlib.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMBlib.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -Wl,-z,relro -shared -Wl,-soname,libMMBlib.so.3.2 -o libMMBlib.so.3.2 CMakeFiles/MMBlib.dir/src/Utils.cpp.o CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMBlib.dir/src/Repel.cpp.o CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o -L/usr/lib/x86_64-linux-gnu64 -L/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu64:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: -lSimTKmolmodel /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.6 -lOpenMM -llapack -lblas -ldl -lrt -lblas -llapack -lblas -llapack -lpthread -ldl -lrt -lm
/usr/bin/cmake -E cmake_symlink_library libMMBlib.so.3.2 libMMBlib.so.3.2 libMMBlib.so
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[ 93%] Built target MMBlib
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Scanning dependencies of target MMB
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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[ 96%] Building CXX object CMakeFiles/MMB.dir/src/RNABuilder.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -o CMakeFiles/MMB.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:15:
/<<PKGBUILDDIR>>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’
33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined")
| ^
[100%] Linking CXX executable MMB
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB.dir/link.txt --verbose=1
/usr/bin/c++ -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -Wl,-z,relro -rdynamic CMakeFiles/MMB.dir/src/RNABuilder.cpp.o -o MMB -L/usr/lib/x86_64-linux-gnu64 -L/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu64:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libMMBlib.so.3.2 -lSimTKmolmodel /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.6 -lOpenMM -llapack -lblas -ldl -lrt -lblas -llapack -lblas -llapack -lpthread -lm -ldl -lrt
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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dh_prep -i
dh_auto_install -i
cd obj-x86_64-linux-gnu && make -j1 install DESTDIR=/<<BUILDDIR>>/macromoleculebuilder-3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.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/MMBlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Nothing to be done for 'CMakeFiles/MMBlib.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 93%] Built target MMBlib
make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.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.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Nothing to be done for 'CMakeFiles/MMB.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[100%] Built target MMB
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/libMMBlib.so.3.2
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/tmp/usr/lib/libMMBlib.so.3.2" to ""
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/libMMBlib.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/MMB
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/tmp/usr/bin/MMB" to ""
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/MMB/parameters.csv
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/extract_FASTA.bak.awk
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/extract_FASTA.awk
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/parse-restraints.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/b-factor-per-residue.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/renumber-loop.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/add-chain-IDs.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/add-precision.awk
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/format-for-pdb.awk
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/renumber.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.disulphide-bonded-cysteines.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1mlb.AB.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/TetR.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.RNA-homology-modeling.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.RBP-fitting.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1ARJ.short.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.TAR.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1UAO-disre-simple.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.DNA-helix.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/.commands.GNRA-NtC.dat.swp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.singlebasepair.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1UAO.atoms-renamed.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.protein-homology-modeling.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.NMR.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/6TNA.short.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1WDN.short.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.antibody-antigen.flexible-interfaces.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1BA2.aligned.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.A_N.32.N.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1dpx.C.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.TetR_threading_TUT.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.GlnBP-thermal-exploration.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/parameters.csv
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/protein-template.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/5MRC.GNRA.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1GID.shifted.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1FC2.C-to-A.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1UAO.short.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.GNRA-NtC.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/tRNA.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.tRNA-fitting.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.template_docking.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.TetRB.scanning.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.long-chain-ID.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/TetRB.scanning.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/antibody-antigen.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.protein-morphing.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1mlc.DEF.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1GGG.short.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.A_N.32.G.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.hairpin-short.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.benzene.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/commands.template-docking.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/2AVY.A.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/examples/1FC2.pdb
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
dh_install -plibmmblib3.2 debian/tmp/usr/lib/libMMBlib.so.* usr/lib/x86_64-linux-gnu
dh_install: warning: All requested packages have been excluded (e.g. via a Build-Profile or due to architecture restrictions).
dh_install -plibmmblib-dev debian/tmp/usr/lib/libMMBlib.so usr/lib/x86_64-linux-gnu
dh_install: warning: All requested packages have been excluded (e.g. via a Build-Profile or due to architecture restrictions).
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -i
dh_installchangelogs -i
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc
a2x: ERROR: "xsltproc" --stringparam callout.graphics 0 --stringparam navig.graphics 0 --stringparam admon.textlabel 1 --stringparam admon.graphics 0 "/etc/asciidoc/docbook-xsl/manpage.xsl" "/<<PKGBUILDDIR>>/debian/tmp/MMB.1.xml" returned non-zero exit status 5
make[1]: *** [debian/rules:23: override_dh_installman] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary-indep] Error 2
dpkg-buildpackage: error: debian/rules binary-indep subprocess returned exit status 2
--------------------------------------------------------------------------------
(The above is just how the build ends and not necessarily the most relevant part)
About the archive rebuild: The build was made using virtual machines
from Hetzner, with enough memory, enough disk, and either one or two
CPUs, using a reduced chroot with only build-essential packages (plus
debhelper).
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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