Package: src:macromoleculebuilder
Version: 4.0.0+dfsg-4
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
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 \
-DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection
-Wformat -Werror=format-security -fcf-protection -O0"
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake
-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var
-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON
"-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu
-DCMAKE_BUILD_TYPE=Release -DENABLE_LEPTON=OFF -DGEMMI_DIR=/usr -DOpenMM_INCLUDE_DIR=/usr/include -DSimTKmolmodel=/usr
"-DCMAKE_CXX_FLAGS=-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0" ..
[... snipped ...]
78 | for (int i = 0; i <
threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
|
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void
AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’
{aka ‘long unsigned int’} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i <
threadingStructVector.size();
i++){threadingStructVector[i].printAlignmentStats();}}
|
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp: In member function ‘virtual void
SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const’:
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:201:30: warning: comparison of
integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long
unsigned int’} and ‘int’ [-Wsign-compare]
201 | if(myEnergies.size() > myParameterReader.convergenceTimeout) {
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused
variable ‘lastEnergy’ [-Wunused-variable]
202 | double lastEnergy = myEnergies.back();
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused
variable ‘compoundNumber’ [-Wunused-variable]
49 | int compoundNumber = 1;
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused
variable ‘requiredPrecision’ [-Wunused-variable]
50 | int requiredPrecision = 12;
| ^~~~~~~~~~~~~~~~~
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:257:17: warning: ‘{anonymous}::digits’ defined
but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined
but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
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:290:10: warning: this ‘if’ clause does not
guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the
latter is misleadingly indented as if it were guarded by the ‘if’
292 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’
[-Wunused-variable]
321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
| ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String
ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions
of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned
int’} and ‘int’ [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning: when initialized here
[-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String
myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index,
SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning: when initialized here
[-Wreorder]
1314 | MMBAtomInfo(String myChain, ResidueID myResidueID,
ResidueInfo::Index myResidueIndex, String myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void
InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
1379 | for (int i = 0; i < myChains.size(); i++)
{myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth;
myInterface.MobilizerString = myMobilizerString;
interfaceVector.push_back(myInterface); };
| ~~^~~~~~~~~~~~~~~~~
/<<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:71:31: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka
‘long unsigned int’} [-Wsign-compare]
71 | 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:78:31: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka
‘long unsigned int’} [-Wsign-compare]
78 | for (int i = 0; i <
threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
|
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void
AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’
{aka ‘long unsigned int’} [-Wsign-compare]
73 | 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())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined
but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined
but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
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:290:10: warning: this ‘if’ clause does not
guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the
latter is misleadingly indented as if it were guarded by the ‘if’
292 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’
[-Wunused-variable]
321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
| ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String
ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions
of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned
int’} and ‘int’ [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning: when initialized here
[-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String
myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index,
SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning: when initialized here
[-Wreorder]
1314 | MMBAtomInfo(String myChain, ResidueID myResidueID,
ResidueInfo::Index myResidueIndex, String myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void
InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
1379 | for (int i = 0; i < myChains.size(); i++)
{myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth;
myInterface.MobilizerString = myMobilizerString;
interfaceVector.push_back(myInterface); };
| ~~^~~~~~~~~~~~~~~~~
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:257:17: warning: ‘{anonymous}::digits’ defined
but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined
but not used [-Wunused-variable]
256 | 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:290:10: warning: this ‘if’ clause does not
guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the
latter is misleadingly indented as if it were guarded by the ‘if’
292 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’
[-Wunused-variable]
321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
| ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String
ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions
of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned
int’} and ‘int’ [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning: when initialized here
[-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String
myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index,
SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning: when initialized here
[-Wreorder]
1314 | MMBAtomInfo(String myChain, ResidueID myResidueID,
ResidueInfo::Index myResidueIndex, String myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void
InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
1379 | for (int i = 0; i < myChains.size(); i++)
{myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth;
myInterface.MobilizerString = myMobilizerString;
interfaceVector.push_back(myInterface); };
| ~~^~~~~~~~~~~~~~~~~
/<<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: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:290:10: warning: this ‘if’ clause does not
guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the
latter is misleadingly indented as if it were guarded by the ‘if’
292 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’
[-Wunused-variable]
321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
| ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String
ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions
of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned
int’} and ‘int’ [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning: when initialized here
[-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String
myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index,
SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning: when initialized here
[-Wreorder]
1314 | MMBAtomInfo(String myChain, ResidueID myResidueID,
ResidueInfo::Index myResidueIndex, String myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void
InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
1379 | for (int i = 0; i < myChains.size(); i++)
{myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth;
myInterface.MobilizerString = myMobilizerString;
interfaceVector.push_back(myInterface); };
| ~~^~~~~~~~~~~~~~~~~
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:71:31: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka
‘long unsigned int’} [-Wsign-compare]
71 | 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:78:31: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka
‘long unsigned int’} [-Wsign-compare]
78 | for (int i = 0; i <
threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
|
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void
AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’
{aka ‘long unsigned int’} [-Wsign-compare]
73 | 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:257:17: warning: ‘{anonymous}::digits’ defined
but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined
but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined
but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined
but not used [-Wunused-variable]
256 | 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-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 -shared -Wl,-soname,libMMB.so.4.0 -o libMMB.so.4.0
CMakeFiles/MMB.dir/src/Utils.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o
CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o
CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o
CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o
CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o
CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMB.dir/src/Repel.cpp.o
CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o CMakeFiles/MMB.dir/src/Spiral.cpp.o
CMakeFiles/MMB.dir/src/ParameterReader.cpp.o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o
CMakeFiles/MMB.dir/src/TetherForce.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o
CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o CMakeFiles/MMB.dir/src/DensityMap.cpp.o
CMakeFiles/MMB.dir/src/DensityForce.cpp.o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o
CMakeFiles/MMB.dir/src/MMBLogger.cpp.o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o
CMakeFiles/MMB.dir/src/CifOutput.cpp.o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o
CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o
CMakeFiles/MMB.dir/src/NtCForces.cpp.o -L/<<PKGBUILDDIR>>/SYSTEM
-Wl,-rpath,/<<PKGBUILDDIR>>/SYSTEM: /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1
/usr/lib/x86_64-linux-gnu/libOpenMM.so /usr/lib/x86_64-linux-gnu/libz.so -lgemmi_cpp
/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
/usr/bin/cmake -E cmake_symlink_library libMMB.so.4.0 libMMB.so.4.0 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 ‘virtual SimTK::Real
ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not
guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the
latter is misleadingly indented as if it were guarded by the ‘if’
292 | return 0;
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’
[-Wunused-variable]
321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
| ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String
ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions
of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned
int’} and ‘int’ [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning: when initialized here
[-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String
myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor
‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index,
SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be
initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning: ‘ResidueID
MMBAtomInfo::residueID’ [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning: when initialized here
[-Wreorder]
1314 | MMBAtomInfo(String myChain, ResidueID myResidueID,
ResidueInfo::Index myResidueIndex, String myAtomName) :
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void
InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions
of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long
unsigned int’} [-Wsign-compare]
1379 | for (int i = 0; i < myChains.size(); i++)
{myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth;
myInterface.MobilizerString = myMobilizerString;
interfaceVector.push_back(myInterface); };
| ~~^~~~~~~~~~~~~~~~~
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:71:31: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka
‘long unsigned int’} [-Wsign-compare]
71 | 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:78:31: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka
‘long unsigned int’} [-Wsign-compare]
78 | for (int i = 0; i <
threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
|
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void
AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer
expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’
{aka ‘long unsigned int’} [-Wsign-compare]
73 | 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:257:17: warning: ‘{anonymous}::digits’ defined
but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined
but not used [-Wunused-variable]
256 | 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/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 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.4.0
/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
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzerror'
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzgetc'
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzgets'
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzopen'
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzread'
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzungetc'
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzclose_r'
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzbuffer'
/usr/bin/ld: libMMB.so.4.0: undefined reference to `gzeof'
collect2: error: ld returned 1 exit status
make[3]: *** [CMakeFiles/MMB_EXEC.dir/build.make:109: MMB] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:114: 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 returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202410/
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 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.
