ld: libMMB.so.4.0: undefined reference to `gzerror')

Debian Bug Tracking System Tue, 26 Nov 2024 23:42:21 -0800

Your message dated Wed, 27 Nov 2024 07:38:21 +0000
with message-id <e1tgccv-00a46x...@fasolo.debian.org>
and subject line Bug#1086362: fixed in macromoleculebuilder 4.0.0+dfsg-5
has caused the Debian Bug report #1086362,
regarding macromoleculebuilder: FTBFS: /usr/bin/ld: libMMB.so.4.0: undefined 
reference to `gzerror'
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1086362: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1086362
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

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.

--- End Message ---

--- Begin Message ---

Source: macromoleculebuilder
Source-Version: 4.0.0+dfsg-5
Done: Andrius Merkys <mer...@debian.org>

We believe that the bug you reported is fixed in the latest version of
macromoleculebuilder, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1086...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated macromoleculebuilder 
package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Wed, 27 Nov 2024 02:07:37 -0500
Source: macromoleculebuilder
Architecture: source
Version: 4.0.0+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1086362
Changes:
 macromoleculebuilder (4.0.0+dfsg-5) unstable; urgency=medium
 .
   * Link MMB_SHARED_TARGET with ZLIB_LIBRARIES via patch (Closes: #1086362)
Checksums-Sha1:
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macromoleculebuilder_4.0.0+dfsg-5.dsc
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macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz
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macromoleculebuilder_4.0.0+dfsg-5_source.buildinfo
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macromoleculebuilder_4.0.0+dfsg-5_source.buildinfo
Files:
 3da8c14c2f0e927fa423dc8728770cdf 2491 science optional 
macromoleculebuilder_4.0.0+dfsg-5.dsc
 69bbd609e8a36fbef46bcfbf9328d2c5 5964 science optional 
macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz
 b3281b5a4608819d97072941ecc19c91 11885 science optional 
macromoleculebuilder_4.0.0+dfsg-5_source.buildinfo

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--- End Message ---

Bug#1086362: marked as done (macromoleculebuilder: FTBFS: /usr/bin/ld: libMMB.so.4.0: undefined reference to `gzerror')

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