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### Running command:
###
###   rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=fmcsR.buildbin-libdir fmcsR_1.37.0.tar.gz
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* installing *source* package 'fmcsR' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c MCS.cpp -o MCS.o
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:108:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
                 for (int i = 0; i < atomCountOne; ++i) {
                                 ~~^~~~~~~~~~~~~~
MCS.cpp:116:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
                 for (int i = 0; i < atomCountTwo; ++i) {
                                 ~~^~~~~~~~~~~~~~
In file included from MCSCompound.h:15,
                 from MCS.h:12,
                 from MCS.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCS.cpp:381:69:   required from here
MCSList.h:143:27: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                         ~~^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:5:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
                 for (int i = 0; i < this->vertexPath.size(); ++i) {
                                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
                 if (vertexIndex < vertexPath.size()-1) {
                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
MCSCompound.cpp: In copy constructor 'FMCS::MCSCompound::MCSCompound(const FMCS::MCSCompound&)':
MCSCompound.cpp:87:74: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct FMCS::MCSCompound::Atom' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
                 memcpy(atoms, other.atoms, sizeof(Atom) * other.atomCount);
                                                                          ^
In file included from MCSCompound.cpp:4:
MCSCompound.h:26:16: note: 'struct FMCS::MCSCompound::Atom' declared here
         struct Atom {
                ^~~~
MCSCompound.cpp: In member function 'const FMCS::MCSCompound& FMCS::MCSCompound::operator=(const FMCS::MCSCompound&)':
MCSCompound.cpp:123:68: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct FMCS::MCSCompound::Atom' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
             memcpy(atoms, that.atoms, sizeof(Atom) * that.atomCount);
                                                                    ^
In file included from MCSCompound.cpp:4:
MCSCompound.h:26:16: note: 'struct FMCS::MCSCompound::Atom' declared here
         struct Atom {
                ^~~~
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)':
MCSCompound.cpp:157:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
         for (int i = 0; i < bondCount; ++i) {
                         ~~^~~~~~~~~~~
MCSCompound.cpp: In member function 'std::__cxx11::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const':
MCSCompound.cpp:194:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
         for (int i = 0; i < indexLength; ++i) {
                         ~~^~~~~~~~~~~~~
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467:26: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
         for(int i = 0; i < bondCount; ++i) {
                        ~~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c MCSMap.cpp -o MCSMap.o
In file included from MCSMap.h:8,
                 from MCSMap.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCSMap.cpp:28:36:   required from here
MCSList.h:143:27: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                         ~~^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.cpp:13:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
                 for (int i = 0; i < this->vertexPath.size(); ++i) {
                                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
                 if (vertexIndex < vertexPath.size()-1) {
                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for (int i = 0; i < vertexQueue.size(); ++i) {
                         ~~^~~~~~~~~~~~~~~~~~~~
MCSRingDetector.cpp:94:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
             for (int j = 0; j < queueSize-1-i; ++j ) {
                             ~~^~~~~~~~~~~~~~~
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
             for (int j = 0; j < degree; ++j) {
                             ~~^~~~~~~~
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
         int aromaticCount = 0;
             ^~~~~~~~~~~~~
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         if (level > vertexPath.size()) {
             ~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
fmcs_R_wrap.cpp: In function 'void fmcs_R_wrap(const char**, const char**, int*, int*, int*, int*, int*, int*, int*, const char**, const char**, const char**, const char**, const char**)':
fmcs_R_wrap.cpp:74:45: warning: 'runningMode' may be used uninitialized in this function [-Wmaybe-uninitialized]
             matchType, runningMode, *timeout);
                                             ^
fmcs_R_wrap.cpp:74:45: warning: 'matchType' may be used uninitialized in this function [-Wmaybe-uninitialized]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c util.cpp -o util.o
util.cpp: In function 'std::__cxx11::string getUpper(const string&)':
util.cpp:11:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (int i = 0; i < upper.length(); ++i) {
                     ~~^~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/fmcsR.buildbin-libdir/00LOCK-fmcsR/00new/fmcsR/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'fmcsR'
    finding HTML links ... done
    MCS-class                               html  
    fmcs                                    html  
    fmcsBatch                               html  
    fmcsR-package                           html  
    fmcstest                                html  
    mcs2sdfset                              html  
    plotMCS                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'fmcsR' as fmcsR_1.37.0.zip
* DONE (fmcsR)