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BUILD BIN report for Rchemcpp on tokay2

This page was generated on 2019-10-16 12:28:19 -0400 (Wed, 16 Oct 2019).

Package 1327/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rchemcpp 2.22.0
Guenter Klambauer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Rchemcpp
Branch: RELEASE_3_9
Last Commit: 9273b46
Last Changed Date: 2019-05-02 11:53:44 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  ERROR  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rchemcpp
Version: 2.22.0
Command: rm -rf Rchemcpp.buildbin-libdir && mkdir Rchemcpp.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rchemcpp.buildbin-libdir Rchemcpp_2.22.0.tar.gz
StartedAt: 2019-10-16 10:01:30 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 10:03:46 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 136.8 seconds
RetCode: 0
Status:  OK  
PackageFile: Rchemcpp_2.22.0.zip
PackageFileSize: 2.479 MiB

Command output

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###
### Running command:
###
###   rm -rf Rchemcpp.buildbin-libdir && mkdir Rchemcpp.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rchemcpp.buildbin-libdir Rchemcpp_2.22.0.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'Rchemcpp' ...
** using staged installation
** libs
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAjUdvf/R.INSTALL10d8591d146b/Rchemcpp/src/chemcpp/src'
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o constant.o constant.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o node.o node.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o atom.o atom.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o bond.o bond.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o cerror.o cerror.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o chemcpp.o chemcpp.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o datacontainer.o datacontainer.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o descriptor.o descriptor.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o elements.o elements.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o jlpioutils.o jlpioutils.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o kcfmolecule.o kcfmolecule.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o molecule.o molecule.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o moleculeset.o moleculeset.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o moleculeutils.o moleculeutils.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o ring.o ring.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=generic -w -fPIC -I../src/   -c -o stringutils.o stringutils.cpp
C:/Rtools/mingw_32/bin/g++  -shared -o ../../libchemcpp.dll -O2 -Wall  -mtune=generic -w -fPIC -I../src/ constant.o node.o atom.o bond.o cerror.o chemcpp.o datacontainer.o descriptor.o elements.o jlpioutils.o kcfmolecule.o molecule.o moleculeset.o moleculeutils.o ring.o stringutils.o
C:/Rtools/mingw_32/bin/g++  -shared -o ../../libchemcpp.so -O2 -Wall  -mtune=generic -w -fPIC -I../src/ constant.o node.o atom.o bond.o cerror.o chemcpp.o datacontainer.o descriptor.o elements.o jlpioutils.o kcfmolecule.o molecule.o moleculeset.o moleculeutils.o ring.o stringutils.o
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpAjUdvf/R.INSTALL10d8591d146b/Rchemcpp/src/chemcpp/src'
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Relements.cpp -o Relements.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Rmolecule.cpp -o Rmolecule.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Rmoleculeset.cpp -o Rmoleculeset.o
In file included from Rmoleculeset.cpp:2:0:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from spectrum3Dhelper.h:38:0,
                 from spectrum3Dhelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
spectrum3Dhelper.cpp: In function 'void gramSpectrum3D_self(SEXP, int, int, int, double, double, bool)':
spectrum3Dhelper.cpp:74:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrum3Dhelper.cpp: In function 'void gramSpectrum3D_test(SEXP, int, int, int, double, double, bool)':
spectrum3Dhelper.cpp:174:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrum3Dhelper.cpp: In function 'void gramComputeSpectrum3D_self(MoleculeSet*, int, int, int, std::vector*, std::vector >*, std::vector*, bool)':
spectrum3Dhelper.cpp:225:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrum3Dhelper.cpp:241:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrum3Dhelper.cpp:242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrum3Dhelper.cpp: In function 'void gramComputeSpectrum3D_test(MoleculeSet*, MoleculeSet*, int, int, int, std::vector*, std::vector*, std::vector >*, std::vector*, bool)':
spectrum3Dhelper.cpp:279:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrum3Dhelper.cpp:295:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrum3Dhelper.cpp:296:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrum3Dhelper.cpp: In function 'void updatePaths3D(MoleculeSet*, std::string, int, std::vector*, std::vector*, int, int)':
spectrum3Dhelper.cpp:384:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:388:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                       ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_self(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:445:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:446:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = i ; j < molPaths->size() ; j++){
                       ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int)':
spectrum3Dhelper.cpp:488:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:489:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < molPaths_test->size() ; j++){
                         ^
spectrum3Dhelper.cpp: In function 'void updateSelfKernel3D(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:530:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i = 0 ; i < molPaths->size() ; i++){
                    ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_self(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:472:75: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);   
                                                                           ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int)':
spectrum3Dhelper.cpp:513:80: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
                                                                                ^
spectrum3Dhelper.cpp: In function 'void updateSelfKernel3D(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:557:34: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
     aMol->addToSelfKernel(update);
                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spectrumhelper.cpp -o spectrumhelper.o
In file included from spectrumhelper.h:38:0,
                 from spectrumhelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
spectrumhelper.cpp: In function 'void gramSpectrum_self(SEXP, int, int, double, bool, bool)':
spectrumhelper.cpp:72:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrumhelper.cpp:75:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < bondTypes.size() ; i++ ){
                          ^
spectrumhelper.cpp: In function 'void gramSpectrum_test(SEXP, int, int, double, bool, bool)':
spectrumhelper.cpp:130:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrumhelper.cpp:133:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < bondTypes.size() ; i++ ){
                          ^
spectrumhelper.cpp: In function 'void gramComputeSpectrum_self(MoleculeSet*, int, int, int, double, std::vector*, std::vector >*, std::vector*, bool, bool)':
spectrumhelper.cpp:161:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrumhelper.cpp:188:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrumhelper.cpp:189:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrumhelper.cpp: In function 'void gramComputeSpectrum_test(MoleculeSet*, MoleculeSet*, int, int, int, double, std::vector*, std::vector*, std::vector >*, std::vector*, bool, bool)':
spectrumhelper.cpp:229:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrumhelper.cpp:258:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrumhelper.cpp:259:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrumhelper.cpp: In function 'void updatePaths(MoleculeSet*, std::string, int, std::vector*, std::vector*, int, int)':
spectrumhelper.cpp:368:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:372:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                       ^
spectrumhelper.cpp: In function 'void updateGram_self(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:453:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:455:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                         ^
spectrumhelper.cpp:467:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:468:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = i ; j < molPaths->size() ; j++){
                       ^
spectrumhelper.cpp: In function 'void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int, double, int)':
spectrumhelper.cpp:518:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:520:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths)[i].path_pointers.size() ; k++){
                         ^
spectrumhelper.cpp:528:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths_test->size() ; i++){
                       ^
spectrumhelper.cpp:530:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths_test)[i].path_pointers.size() ; k++){
                         ^
spectrumhelper.cpp:543:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:544:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < molPaths_test->size() ; j++){
                         ^
spectrumhelper.cpp: In function 'void updateSelfKernel(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:592:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:594:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                         ^
spectrumhelper.cpp:606:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i = 0 ; i < molPaths->size() ; i++){
                    ^
spectrumhelper.cpp:630:34: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
     aMol->addToSelfKernel(update);
                                  ^
spectrumhelper.cpp: In function 'void updateGram_self(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:499:75: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);   
                                                                           ^
spectrumhelper.cpp: In function 'void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int, double, int)':
spectrumhelper.cpp:570:80: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
                                                                                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subtreehelper.cpp -o subtreehelper.o
In file included from subtreehelper.h:37:0,
                 from subtreehelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
subtreehelper.cpp: In function 'void gramSubtree_self(SEXP, double, int, bool, bool, bool, bool)':
subtreehelper.cpp:59:6: warning: unused variable 'depth' [-Wunused-variable]
  int depth = -1;
      ^
subtreehelper.cpp: In function 'void gramSubtree_test(SEXP, double, int, bool, bool, bool, bool)':
subtreehelper.cpp:138:6: warning: unused variable 'depth' [-Wunused-variable]
  int depth = -1;
      ^
subtreehelper.cpp: In function 'void initialize_extended(MoleculeSet*, std::vector > >*)':
subtreehelper.cpp:215:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int k=0; k < edges->at(n)[i].size() ; k++){
                      ^
subtreehelper.cpp: In function 'double subTreeKernel(Molecule*, Molecule*, std::vector >*, std::vector >*, int, double, bool, bool, bool)':
subtreehelper.cpp:297:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int istep=0 ; istep < toupdate1.size() ; istep++) {
                            ^
subtreehelper.cpp:304:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                ^
subtreehelper.cpp:304:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                                                  ^
subtreehelper.cpp:321:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(int l = 0 ; l < tuples[natoms1-1][d-1].size() ; l++){
                        ^
subtreehelper.cpp:322:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int m = 0 ; m < tuples[natoms2-1][d-1].size() ; m++){
                         ^
subtreehelper.cpp:350:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n = 1 ; n < tempKernel.size() ; n++){
                        ^
subtreehelper.cpp: In function 'void initialize_tuples(int)':
subtreehelper.cpp:451:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0 ; i= MoleculeSet::numMolecules())
                          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from spectrum3Dhelper.h:38:0,
                 from spectrum3Dhelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
spectrum3Dhelper.cpp: In function 'void gramSpectrum3D_self(SEXP, int, int, int, double, double, bool)':
spectrum3Dhelper.cpp:74:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrum3Dhelper.cpp: In function 'void gramSpectrum3D_test(SEXP, int, int, int, double, double, bool)':
spectrum3Dhelper.cpp:174:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrum3Dhelper.cpp: In function 'void gramComputeSpectrum3D_self(MoleculeSet*, int, int, int, std::vector*, std::vector >*, std::vector*, bool)':
spectrum3Dhelper.cpp:225:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrum3Dhelper.cpp:241:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrum3Dhelper.cpp:242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrum3Dhelper.cpp: In function 'void gramComputeSpectrum3D_test(MoleculeSet*, MoleculeSet*, int, int, int, std::vector*, std::vector*, std::vector >*, std::vector*, bool)':
spectrum3Dhelper.cpp:279:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrum3Dhelper.cpp:295:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrum3Dhelper.cpp:296:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrum3Dhelper.cpp: In function 'void updatePaths3D(MoleculeSet*, std::string, int, std::vector*, std::vector*, int, int)':
spectrum3Dhelper.cpp:384:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:388:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                       ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_self(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:445:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:446:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = i ; j < molPaths->size() ; j++){
                       ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int)':
spectrum3Dhelper.cpp:488:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:489:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < molPaths_test->size() ; j++){
                         ^
spectrum3Dhelper.cpp: In function 'void updateSelfKernel3D(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:530:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i = 0 ; i < molPaths->size() ; i++){
                    ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_self(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:472:75: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);   
                                                                           ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int)':
spectrum3Dhelper.cpp:513:80: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
                                                                                ^
spectrum3Dhelper.cpp: In function 'void updateSelfKernel3D(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:557:34: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
     aMol->addToSelfKernel(update);
                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spectrumhelper.cpp -o spectrumhelper.o
In file included from spectrumhelper.h:38:0,
                 from spectrumhelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
spectrumhelper.cpp: In function 'void gramSpectrum_self(SEXP, int, int, double, bool, bool)':
spectrumhelper.cpp:72:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrumhelper.cpp:75:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < bondTypes.size() ; i++ ){
                          ^
spectrumhelper.cpp: In function 'void gramSpectrum_test(SEXP, int, int, double, bool, bool)':
spectrumhelper.cpp:130:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrumhelper.cpp:133:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < bondTypes.size() ; i++ ){
                          ^
spectrumhelper.cpp: In function 'void gramComputeSpectrum_self(MoleculeSet*, int, int, int, double, std::vector*, std::vector >*, std::vector*, bool, bool)':
spectrumhelper.cpp:161:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrumhelper.cpp:188:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrumhelper.cpp:189:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrumhelper.cpp: In function 'void gramComputeSpectrum_test(MoleculeSet*, MoleculeSet*, int, int, int, double, std::vector*, std::vector*, std::vector >*, std::vector*, bool, bool)':
spectrumhelper.cpp:229:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrumhelper.cpp:258:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrumhelper.cpp:259:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrumhelper.cpp: In function 'void updatePaths(MoleculeSet*, std::string, int, std::vector*, std::vector*, int, int)':
spectrumhelper.cpp:368:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:372:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                       ^
spectrumhelper.cpp: In function 'void updateGram_self(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:453:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:455:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                         ^
spectrumhelper.cpp:467:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:468:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = i ; j < molPaths->size() ; j++){
                       ^
spectrumhelper.cpp: In function 'void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int, double, int)':
spectrumhelper.cpp:518:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:520:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths)[i].path_pointers.size() ; k++){
                         ^
spectrumhelper.cpp:528:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths_test->size() ; i++){
                       ^
spectrumhelper.cpp:530:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths_test)[i].path_pointers.size() ; k++){
                         ^
spectrumhelper.cpp:543:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:544:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < molPaths_test->size() ; j++){
                         ^
spectrumhelper.cpp: In function 'void updateSelfKernel(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:592:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:594:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                         ^
spectrumhelper.cpp:606:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i = 0 ; i < molPaths->size() ; i++){
                    ^
spectrumhelper.cpp: In function 'void updateGram_self(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:499:75: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);   
                                                                           ^
spectrumhelper.cpp: In function 'void updateSelfKernel(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:630:34: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
     aMol->addToSelfKernel(update);
                                  ^
spectrumhelper.cpp: In function 'void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int, double, int)':
spectrumhelper.cpp:570:80: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
                                                                                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subtreehelper.cpp -o subtreehelper.o
In file included from subtreehelper.h:37:0,
                 from subtreehelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
subtreehelper.cpp: In function 'void gramSubtree_self(SEXP, double, int, bool, bool, bool, bool)':
subtreehelper.cpp:59:6: warning: unused variable 'depth' [-Wunused-variable]
  int depth = -1;
      ^
subtreehelper.cpp: In function 'void gramSubtree_test(SEXP, double, int, bool, bool, bool, bool)':
subtreehelper.cpp:138:6: warning: unused variable 'depth' [-Wunused-variable]
  int depth = -1;
      ^
subtreehelper.cpp: In function 'void initialize_extended(MoleculeSet*, std::vector > >*)':
subtreehelper.cpp:215:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int k=0; k < edges->at(n)[i].size() ; k++){
                      ^
subtreehelper.cpp: In function 'double subTreeKernel(Molecule*, Molecule*, std::vector >*, std::vector >*, int, double, bool, bool, bool)':
subtreehelper.cpp:297:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int istep=0 ; istep < toupdate1.size() ; istep++) {
                            ^
subtreehelper.cpp:304:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                ^
subtreehelper.cpp:304:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                                                  ^
subtreehelper.cpp:321:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(int l = 0 ; l < tuples[natoms1-1][d-1].size() ; l++){
                        ^
subtreehelper.cpp:322:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int m = 0 ; m < tuples[natoms2-1][d-1].size() ; m++){
                         ^
subtreehelper.cpp:350:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n = 1 ; n < tempKernel.size() ; n++){
                        ^
subtreehelper.cpp: In function 'void initialize_tuples(int)':
subtreehelper.cpp:451:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0 ; i