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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Rchemcpp_2.21.1.tar.gz && 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_2.21.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Rchemcpp_2.21.1.zip && rm Rchemcpp_2.21.1.tar.gz Rchemcpp_2.21.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 497k 100 497k 0 0 7133k 0 --:--:-- --:--:-- --:--:-- 7768k
install for i386
* installing *source* package 'Rchemcpp' ...
** libs
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpcbqFMy/R.INSTALL6a865087126/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/RtmpcbqFMy/R.INSTALL6a865087126/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<pathsInMol3D>*, std::vector<std::basic_string<char> >*, std::vector<int>*, 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<pathsInMol3D>*, std::vector<pathsInMol3D>*, std::vector<std::basic_string<char> >*, std::vector<int>*, 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<pathsInMol3D>*, std::vector<pathsInMol3D>*, 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<pathsInMol3D>*, 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<pathsInMol3D>*, std::vector<pathsInMol3D>*, 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<pathsInMol3D>*, 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<pathsInMol3D>*, 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<pathsInMol3D>*, std::vector<pathsInMol3D>*, 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<pathsInMol3D>*, 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<pathsInMol>*, std::vector<std::basic_string<char> >*, std::vector<int>*, 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<pathsInMol>*, std::vector<pathsInMol>*, std::vector<std::basic_string<char> >*, std::vector<int>*, 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<pathsInMol>*, std::vector<pathsInMol>*, 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<pathsInMol>*, 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<pathsInMol>*, std::vector<pathsInMol>*, 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<pathsInMol>*, 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<pathsInMol>*, 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<pathsInMol>*, std::vector<pathsInMol>*, 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<std::vector<std::vector<Nextatom> > >*)':
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<Nextatom> >*, std::vector<std::vector<Nextatom> >*, 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<tuples[n][p-1].size() ; i++) {
^
subtreehelper.cpp:457:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0 ; j<tuples[n][p-1][i].size() ; j++) {
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rchemcpp.dll tmp.def Relements.o Rmolecule.o Rmoleculeset.o spectrum3Dhelper.o spectrumhelper.o subtreehelper.o -L./ -lchemcpp -Wl,-rpath,C:/Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/00LOCK-Rchemcpp/00new/Rchemcpp/libs -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/00LOCK-Rchemcpp/00new/Rchemcpp/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'length' with signature '"Rcpp_Rmoleculeset"': no definition for class "Rcpp_Rmoleculeset"
** help
*** installing help indices
converting help for package 'Rchemcpp'
finding HTML links ... done
Rchemcpp-package html
Rcpp_Rmolecule-class html
Rcpp_Rmoleculeset-class html
createRMolecule html
getMoleculeNamesFromSDF html
getMoleculePropertyFromSDF html
readRmoleculeset html
sd2gram html
sd2gram3Dpharma html
sd2gram3Dspectrum html
sd2gramSpectrum html
sd2gramSubtree 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
install for x64
* installing *source* package 'Rchemcpp' ...
** libs
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8sJ0A0/R.INSTALLd6436d0153f/Rchemcpp/src/chemcpp/src'
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o constant.o constant.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o node.o node.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o atom.o atom.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o bond.o bond.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o cerror.o cerror.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o chemcpp.o chemcpp.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o datacontainer.o datacontainer.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o descriptor.o descriptor.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o elements.o elements.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o jlpioutils.o jlpioutils.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o kcfmolecule.o kcfmolecule.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o molecule.o molecule.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o moleculeset.o moleculeset.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o moleculeutils.o moleculeutils.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o ring.o ring.cpp
C:/Rtools/mingw_64/bin/g++ -O2 -Wall -mtune=generic -w -fPIC -I../src/ -c -o stringutils.o stringutils.cpp
C:/Rtools/mingw_64/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_64/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/Rtmp8sJ0A0/R.INSTALLd6436d0153f/Rchemcpp/src/chemcpp/src'
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 Relements.cpp -o Relements.o
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 Rmolecule.cpp -o Rmolecule.o
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 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_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<pathsInMol3D>*, std::vector<std::basic_string<char> >*, std::vector<int>*, 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<pathsInMol3D>*, std::vector<pathsInMol3D>*, std::vector<std::basic_string<char> >*, std::vector<int>*, 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<pathsInMol3D>*, std::vector<pathsInMol3D>*, 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<pathsInMol3D>*, 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<pathsInMol3D>*, std::vector<pathsInMol3D>*, 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<pathsInMol3D>*, 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<pathsInMol3D>*, 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<pathsInMol3D>*, std::vector<pathsInMol3D>*, 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<pathsInMol3D>*, 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<pathsInMol>*, std::vector<std::basic_string<char> >*, std::vector<int>*, 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<pathsInMol>*, std::vector<pathsInMol>*, std::vector<std::basic_string<char> >*, std::vector<int>*, 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<pathsInMol>*, std::vector<pathsInMol>*, 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<pathsInMol>*, 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<pathsInMol>*, std::vector<pathsInMol>*, 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<pathsInMol>*, 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<pathsInMol>*, 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<pathsInMol>*, 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<pathsInMol>*, std::vector<pathsInMol>*, 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<std::vector<std::vector<Nextatom> > >*)':
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<Nextatom> >*, std::vector<std::vector<Nextatom> >*, 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<tuples[n][p-1].size() ; i++) {
^
subtreehelper.cpp:457:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j=0 ; j<tuples[n][p-1][i].size() ; j++) {
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rchemcpp.dll tmp.def Relements.o Rmolecule.o Rmoleculeset.o spectrum3Dhelper.o spectrumhelper.o subtreehelper.o -L./ -lchemcpp -Wl,-rpath,C:/Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rchemcpp' as Rchemcpp_2.21.1.zip
* DONE (Rchemcpp)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Rchemcpp' successfully unpacked and MD5 sums checked
