Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for Rchemcpp on moscato1

This page was generated on 2016-09-21 03:45:00 -0700 (Wed, 21 Sep 2016).

Package 985/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rchemcpp 2.11.0
Guenter Klambauer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rchemcpp
Last Changed Rev: 120616 / Revision: 121152
Last Changed Date: 2016-08-31 02:33:08 -0700 (Wed, 31 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rchemcpp
Version: 2.11.0
Command: rm -rf Rchemcpp.buildbin-libdir Rchemcpp.Rcheck && mkdir Rchemcpp.buildbin-libdir Rchemcpp.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rchemcpp.buildbin-libdir Rchemcpp_2.11.0.tar.gz >Rchemcpp.Rcheck\00install.out 2>&1 && cp Rchemcpp.Rcheck\00install.out Rchemcpp-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Rchemcpp.buildbin-libdir --install="check:Rchemcpp-install.out" --force-multiarch --no-vignettes --timings Rchemcpp_2.11.0.tar.gz
StartedAt: 2016-09-20 14:57:17 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:01:08 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 230.9 seconds
RetCode: 0
Status:  OK  
CheckDir: Rchemcpp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rchemcpp.buildbin-libdir Rchemcpp.Rcheck && mkdir Rchemcpp.buildbin-libdir Rchemcpp.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rchemcpp.buildbin-libdir Rchemcpp_2.11.0.tar.gz >Rchemcpp.Rcheck\00install.out 2>&1 && cp Rchemcpp.Rcheck\00install.out Rchemcpp-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Rchemcpp.buildbin-libdir --install="check:Rchemcpp-install.out" --force-multiarch --no-vignettes --timings Rchemcpp_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Rchemcpp.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rchemcpp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rchemcpp' version '2.11.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rchemcpp' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      6.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotStruc: no visible global function definition for 'lines'
plotStruc: no visible global function definition for 'points'
plotStruc: no visible global function definition for 'text'
plot,SDFset: no visible global function definition for 'par'
Undefined global functions or variables:
  lines par points text
Consider adding
  importFrom("graphics", "lines", "par", "points", "text")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs/i386/Rchemcpp.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbld/bbs-3.4-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs/i386/libchemcpp.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/Rchemcpp.Rcheck/00check.log'
for details.

Rchemcpp.Rcheck/00install.out:


install for i386

* installing *source* package 'Rchemcpp' ...
** libs
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.4-bioc/tmpdir/Rtmp0ynwOB/R.INSTALLbe84fd03965/Rchemcpp/src/chemcpp/src'
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o constant.o constant.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o node.o node.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o atom.o atom.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o bond.o bond.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o cerror.o cerror.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o chemcpp.o chemcpp.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o datacontainer.o datacontainer.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o descriptor.o descriptor.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o elements.o elements.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o jlpioutils.o jlpioutils.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o kcfmolecule.o kcfmolecule.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o molecule.o molecule.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o moleculeset.o moleculeset.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o moleculeutils.o moleculeutils.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o ring.o ring.cpp
C:/Rtools/mingw_32/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o stringutils.o stringutils.cpp
C:/Rtools/mingw_32/bin/g++  -shared -o ../../libchemcpp.dll -O2 -Wall  -mtune=core2 -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=core2 -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/d/biocbld/bbs-3.4-bioc/tmpdir/Rtmp0ynwOB/R.INSTALLbe84fd03965/Rchemcpp/src/chemcpp/src'
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Relements.cpp -o Relements.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Rmolecule.cpp -o Rmolecule.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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,D:/biocbld/bbs-3.4-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs/i386
** R
** inst
** preparing package for lazy loading
in method for 'length' with signature '"Rcpp_Rmoleculeset"': no definition for class "Rcpp_Rmoleculeset"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Rchemcpp' ...
** libs
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-3.4-bioc/tmpdir/Rtmp8UcM9G/R.INSTALL11883dad6491/Rchemcpp/src/chemcpp/src'
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o constant.o constant.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o node.o node.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o atom.o atom.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o bond.o bond.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o cerror.o cerror.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o chemcpp.o chemcpp.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o datacontainer.o datacontainer.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o descriptor.o descriptor.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o elements.o elements.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o jlpioutils.o jlpioutils.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o kcfmolecule.o kcfmolecule.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o molecule.o molecule.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o moleculeset.o moleculeset.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o moleculeutils.o moleculeutils.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o ring.o ring.cpp
C:/Rtools/mingw_64/bin/g++  -O2 -Wall  -mtune=core2 -w -fPIC -I../src/   -c -o stringutils.o stringutils.cpp
C:/Rtools/mingw_64/bin/g++  -shared -o ../../libchemcpp.dll -O2 -Wall  -mtune=core2 -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=core2 -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/d/biocbld/bbs-3.4-bioc/tmpdir/Rtmp8UcM9G/R.INSTALL11883dad6491/Rchemcpp/src/chemcpp/src'
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Relements.cpp -o Relements.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c Rmolecule.cpp -o Rmolecule.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I./chemcpp/src   -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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,D:/biocbld/bbs-3.4-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Rchemcpp.buildbin-libdir/Rchemcpp/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rchemcpp' as Rchemcpp_2.11.0.zip
* DONE (Rchemcpp)

Rchemcpp.Rcheck/examples_i386/Rchemcpp-Ex.timings:

nameusersystemelapsed
Rchemcpp-package2.280.042.36
Rcpp_Rmolecule-class000
Rcpp_Rmoleculeset-class0.020.000.01
createRMolecule000
getMoleculeNamesFromSDF000
getMoleculePropertyFromSDF0.010.000.02
sd2gram1.020.021.03
sd2gram3Dpharma0.670.000.67
sd2gram3Dspectrum0.270.000.27
sd2gramSpectrum0.050.000.05
sd2gramSubtree0.240.020.26

Rchemcpp.Rcheck/examples_x64/Rchemcpp-Ex.timings:

nameusersystemelapsed
Rchemcpp-package2.370.012.39
Rcpp_Rmolecule-class0.010.000.01
Rcpp_Rmoleculeset-class000
createRMolecule000
getMoleculeNamesFromSDF0.020.000.02
getMoleculePropertyFromSDF000
sd2gram1.150.021.17
sd2gram3Dpharma0.70.00.7
sd2gram3Dspectrum0.290.000.28
sd2gramSpectrum0.030.010.05
sd2gramSubtree0.250.000.25