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BioC 3.3: CHECK report for Rchemcpp on zin2

This page was generated on 2016-10-13 12:44:03 -0700 (Thu, 13 Oct 2016).

Package 942/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rchemcpp 2.10.0
Guenter Klambauer
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/Rchemcpp
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rchemcpp
Version: 2.10.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rchemcpp_2.10.0.tar.gz
StartedAt: 2016-10-13 05:48:27 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 05:50:09 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 102.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Rchemcpp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rchemcpp_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Rchemcpp.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rchemcpp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rchemcpp’ version ‘2.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rchemcpp’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs     10.2Mb
* 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/Rchemcpp.Rcheck/00check.log’
for details.

Rchemcpp.Rcheck/00install.out:

* installing *source* package ‘Rchemcpp’ ...
** libs
make[1]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/Rchemcpp.Rcheck/00_pkg_src/Rchemcpp/src/chemcpp/src'
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o constant.o constant.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o node.o node.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o atom.o atom.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o bond.o bond.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o cerror.o cerror.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o chemcpp.o chemcpp.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o datacontainer.o datacontainer.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o descriptor.o descriptor.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o elements.o elements.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o jlpioutils.o jlpioutils.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o kcfmolecule.o kcfmolecule.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o molecule.o molecule.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o moleculeset.o moleculeset.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o moleculeutils.o moleculeutils.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o ring.o ring.cpp
g++ -g -O2  -Wall -w -fPIC -I../src/   -c -o stringutils.o stringutils.cpp
g++ -shared -o ../../libchemcpp.dll -g -O2  -Wall -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
g++ -shared -o ../../libchemcpp.so -g -O2  -Wall -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 `/home/biocbuild/bbs-3.3-bioc/meat/Rchemcpp.Rcheck/00_pkg_src/Rchemcpp/src/chemcpp/src'
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Relements.cpp -o Relements.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Rmolecule.cpp -o Rmolecule.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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:330:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                                                       ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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:330:55: 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:74:44: 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:174:44: 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:225:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                                           ^
spectrum3Dhelper.cpp:241:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                                       ^
spectrum3Dhelper.cpp:242:39: 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:279:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                                           ^
spectrum3Dhelper.cpp:295:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                                       ^
spectrum3Dhelper.cpp:296:39: 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:384:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                                      ^
spectrum3Dhelper.cpp:388:59: 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:445:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                                      ^
spectrum3Dhelper.cpp:446:40: 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:488:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                                      ^
spectrum3Dhelper.cpp:489:47: 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:530:37: 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);
                                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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:330:55: 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:72:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                                            ^
spectrumhelper.cpp:75:43: 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:130:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                                            ^
spectrumhelper.cpp:133:43: 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:161:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                                           ^
spectrumhelper.cpp:188:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                                       ^
spectrumhelper.cpp:189:39: 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:229:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                                           ^
spectrumhelper.cpp:258:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                                       ^
spectrumhelper.cpp:259:39: 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:368:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                                      ^
spectrumhelper.cpp:372:59: 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:453:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                                        ^
spectrumhelper.cpp:455:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                                                             ^
spectrumhelper.cpp:467:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                                      ^
spectrumhelper.cpp:468:40: 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:518:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                                        ^
spectrumhelper.cpp:520:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths)[i].path_pointers.size() ; k++){
                                                             ^
spectrumhelper.cpp:528:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths_test->size() ; i++){
                                             ^
spectrumhelper.cpp:530:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths_test)[i].path_pointers.size() ; k++){
                                                                  ^
spectrumhelper.cpp:543:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                                      ^
spectrumhelper.cpp:544:47: 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:592:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                                        ^
spectrumhelper.cpp:594:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                                                             ^
spectrumhelper.cpp:606:37: 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);
                                                                                ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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:330:55: 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:215:45: 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:297:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int istep=0 ; istep < toupdate1.size() ; istep++) {
                                             ^
subtreehelper.cpp:304:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                                        ^
subtreehelper.cpp:304:74: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                                                                          ^
subtreehelper.cpp:321:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(int l = 0 ; l < tuples[natoms1-1][d-1].size() ; l++){
                                                      ^
subtreehelper.cpp:322:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int m = 0 ; m < tuples[natoms2-1][d-1].size() ; m++){
                                                       ^
subtreehelper.cpp:350:42: 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:451:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0 ; i<tuples[n][p-1].size() ; i++) {
                                          ^
subtreehelper.cpp:457:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int j=0 ; j<tuples[n][p-1][i].size() ; j++) {
                                               ^
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o Rchemcpp.so Relements.o Rmolecule.o Rmoleculeset.o spectrum3Dhelper.o spectrumhelper.o subtreehelper.o -L./ -lchemcpp -Wl,-rpath,/home/biocbuild/bbs-3.3-bioc/meat/Rchemcpp.Rcheck/Rchemcpp/libs -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/Rchemcpp.Rcheck/Rchemcpp/libs
** 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
* DONE (Rchemcpp)

Rchemcpp.Rcheck/Rchemcpp-Ex.timings:

nameusersystemelapsed
Rchemcpp-package2.2830.0402.327
Rcpp_Rmolecule-class0.0020.0000.002
Rcpp_Rmoleculeset-class0.0050.0000.006
createRMolecule0.0040.0000.004
getMoleculeNamesFromSDF0.0050.0000.006
getMoleculePropertyFromSDF0.0020.0000.002
sd2gram0.8980.0000.898
sd2gram3Dpharma0.7930.0120.806
sd2gram3Dspectrum0.230.000.23
sd2gramSpectrum0.0280.0000.031
sd2gramSubtree0.2060.0080.214