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CHECK report for Rchemcpp on tokay2

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

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

Summary

Package: Rchemcpp
Version: 2.22.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rchemcpp.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rchemcpp_2.22.0.tar.gz
StartedAt: 2019-10-16 06:23:05 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:25:29 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 144.4 seconds
RetCode: 0
Status:  OK  
CheckDir: Rchemcpp.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rchemcpp.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rchemcpp_2.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.22.0'
* 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  9.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      6.3Mb
* 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
* 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 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 shell scripts ... 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 include directives in Makefiles ... 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 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/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 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rchemcpp/libs/x64/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 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rchemcpp/libs/x64/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 use Fortran I/O
nor system RNGs. 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 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rchemcpp.Rcheck/00check.log'
for details.

Installation output

Rchemcpp.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Rchemcpp_2.22.0.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_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Rchemcpp_2.22.0.zip && rm Rchemcpp_2.22.0.tar.gz Rchemcpp_2.22.0.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
100  497k  100  497k    0     0  7284k      0 --:--:-- --:--:-- --:--:-- 8285k

install for i386

* installing *source* package 'Rchemcpp' ...
** using staged installation
** libs
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpmwwzNk/R.INSTALL1260656732f1/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/RtmpmwwzNk/R.INSTALL1260656732f1/Rchemcpp/src/chemcpp/src'
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Relements.cpp -o Relements.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Rmolecule.cpp -o Rmolecule.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Rmoleculeset.cpp -o Rmoleculeset.o
In file included from Rmoleculeset.cpp:2:0:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from spectrum3Dhelper.h:38:0,
                 from spectrum3Dhelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
spectrum3Dhelper.cpp: In function 'void gramSpectrum3D_self(SEXP, int, int, int, double, double, bool)':
spectrum3Dhelper.cpp:74:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrum3Dhelper.cpp: In function 'void gramSpectrum3D_test(SEXP, int, int, int, double, double, bool)':
spectrum3Dhelper.cpp:174:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrum3Dhelper.cpp: In function 'void gramComputeSpectrum3D_self(MoleculeSet*, int, int, int, std::vector*, std::vector >*, std::vector*, bool)':
spectrum3Dhelper.cpp:225:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrum3Dhelper.cpp:241:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrum3Dhelper.cpp:242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrum3Dhelper.cpp: In function 'void gramComputeSpectrum3D_test(MoleculeSet*, MoleculeSet*, int, int, int, std::vector*, std::vector*, std::vector >*, std::vector*, bool)':
spectrum3Dhelper.cpp:279:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrum3Dhelper.cpp:295:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrum3Dhelper.cpp:296:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrum3Dhelper.cpp: In function 'void updatePaths3D(MoleculeSet*, std::string, int, std::vector*, std::vector*, int, int)':
spectrum3Dhelper.cpp:384:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:388:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                       ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_self(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:445:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:446:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = i ; j < molPaths->size() ; j++){
                       ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int)':
spectrum3Dhelper.cpp:488:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:489:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < molPaths_test->size() ; j++){
                         ^
spectrum3Dhelper.cpp: In function 'void updateSelfKernel3D(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:530:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i = 0 ; i < molPaths->size() ; i++){
                    ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_self(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:472:75: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);   
                                                                           ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int)':
spectrum3Dhelper.cpp:513:80: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
                                                                                ^
spectrum3Dhelper.cpp: In function 'void updateSelfKernel3D(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:557:34: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
     aMol->addToSelfKernel(update);
                                  ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spectrumhelper.cpp -o spectrumhelper.o
In file included from spectrumhelper.h:38:0,
                 from spectrumhelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
spectrumhelper.cpp: In function 'void gramSpectrum_self(SEXP, int, int, double, bool, bool)':
spectrumhelper.cpp:72:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrumhelper.cpp:75:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < bondTypes.size() ; i++ ){
                          ^
spectrumhelper.cpp: In function 'void gramSpectrum_test(SEXP, int, int, double, bool, bool)':
spectrumhelper.cpp:130:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrumhelper.cpp:133:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < bondTypes.size() ; i++ ){
                          ^
spectrumhelper.cpp: In function 'void gramComputeSpectrum_self(MoleculeSet*, int, int, int, double, std::vector*, std::vector >*, std::vector*, bool, bool)':
spectrumhelper.cpp:161:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrumhelper.cpp:188:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrumhelper.cpp:189:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrumhelper.cpp: In function 'void gramComputeSpectrum_test(MoleculeSet*, MoleculeSet*, int, int, int, double, std::vector*, std::vector*, std::vector >*, std::vector*, bool, bool)':
spectrumhelper.cpp:229:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrumhelper.cpp:258:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrumhelper.cpp:259:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrumhelper.cpp: In function 'void updatePaths(MoleculeSet*, std::string, int, std::vector*, std::vector*, int, int)':
spectrumhelper.cpp:368:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:372:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                       ^
spectrumhelper.cpp: In function 'void updateGram_self(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:453:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:455:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                         ^
spectrumhelper.cpp:467:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:468:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = i ; j < molPaths->size() ; j++){
                       ^
spectrumhelper.cpp: In function 'void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int, double, int)':
spectrumhelper.cpp:518:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:520:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths)[i].path_pointers.size() ; k++){
                         ^
spectrumhelper.cpp:528:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths_test->size() ; i++){
                       ^
spectrumhelper.cpp:530:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths_test)[i].path_pointers.size() ; k++){
                         ^
spectrumhelper.cpp:543:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:544:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < molPaths_test->size() ; j++){
                         ^
spectrumhelper.cpp: In function 'void updateSelfKernel(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:592:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:594:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                         ^
spectrumhelper.cpp:606:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i = 0 ; i < molPaths->size() ; i++){
                    ^
spectrumhelper.cpp:630:34: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
     aMol->addToSelfKernel(update);
                                  ^
spectrumhelper.cpp: In function 'void updateGram_self(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:499:75: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);   
                                                                           ^
spectrumhelper.cpp: In function 'void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int, double, int)':
spectrumhelper.cpp:570:80: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
                                                                                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subtreehelper.cpp -o subtreehelper.o
In file included from subtreehelper.h:37:0,
                 from subtreehelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
subtreehelper.cpp: In function 'void gramSubtree_self(SEXP, double, int, bool, bool, bool, bool)':
subtreehelper.cpp:59:6: warning: unused variable 'depth' [-Wunused-variable]
  int depth = -1;
      ^
subtreehelper.cpp: In function 'void gramSubtree_test(SEXP, double, int, bool, bool, bool, bool)':
subtreehelper.cpp:138:6: warning: unused variable 'depth' [-Wunused-variable]
  int depth = -1;
      ^
subtreehelper.cpp: In function 'void initialize_extended(MoleculeSet*, std::vector > >*)':
subtreehelper.cpp:215:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int k=0; k < edges->at(n)[i].size() ; k++){
                      ^
subtreehelper.cpp: In function 'double subTreeKernel(Molecule*, Molecule*, std::vector >*, std::vector >*, int, double, bool, bool, bool)':
subtreehelper.cpp:297:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int istep=0 ; istep < toupdate1.size() ; istep++) {
                            ^
subtreehelper.cpp:304:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                ^
subtreehelper.cpp:304:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                                                  ^
subtreehelper.cpp:321:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(int l = 0 ; l < tuples[natoms1-1][d-1].size() ; l++){
                        ^
subtreehelper.cpp:322:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int m = 0 ; m < tuples[natoms2-1][d-1].size() ; m++){
                         ^
subtreehelper.cpp:350:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n = 1 ; n < tempKernel.size() ; n++){
                        ^
subtreehelper.cpp: In function 'void initialize_tuples(int)':
subtreehelper.cpp:451:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0 ; i= MoleculeSet::numMolecules())
                          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spectrum3Dhelper.cpp -o spectrum3Dhelper.o
In file included from spectrum3Dhelper.h:38:0,
                 from spectrum3Dhelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
spectrum3Dhelper.cpp: In function 'void gramSpectrum3D_self(SEXP, int, int, int, double, double, bool)':
spectrum3Dhelper.cpp:74:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrum3Dhelper.cpp: In function 'void gramSpectrum3D_test(SEXP, int, int, int, double, double, bool)':
spectrum3Dhelper.cpp:174:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrum3Dhelper.cpp: In function 'void gramComputeSpectrum3D_self(MoleculeSet*, int, int, int, std::vector*, std::vector >*, std::vector*, bool)':
spectrum3Dhelper.cpp:225:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrum3Dhelper.cpp:241:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrum3Dhelper.cpp:242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrum3Dhelper.cpp: In function 'void gramComputeSpectrum3D_test(MoleculeSet*, MoleculeSet*, int, int, int, std::vector*, std::vector*, std::vector >*, std::vector*, bool)':
spectrum3Dhelper.cpp:279:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrum3Dhelper.cpp:295:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrum3Dhelper.cpp:296:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrum3Dhelper.cpp: In function 'void updatePaths3D(MoleculeSet*, std::string, int, std::vector*, std::vector*, int, int)':
spectrum3Dhelper.cpp:384:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:388:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                       ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_self(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:445:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:446:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = i ; j < molPaths->size() ; j++){
                       ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int)':
spectrum3Dhelper.cpp:488:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrum3Dhelper.cpp:489:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < molPaths_test->size() ; j++){
                         ^
spectrum3Dhelper.cpp: In function 'void updateSelfKernel3D(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:530:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i = 0 ; i < molPaths->size() ; i++){
                    ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_self(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:472:75: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);   
                                                                           ^
spectrum3Dhelper.cpp: In function 'void updateGram3D_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int)':
spectrum3Dhelper.cpp:513:80: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
                                                                                ^
spectrum3Dhelper.cpp: In function 'void updateSelfKernel3D(MoleculeSet*, std::vector*, int)':
spectrum3Dhelper.cpp:557:34: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
     aMol->addToSelfKernel(update);
                                  ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c spectrumhelper.cpp -o spectrumhelper.o
In file included from spectrumhelper.h:38:0,
                 from spectrumhelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
spectrumhelper.cpp: In function 'void gramSpectrum_self(SEXP, int, int, double, bool, bool)':
spectrumhelper.cpp:72:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrumhelper.cpp:75:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < bondTypes.size() ; i++ ){
                          ^
spectrumhelper.cpp: In function 'void gramSpectrum_test(SEXP, int, int, double, bool, bool)':
spectrumhelper.cpp:130:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < atomLabels.size() ; i++ ){
                          ^
spectrumhelper.cpp:133:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for( int i = 0 ; i < bondTypes.size() ; i++ ){
                          ^
spectrumhelper.cpp: In function 'void gramComputeSpectrum_self(MoleculeSet*, int, int, int, double, std::vector*, std::vector >*, std::vector*, bool, bool)':
spectrumhelper.cpp:161:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrumhelper.cpp:188:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrumhelper.cpp:189:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrumhelper.cpp: In function 'void gramComputeSpectrum_test(MoleculeSet*, MoleculeSet*, int, int, int, double, std::vector*, std::vector*, std::vector >*, std::vector*, bool, bool)':
spectrumhelper.cpp:229:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ;  i < atomLabels->size() ; i++){
                        ^
spectrumhelper.cpp:258:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0 ; j < atomLabels->size() ; j++){
                    ^
spectrumhelper.cpp:259:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int k = 0 ; k < bondTypes->size() ; k++){
                     ^
spectrumhelper.cpp: In function 'void updatePaths(MoleculeSet*, std::string, int, std::vector*, std::vector*, int, int)':
spectrumhelper.cpp:368:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:372:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                       ^
spectrumhelper.cpp: In function 'void updateGram_self(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:453:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:455:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                         ^
spectrumhelper.cpp:467:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:468:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = i ; j < molPaths->size() ; j++){
                       ^
spectrumhelper.cpp: In function 'void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int, double, int)':
spectrumhelper.cpp:518:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:520:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths)[i].path_pointers.size() ; k++){
                         ^
spectrumhelper.cpp:528:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths_test->size() ; i++){
                       ^
spectrumhelper.cpp:530:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int k = 0 ; k < (*molPaths_test)[i].path_pointers.size() ; k++){
                         ^
spectrumhelper.cpp:543:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0 ; i < molPaths->size() ; i++){
                     ^
spectrumhelper.cpp:544:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < molPaths_test->size() ; j++){
                         ^
spectrumhelper.cpp: In function 'void updateSelfKernel(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:592:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < molPaths->size() ; i++){
                       ^
spectrumhelper.cpp:594:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j = 0 ; j < (*molPaths)[i].path_pointers.size() ; j++ ){
                         ^
spectrumhelper.cpp:606:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i = 0 ; i < molPaths->size() ; i++){
                    ^
spectrumhelper.cpp: In function 'void updateGram_self(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:499:75: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[j].molInd , (*molPaths)[i].molInd, update);   
                                                                           ^
spectrumhelper.cpp: In function 'void updateSelfKernel(MoleculeSet*, std::vector*, int, double, int)':
spectrumhelper.cpp:630:34: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
     aMol->addToSelfKernel(update);
                                  ^
spectrumhelper.cpp: In function 'void updateGram_test(MoleculeSet*, MoleculeSet*, std::vector*, std::vector*, int, double, int)':
spectrumhelper.cpp:570:80: warning: 'update' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (*aSet).addToGram( (*molPaths)[i].molInd , (*molPaths_test)[j].molInd, update);
                                                                                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I./chemcpp/src -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subtreehelper.cpp -o subtreehelper.o
In file included from subtreehelper.h:37:0,
                 from subtreehelper.cpp:32:
Rmoleculeset.h: In member function 'SEXPREC* Rmoleculeset::getMolByIndex(int)':
Rmoleculeset.h:330:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (anInd < 0 || anInd >= MoleculeSet::numMolecules())
                          ^
subtreehelper.cpp: In function 'void gramSubtree_self(SEXP, double, int, bool, bool, bool, bool)':
subtreehelper.cpp:59:6: warning: unused variable 'depth' [-Wunused-variable]
  int depth = -1;
      ^
subtreehelper.cpp: In function 'void gramSubtree_test(SEXP, double, int, bool, bool, bool, bool)':
subtreehelper.cpp:138:6: warning: unused variable 'depth' [-Wunused-variable]
  int depth = -1;
      ^
subtreehelper.cpp: In function 'void initialize_extended(MoleculeSet*, std::vector > >*)':
subtreehelper.cpp:215:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (int k=0; k < edges->at(n)[i].size() ; k++){
                      ^
subtreehelper.cpp: In function 'double subTreeKernel(Molecule*, Molecule*, std::vector >*, std::vector >*, int, double, bool, bool, bool)':
subtreehelper.cpp:297:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int istep=0 ; istep < toupdate1.size() ; istep++) {
                            ^
subtreehelper.cpp:304:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                ^
subtreehelper.cpp:304:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while ( (n1 < (*edges1)[atom1].size()) && (n2 < (*edges2)[atom2].size() ) ) {
                                                  ^
subtreehelper.cpp:321:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(int l = 0 ; l < tuples[natoms1-1][d-1].size() ; l++){
                        ^
subtreehelper.cpp:322:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int m = 0 ; m < tuples[natoms2-1][d-1].size() ; m++){
                         ^
subtreehelper.cpp:350:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int n = 1 ; n < tempKernel.size() ; n++){
                        ^
subtreehelper.cpp: In function 'void initialize_tuples(int)':
subtreehelper.cpp:451:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0 ; i

Tests output

Example timings

Rchemcpp.Rcheck/examples_i386/Rchemcpp-Ex.timings

nameusersystemelapsed
Rchemcpp-package3.050.024.19
Rcpp_Rmolecule-class000
Rcpp_Rmoleculeset-class0.020.000.01
createRMolecule000
getMoleculeNamesFromSDF000
getMoleculePropertyFromSDF0.000.020.02
sd2gram1.010.001.01
sd2gram3Dpharma0.680.030.71
sd2gram3Dspectrum0.230.000.23
sd2gramSpectrum0.020.000.02
sd2gramSubtree0.260.000.26

Rchemcpp.Rcheck/examples_x64/Rchemcpp-Ex.timings

nameusersystemelapsed
Rchemcpp-package2.360.042.46
Rcpp_Rmolecule-class000
Rcpp_Rmoleculeset-class000
createRMolecule000
getMoleculeNamesFromSDF000
getMoleculePropertyFromSDF000
sd2gram0.830.000.83
sd2gram3Dpharma0.780.010.79
sd2gram3Dspectrum0.200.000.21
sd2gramSpectrum0.030.000.03
sd2gramSubtree0.240.000.23