Rchemcpp 2.0.2 Guenter Klambauer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Rchemcpp | Last Changed Rev: 86082 / Revision: 88450 | Last Changed Date: 2014-02-04 15:36:04 -0800 (Tue, 04 Feb 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* installing *source* package ‘Rchemcpp’ ...
** libs
make[1]: Entering directory `/home/biocbuild/bbs-2.13-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-2.13-bioc/meat/Rchemcpp.Rcheck/00_pkg_src/Rchemcpp/src/chemcpp/src'
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c Relements.cpp -o Relements.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c Rmolecule.cpp -o Rmolecule.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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]
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]
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]
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]
spectrum3Dhelper.cpp:241:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:242:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrum3Dhelper.cpp:295:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrum3Dhelper.cpp:296:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrum3Dhelper.cpp:388:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrum3Dhelper.cpp:446:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrum3Dhelper.cpp:489:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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 [-Wuninitialized]
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 [-Wuninitialized]
spectrum3Dhelper.cpp: In function ‘void updateSelfKernel3D(MoleculeSet*, std::vector<pathsInMol3D>*, int)’:
spectrum3Dhelper.cpp:557:34: warning: ‘update’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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]
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]
spectrumhelper.cpp:75:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrumhelper.cpp:133:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrumhelper.cpp:188:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:189:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrumhelper.cpp:258:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:259:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrumhelper.cpp:372:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrumhelper.cpp:455:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:467:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:468:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrumhelper.cpp:520:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:528:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:530:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:543:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:544:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
spectrumhelper.cpp:594:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
spectrumhelper.cpp:606:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wuninitialized]
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 [-Wuninitialized]
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 [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I./chemcpp/src -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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]
subtreehelper.cpp: In function ‘void gramSubtree_self(SEXP, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:59:6: warning: unused variable ‘depth’ [-Wunused-variable]
subtreehelper.cpp: In function ‘void gramSubtree_test(SEXP, double, int, bool, bool, bool, bool)’:
subtreehelper.cpp:138:6: warning: unused variable ‘depth’ [-Wunused-variable]
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]
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]
subtreehelper.cpp:304:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:304:74: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:321:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:322:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:350:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp: In function ‘void initialize_tuples(int)’:
subtreehelper.cpp:451:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
subtreehelper.cpp:457:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -shared -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-2.13-bioc/meat/Rchemcpp.Rcheck/Rchemcpp/libs -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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)