Rdisop 1.31.0
Steffen Neumann
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rdisop | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL Rdisop
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* installing to library ‘/home/biocbuild/bbs-3.3-bioc/R/library’
* installing *source* package ‘Rdisop’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c disop.cpp -o disop.o
In file included from /home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:53:0,
from /home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include/RcppCommon.h:29,
from /home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include/RcppClassic.h:27,
from disop.cpp:33:
disop.cpp: In function ‘void initializeAlphabet(SEXP, alphabet_t&, int)’:
disop.cpp:825:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
const char *symbol = CHAR(Rf_asChar(getListElement(l, "name")));
^
/home/biocbuild/bbs-3.3-bioc/R/include/Rinternals.h:440:25: note: in definition of macro ‘CHAR’
#define CHAR(x) R_CHAR(x)
^
disop.cpp:827:86: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
nominal_mass_type nominalmass = (nominal_mass_type) REAL(getListElement(l, "mass"))[0];
^
disop.cpp:829:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
SEXP isotope = getListElement(l, "isotope");
^
disop.cpp:831:63: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
int numisotopes = Rf_length(getListElement(isotope, "mass"));
^
disop.cpp:832:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
double *mass = REAL(getListElement(isotope, "mass"));
^
disop.cpp:833:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
double *abundance = REAL(getListElement(isotope, "abundance"));
^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -L/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/lib -lRcppClassic -Wl,-rpath,/home/biocbuild/bbs-3.3-bioc/R/library/RcppClassic/lib -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/R/library/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘Rdisop.Rnw’
** testing if installed package can be loaded
* DONE (Rdisop)