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Rdisop

Package: Rdisop
Title: Decomposition of Isotopic Patterns
Version: 1.32.0
Date: 2015-12-08
Author: Anton Pervukhin <apervukh@minet.uni-jena.de>, Steffen Neumann <sneumann@ipb-halle.de>
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
Description: Identification of metabolites using high precision mass
spectrometry. MS Peaks are used to derive a ranked list
of sum formulae, alternatively for a given sum formula
the theoretical isotope distribution can be calculated
to search in MS peak lists.
Depends: R (>= 2.0.0), RcppClassic
LinkingTo: RcppClassic, Rcpp
Suggests: RUnit
SystemRequirements: None
License: GPL-2
URL: https://github.com/sneumann/Rdisop
BugReports: https://github.com/sneumann/Rdisop/issues/new
biocViews: MassSpectrometry, Metabolomics
Packaged: 2016-05-04 03:04:12 UTC; biocbuild
NeedsCompilation: yes
● BiocViews: MassSpectrometry, Metabolomics
● 0 images, 4 functions, 0 datasets
● Reverse Depends: 0
Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'Rdisop' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"  -I./imslib/src/ -fpic  -g -O2  -c disop.cpp -o disop.o
In file included from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/r/headers.h:53:0,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/ddbj/local/lib64/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/ddbj/local/lib64/R/include/Rinternals.h:448:25: 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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/RcppClassic/include" -I"/home/ddbj/local/lib64/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/ddbj/local/lib64/R/lib -L/usr/local/lib64 -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/ddbj/local/lib64/R/library/RcppClassic/lib -lRcppClassic -Wl,-rpath,/home/ddbj/local/lib64/R/library/RcppClassic/lib -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Rdisop'
    finding HTML links ... done
    addMolecules                            html  
    decomposeMass                           html  
    getMolecule                             html  
    initializeCHNOPS                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rdisop)
Making 'packages.html' ... done