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BioC 3.4: INSTALL report for Rdisop on moscato1

This page was generated on 2016-09-21 03:42:22 -0700 (Wed, 21 Sep 2016).

Package 993/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.33.0
Steffen Neumann
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rdisop
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rdisop
Version: 1.33.0
Command: rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/Rdisop_1.33.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=Rdisop.buildbin-libdir --merge-multiarch Rdisop_1.33.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL Rdisop_1.33.0.zip && rm Rdisop_1.33.0.tar.gz Rdisop_1.33.0.zip
StartedAt: 2016-09-19 20:20:36 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:22:31 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 115.2 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/Rdisop_1.33.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=Rdisop.buildbin-libdir --merge-multiarch Rdisop_1.33.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL Rdisop_1.33.0.zip  && rm Rdisop_1.33.0.tar.gz Rdisop_1.33.0.zip
###
##############################################################################
##############################################################################


  % 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  684k  100  684k    0     0  29.2M      0 --:--:-- --:--:-- --:--:-- 35.1M

install for i386

* installing *source* package 'Rdisop' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from disop.cpp:18:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
In file included from disop.cpp:28:0:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
  typedef typename DecompositionWeights::weight_type weight_type;
                                                     ^
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
   bool parityeven = !parityodd;
        ^
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:218:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:221:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:229:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
                                              ^
disop.cpp:229:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
                                                                    ^
disop.cpp:181:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
  int number_molecules_shown = 100;
      ^
disop.cpp:159:39: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
     typedef distribution_t::mass_type mass_type;
                                       ^
disop.cpp:161:47: warning: typedef 'nominal_mass_type' locally defined but not used [-Wunused-local-typedefs]
     typedef distribution_t::nominal_mass_type nominal_mass_type;
                                               ^
disop.cpp:164:42: warning: typedef 'decomposition_type' locally defined but not used [-Wunused-local-typedefs]
     typedef decompositions_t::value_type decomposition_type;
                                          ^
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:378:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                              ^
disop.cpp:378:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                                                    ^
disop.cpp:395:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:398:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:402:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                              ^
disop.cpp:402:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                                                    ^
disop.cpp:365:40: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
      typedef distribution_t::mass_type mass_type;
                                        ^
disop.cpp: In function 'SEXPREC* rlistScores(std::multimap<score_type, ims::ComposedElement, std::greater<score_type> >, int)':
disop.cpp:623:43: warning: typedef 'scorer_type' locally defined but not used [-Wunused-local-typedefs]
     typedef DistributionProbabilityScorer scorer_type;
                                           ^
disop.cpp: In function 'void initializeCHNOPS(alphabet_t&, int)':
disop.cpp:712:32: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
  typedef alphabet_t::container elements_type;
                                ^
In file included from D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:53:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from D:/biocbld/bbs-3.4-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")));
                                                                 ^
D:/biocbld/BBS-3˜1.4-B/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")); 
                                                                 ^
disop.cpp:817:33: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
   typedef alphabet_t::container elements_type;
                                 ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:0:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
                 from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/distributedalphabet.h:7,
                 from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function 'virtual void ims::KeggLigandCompoundsParser::parse(const sequence_type&)':
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  for (; letter_pos < last_pos && 
                               ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/decomp/decomputils.h:12,
                 from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:0:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
  typedef typename DecompositionWeights::weight_type weight_type;
                                                     ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/characteralphabet.h:6,
                 from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
                 from ./imslib/src/ims/nitrogenrulefilter.h:4,
                 from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rdisop.dll tmp.def 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 D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/lib/i386/libRcppClassic.a -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/i386
** 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

install for x64

* installing *source* package 'Rdisop' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from disop.cpp:18:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
In file included from disop.cpp:28:0:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
  typedef typename DecompositionWeights::weight_type weight_type;
                                                     ^
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
   bool parityeven = !parityodd;
        ^
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:218:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:221:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:229:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
                                              ^
disop.cpp:229:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
                                                                    ^
disop.cpp:181:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
  int number_molecules_shown = 100;
      ^
disop.cpp:159:39: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
     typedef distribution_t::mass_type mass_type;
                                       ^
disop.cpp:161:47: warning: typedef 'nominal_mass_type' locally defined but not used [-Wunused-local-typedefs]
     typedef distribution_t::nominal_mass_type nominal_mass_type;
                                               ^
disop.cpp:164:42: warning: typedef 'decomposition_type' locally defined but not used [-Wunused-local-typedefs]
     typedef decompositions_t::value_type decomposition_type;
                                          ^
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:378:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                              ^
disop.cpp:378:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                                                    ^
disop.cpp:395:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:398:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:402:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                              ^
disop.cpp:402:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
                                                                    ^
disop.cpp:365:40: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
      typedef distribution_t::mass_type mass_type;
                                        ^
disop.cpp: In function 'SEXPREC* rlistScores(std::multimap<score_type, ims::ComposedElement, std::greater<score_type> >, int)':
disop.cpp:623:43: warning: typedef 'scorer_type' locally defined but not used [-Wunused-local-typedefs]
     typedef DistributionProbabilityScorer scorer_type;
                                           ^
disop.cpp: In function 'void initializeCHNOPS(alphabet_t&, int)':
disop.cpp:712:32: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
  typedef alphabet_t::container elements_type;
                                ^
In file included from D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:53:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from D:/biocbld/bbs-3.4-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")));
                                                                 ^
D:/biocbld/BBS-3˜1.4-B/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")); 
                                                                 ^
disop.cpp:817:33: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
   typedef alphabet_t::container elements_type;
                                 ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:0:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
                 from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/distributedalphabet.h:7,
                 from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function 'virtual void ims::KeggLigandCompoundsParser::parse(const sequence_type&)':
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  for (; letter_pos < last_pos && 
                               ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/decomp/decomputils.h:12,
                 from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:0:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
  typedef typename DecompositionWeights::weight_type weight_type;
                                                     ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
                 from ./imslib/src/ims/characteralphabet.h:6,
                 from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
                 from ./imslib/src/ims/nitrogenrulefilter.h:4,
                 from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rdisop.dll tmp.def 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 D:/biocbld/bbs-3.4-bioc/R/library/RcppClassic/lib/x64/libRcppClassic.a -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rdisop' as Rdisop_1.33.0.zip
* DONE (Rdisop)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'Rdisop' successfully unpacked and MD5 sums checked