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BUILD BIN report for Rdisop on tokay1

This page was generated on 2019-04-13 11:20:34 -0400 (Sat, 13 Apr 2019).

Package 1273/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.42.1
Steffen Neumann
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/Rdisop
Branch: RELEASE_3_8
Last Commit: d0383fe
Last Changed Date: 2019-01-04 13:12:02 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ ERROR ]
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rdisop
Version: 1.42.1
Command: rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.42.1.tar.gz
StartedAt: 2019-04-13 07:50:44 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 07:50:58 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 14.0 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.42.1.tar.gz
###
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install for i386

* installing *source* package 'Rdisop' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -I./imslib/src/   -O2 -Wall  -mtune=generic -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 C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:64:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from C:/Users/biocbuild/bbs-3.8-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")));
                                                                 ^
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:478:25: 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\nm.exe: imslib/src/ims/element.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/composedelement.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/isotopedistribution.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/alphabet.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/weights.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/distributedalphabet.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/transformation.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/isotopespecies.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/base/parser/alphabettextparser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/base/parser/distributedalphabettextparser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/base/parser/massestextparser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/base/parser/moleculesequenceparser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/base/parser/standardmoleculesequenceparser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/base/parser/keggligandcompoundsparser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/base/parser/moleculeionchargemodificationparser.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/calib/linepairstabber.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/calib/matchmatrix.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/calib/linearpointsetmatcher.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/decomp/realmassdecomposer.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/utils/distribution.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/distributionprobabilityscorer.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/characteralphabet.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: imslib/src/ims/nitrogenrulefilter.o: File format not recognized
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 C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppClassic/lib/i386/libRcppClassic.a -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
imslib/src/ims/element.o: file not recognized: File format not recognized
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'Rdisop'
* removing 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Rdisop.buildbin-libdir/Rdisop'
In R CMD INSTALL
In R CMD INSTALL