Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

BUILD BIN report for Rdisop on tokay2

This page was generated on 2019-04-09 11:56:04 -0400 (Tue, 09 Apr 2019).

Package 1312/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.43.3
Steffen Neumann
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Rdisop
Branch: master
Last Commit: 88541a7
Last Changed Date: 2019-04-05 15:10:53 -0400 (Fri, 05 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ ERROR ]
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: Rdisop
Version: 1.43.3
Command: rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.43.3.tar.gz
StartedAt: 2019-04-09 08:48:02 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 08:48:25 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 23.4 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.43.3.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'Rdisop' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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:380:46: 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:380:68: 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:397:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:400:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
                                           ^
disop.cpp:404:46: 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:404:68: 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:367:40: 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:616:43: 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:699:32: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
  typedef alphabet_t::container elements_type;
                                ^
disop.cpp: In function 'void initializeAlphabet(SEXP, alphabet_t&, int)':
disop.cpp:804:33: 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-3.9-bioc/R/library/RcppClassic/lib/i386/libRcppClassic.a -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-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-3.9-bioc/meat/Rdisop.buildbin-libdir/Rdisop'