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BioC 2.12: BUILD BIN report for Rdisop on moscato2

This page was generated on 2013-10-09 09:38:32 -0700 (Wed, 09 Oct 2013).

Package 531/671HostnameOS / ArchBUILDCHECKBUILD BIN
Rdisop 1.20.0
Steffen Neumann
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Rdisop
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS [ OK ]
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Rdisop
Version: 1.20.0
Command: rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rdisop.buildbin-libdir Rdisop_1.20.0.tar.gz
StartedAt: 2013-10-09 05:22:44 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 05:25:20 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 155.7 seconds
RetCode: 0
Status:  OK  
PackageFile: Rdisop_1.20.0.zip
PackageFileSize: 937.7 KiB

Command output


install for i386

* installing *source* package 'Rdisop' ...
** libs
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:218:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:221:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:229:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:229:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:181:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:378:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:378:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:395:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:398:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:402:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:402:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp: In function 'void initializeAlphabet(SEXP, alphabet_t&, int)':
disop.cpp:825:26: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:827:86: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:829:47: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:831:63: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:832:55: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:833:65: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:55:65: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -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 E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/lib/i386/libRcppClassic.a E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/lib/i386/libRcpp.a -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: package 'RcppClassic' was built under R version 3.0.2
Warning: package 'Rcpp' was built under R version 3.0.2
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'RcppClassic' was built under R version 3.0.2
Warning: package 'Rcpp' was built under R version 3.0.2

install for x64

* installing *source* package 'Rdisop' ...
** libs
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:218:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:221:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:229:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:229:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:181:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:378:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:378:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:395:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:398:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:402:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:402:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp: In function 'void initializeAlphabet(SEXP, alphabet_t&, int)':
disop.cpp:825:26: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:827:86: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:829:47: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:831:63: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:832:55: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:833:65: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:55:65: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -I./imslib/src/   -O2 -Wall  -mtune=core2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/include" -I"E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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:166:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -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 E:/biocbld/bbs-2.12-bioc/R/library/RcppClassic/lib/x64/libRcppClassic.a E:/biocbld/bbs-2.12-bioc/R/library/Rcpp/lib/x64/libRcpp.a -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/x64
** testing if installed package can be loaded
Warning: package 'RcppClassic' was built under R version 3.0.2
Warning: package 'Rcpp' was built under R version 3.0.2
* MD5 sums
packaged installation of 'Rdisop' as Rdisop_1.20.0.zip
* DONE (Rdisop)