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Package 484/609HostnameOS / ArchBUILDCHECKBUILD BIN
Rdisop 1.18.0
Steffen Neumann
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/Rdisop
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ]
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: Rdisop
Version: 1.18.0
Command: rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rdisop.buildbin-libdir Rdisop_1.18.0.tar.gz
StartedAt: 2013-03-25 04:15:02 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:17:35 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 152.5 seconds
RetCode: 0
Status:  OK  
PackageFile: Rdisop_1.18.0.zip
PackageFileSize: 931.6 KiB

Command output


install for i386

* installing *source* package 'Rdisop' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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:107:8: warning: unused variable 'parityeven' [-Wunused-variable]
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:194:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:197:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:205:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:205:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:157:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:340:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:340:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:357:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:360:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:364:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:364:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp: In function 'void initializeAlphabet(SEXP, alphabet_t&, int)':
disop.cpp:787:26: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:789:86: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:791:47: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:793:63: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:794:55: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:795:65: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
g++ -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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 D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/lib/i386/libRcppClassic.a D:/biocbld/bbs-2.11-bioc/R/library/Rcpp/lib/i386/libRcpp.a -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lR
D:/biocbld/bbs-2.11-bioc/R/library/Rcpp/lib/i386/libRcpp.a(api.o): duplicate section `.rdata$_ZTVN4Rcpp6VectorILi14EEE[vtable for Rcpp::Vector<14>]' has different size
installing to D:/biocbld/bbs-2.11-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
g++ -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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:107:8: warning: unused variable 'parityeven' [-Wunused-variable]
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:194:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:197:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:205:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:205:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:157:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:340:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:340:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:357:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:360:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:364:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp:364:86: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
disop.cpp: In function 'void initializeAlphabet(SEXP, alphabet_t&, int)':
disop.cpp:787:26: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:789:86: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:791:47: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:793:63: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:794:55: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
disop.cpp:795:65: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
g++ -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/include" -I"D:/biocbld/bbs-2.11-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 D:/biocbld/bbs-2.11-bioc/R/library/RcppClassic/lib/x64/libRcppClassic.a D:/biocbld/bbs-2.11-bioc/R/library/Rcpp/lib/x64/libRcpp.a -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lR
D:/biocbld/bbs-2.11-bioc/R/library/Rcpp/lib/x64/libRcpp.a(api.o): duplicate section `.data$_ZTVN4Rcpp6VectorILi14EEE[_ZTVN4Rcpp6VectorILi14EEE]' has different size
installing to D:/biocbld/bbs-2.11-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rdisop' as Rdisop_1.18.0.zip

* DONE (Rdisop)