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BioC 3.0: INSTALL report for Rdisop on perceval

This page was generated on 2015-04-10 09:53:43 -0700 (Fri, 10 Apr 2015).

Package 730/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.26.0
Steffen Neumann
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Rdisop
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: Rdisop
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rdisop
StartedAt: 2015-04-09 17:06:08 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 17:06:53 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 45.0 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rdisop
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
* installing *source* package ‘Rdisop’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from disop.cpp:18:
./imslib/src/ims/element.h: In member function ‘double ims::Element::getMass(size_t) const’:
./imslib/src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’:
disop.cpp:106: warning: unused variable ‘parityeven’
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:218: warning: comparison between signed and unsigned integer expressions
disop.cpp:221: warning: comparison between signed and unsigned integer expressions
disop.cpp:229: warning: comparison between signed and unsigned integer expressions
disop.cpp:229: warning: comparison between signed and unsigned integer expressions
disop.cpp:181: warning: unused variable ‘number_molecules_shown’
disop.cpp: In function ‘SEXPREC* calculateScore(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:378: warning: comparison between signed and unsigned integer expressions
disop.cpp:378: warning: comparison between signed and unsigned integer expressions
disop.cpp:395: warning: comparison between signed and unsigned integer expressions
disop.cpp:398: warning: comparison between signed and unsigned integer expressions
disop.cpp:402: warning: comparison between signed and unsigned integer expressions
disop.cpp:402: warning: comparison between signed and unsigned integer expressions
disop.cpp: In function ‘void initializeAlphabet(SEXPREC*, alphabet_t&, int)’:
disop.cpp:825: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:827: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:829: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:831: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:832: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:833: warning: deprecated conversion from string constant to ‘char*’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:
./imslib/src/ims/element.h: In member function ‘double ims::Element::getMass(size_t) const’:
./imslib/src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7,
                 from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function ‘double ims::Element::getMass(size_t) const’:
./imslib/src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function ‘double ims::Element::getMass(size_t) const’:
./imslib/src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from ./imslib/src/ims/distributedalphabet.h:7,
                 from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function ‘double ims::Element::getMass(size_t) const’:
./imslib/src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from ./imslib/src/ims/decomp/decomputils.h:12,
                 from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function ‘double ims::Element::getMass(size_t) const’:
./imslib/src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from ./imslib/src/ims/characteralphabet.h:6,
                 from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function ‘double ims::Element::getMass(size_t) const’:
./imslib/src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"  -I./imslib/src/ -fPIC  -mtune=core2 -g -O2 -Wall  -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7,
                 from ./imslib/src/ims/nitrogenrulefilter.h:4,
                 from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function ‘double ims::Element::getMass(size_t) const’:
./imslib/src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o Rdisop.so 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 /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppClassic/lib/libRcppClassic.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rdisop/libs
** 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
* DONE (Rdisop)