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BioC 2.14: BUILD report for Rdisop on petty

This page was generated on 2014-10-08 08:58:09 -0700 (Wed, 08 Oct 2014).

Package 644/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.24.1
Steffen Neumann
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Rdisop
Last Changed Rev: 89375 / Revision: 95116
Last Changed Date: 2014-04-22 17:24:00 -0700 (Tue, 22 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  ERROR [ ERROR ] skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: Rdisop
Version: 1.24.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rdisop
StartedAt: 2014-10-07 18:34:31 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:35:16 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 45.6 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rdisop
###
##############################################################################
##############################################################################


* checking for file ‘Rdisop/DESCRIPTION’ ... OK
* preparing ‘Rdisop’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
      -----------------------------------
* 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/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 /private/tmp/RtmpUjqQoK/Rinst233214213473/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
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/private/tmp/RtmpUjqQoK/Rinst233214213473/Rdisop/libs/Rdisop.so':
  dlopen(/private/tmp/RtmpUjqQoK/Rinst233214213473/Rdisop/libs/Rdisop.so, 6): Symbol not found: __ZTIN4Rcpp7RObjectE
  Referenced from: /private/tmp/RtmpUjqQoK/Rinst233214213473/Rdisop/libs/Rdisop.so
  Expected in: flat namespace
 in /private/tmp/RtmpUjqQoK/Rinst233214213473/Rdisop/libs/Rdisop.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/private/tmp/RtmpUjqQoK/Rinst233214213473/Rdisop’
      -----------------------------------
ERROR: package installation failed