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 |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD INSTALL Rdisop
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* installing to library ‘/home/biocbuild/bbs-2.14-bioc/R/library’
* installing *source* package ‘Rdisop’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:0:
./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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -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:8:0,
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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
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++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include" -I./imslib/src/ -fpic -g -O2 -Wall -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
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++ -shared -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 -L/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/lib -lRcppClassic -Wl,-rpath,/home/biocbuild/bbs-2.14-bioc/R/library/RcppClassic/lib -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/R/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)