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Package 332/419HostnameOS / ArchBUILDCHECKBUILD BIN
Rdisop 1.10.0
Steffen Neumann
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/Rdisop
Last Changed Rev: 50293 / Revision: 54281
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: Rdisop
Version: 1.10.0
Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings Rdisop_1.10.0.tar.gz
StartedAt: 2011-03-31 10:10:56 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 10:12:03 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 66.8 seconds
RetCode: 0
Status:  OK  
CheckDir: Rdisop.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/Rdisop.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rdisop/DESCRIPTION' ... OK
* this is package 'Rdisop' version '1.10.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rdisop' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

Rdisop.Rcheck/00install.out:

* installing *source* package 'Rdisop' ...
Building libRcpp.a in RcppSrc...
... using <x86_64-w64-mingw32-gcc> and <x86_64-w64-mingw32-g++>
x86_64-w64-mingw32-g++ -c Rcpp.cpp -o Rcpp.o -I"D:/biocbld/BBS-2˜1.7-B/R/include" -I"D:/biocbld/BBS-2˜1.7-B/R/src/include"  -Wall -O2
x86_64-w64-mingw32-ar rs libRcpp.a Rcpp.o
rm -f Rcpp.o
Building imslib.dll in src/imslib... with <x86_64-w64-mingw32-gcc> and <x86_64-w64-mingw32-g++>
configure: not found
Makefile:1204: src/ims/.deps/alphabet.Plo: No such file or directory
Makefile:1205: src/ims/.deps/characteralphabet.Plo: No such file or directory
Makefile:1206: src/ims/.deps/composedelement.Plo: No such file or directory
Makefile:1207: src/ims/.deps/distributedalphabet.Plo: No such file or directory
Makefile:1208: src/ims/.deps/distributionprobabilityscorer.Plo: No such file or directory
Makefile:1209: src/ims/.deps/element.Plo: No such file or directory
Makefile:1210: src/ims/.deps/isotopedistribution.Plo: No such file or directory
Makefile:1211: src/ims/.deps/isotopespecies.Plo: No such file or directory
Makefile:1212: src/ims/.deps/nitrogenrulefilter.Plo: No such file or directory
Makefile:1213: src/ims/.deps/transformation.Plo: No such file or directory
Makefile:1214: src/ims/.deps/weights.Plo: No such file or directory
Makefile:1215: src/ims/base/parser/.deps/alphabettextparser.Plo: No such file or directory
Makefile:1216: src/ims/base/parser/.deps/distributedalphabettextparser.Plo: No such file or directory
Makefile:1217: src/ims/base/parser/.deps/keggligandcompoundsparser.Plo: No such file or directory
Makefile:1218: src/ims/base/parser/.deps/massestextparser.Plo: No such file or directory
Makefile:1219: src/ims/base/parser/.deps/moleculeionchargemodificationparser.Plo: No such file or directory
Makefile:1220: src/ims/base/parser/.deps/moleculesequenceparser.Plo: No such file or directory
Makefile:1221: src/ims/base/parser/.deps/standardmoleculesequenceparser.Plo: No such file or directory
Makefile:1222: src/ims/calib/.deps/linearpointsetmatcher.Plo: No such file or directory
Makefile:1223: src/ims/calib/.deps/linepairstabber.Plo: No such file or directory
Makefile:1224: src/ims/calib/.deps/matchmatrix.Plo: No such file or directory
Makefile:1225: src/ims/decomp/.deps/realmassdecomposer.Plo: No such file or directory
Makefile:1226: src/ims/utils/.deps/distribution.Plo: No such file or directory
Makefile:1281: tools/.deps/scoredecompositions.Po: No such file or directory
make: *** No rule to make target `tools/.deps/scoredecompositions.Po'.  Stop.
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c disop.cpp -o disop.o
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:124:8: warning: unused variable 'parityeven'
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
disop.cpp:211:61: warning: comparison between signed and unsigned integer expressions
disop.cpp:214:61: warning: comparison between signed and unsigned integer expressions
disop.cpp:222:60: warning: comparison between signed and unsigned integer expressions
disop.cpp:222:86: warning: comparison between signed and unsigned integer expressions
disop.cpp:174:6: warning: unused variable 'number_molecules_shown'
disop.cpp: In function 'SEXPREC* calculateScore(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
disop.cpp:357:60: warning: comparison between signed and unsigned integer expressions
disop.cpp:357:86: warning: comparison between signed and unsigned integer expressions
disop.cpp:374:61: warning: comparison between signed and unsigned integer expressions
disop.cpp:377:61: warning: comparison between signed and unsigned integer expressions
disop.cpp:381:60: warning: comparison between signed and unsigned integer expressions
disop.cpp:381:86: warning: comparison between signed and unsigned integer expressions
disop.cpp: In function 'void initializeAlphabet(SEXPREC*, alphabet_t&, int)':
disop.cpp:797:26: warning: deprecated conversion from string constant to 'char*'
disop.cpp:799:86: warning: deprecated conversion from string constant to 'char*'
disop.cpp:801:47: warning: deprecated conversion from string constant to 'char*'
disop.cpp:803:23: warning: deprecated conversion from string constant to 'char*'
disop.cpp:804:55: warning: deprecated conversion from string constant to 'char*'
disop.cpp:805:65: warning: deprecated conversion from string constant to 'char*'
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -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 ims::AbstractMoleculeSequenceParser::sequence_type&)':
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:55:65: warning: suggest parentheses around '&&' within '||'
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"      -I../RcppSrc -I./imslib/src/   -O2 -Wall  -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
x86_64-w64-mingw32-g++ -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 -L../RcppSrc -lRcpp -LD:/biocbld/BBS-2˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-bioc/meat/Rdisop.Rcheck/Rdisop/libs/x64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Rdisop)

Rdisop.Rcheck/Rdisop-Ex.timings:

nameusersystemelapsed
RcppVersion000
addMolecules000
decomposeMass0.020.000.01
getMolecule000
initializeCHNOPS000