Rdisop 1.13.0
Steffen Neumann
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rdisop | | Last Changed Rev: 54802 / Revision: 56603 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / 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 |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/Rdisop.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* 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 '1.13.0'
* 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 installed package size ... 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* 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˜1.9-B/R/include" -I"D:/biocbld/BBS-2˜1.9-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
make: *** No rule to make target `src/libims.la'. Stop.
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I../RcppSrc -I./imslib/src/ -O2 -Wall -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from disop.cpp:35:
./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
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˜1.9-B/R/include" -I../RcppSrc -I./imslib/src/ -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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I../RcppSrc -I./imslib/src/ -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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-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˜1.9-B/R/include" -I../RcppSrc -I./imslib/src/ -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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-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˜1.9-B/R/include" -I../RcppSrc -I./imslib/src/ -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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-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˜1.9-B/R/include" -I../RcppSrc -I./imslib/src/ -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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-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˜1.9-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˜1.9-B/R/include" -I../RcppSrc -I./imslib/src/ -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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I../RcppSrc -I./imslib/src/ -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
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˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/Rdisop.Rcheck/Rdisop/libs/x64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'Rdisop.Rnw'
** testing if installed package can be loaded
* DONE (Rdisop)