Rdisop 1.16.0
Steffen Neumann
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/Rdisop | | Last Changed Rev: 64678 / Revision: 69725 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Rdisop.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rdisop/DESCRIPTION’ ... OK
* this is package ‘Rdisop’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘Rdisop’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
libs 5.4Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Rdisop.Rcheck/Rdisop/libs/Rdisop.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Object: ‘imslib/src/ims/distributionprobabilityscorer.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
‘Makefile’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘doRUnit.R’
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
NOTE: There were 3 notes.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Rdisop.Rcheck/00check.log’
for details.
* installing *source* package ‘Rdisop’ ...
** libs
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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
disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’:
disop.cpp:107:8: warning: unused variable ‘parityeven’
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:194:61: warning: comparison between signed and unsigned integer expressions
disop.cpp:197:61: warning: comparison between signed and unsigned integer expressions
disop.cpp:205:60: warning: comparison between signed and unsigned integer expressions
disop.cpp:205:86: warning: comparison between signed and unsigned integer expressions
disop.cpp:157:6: warning: unused variable ‘number_molecules_shown’
disop.cpp: In function ‘SEXPREC* calculateScore(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:340:60: warning: comparison between signed and unsigned integer expressions
disop.cpp:340:86: warning: comparison between signed and unsigned integer expressions
disop.cpp:357:61: warning: comparison between signed and unsigned integer expressions
disop.cpp:360:61: warning: comparison between signed and unsigned integer expressions
disop.cpp:364:60: warning: comparison between signed and unsigned integer expressions
disop.cpp:364:86: warning: comparison between signed and unsigned integer expressions
disop.cpp: In function ‘void initializeAlphabet(SEXPREC*, alphabet_t&, int)’:
disop.cpp:787:26: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:789:86: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:791:47: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:793:63: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:794:55: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:795:65: warning: deprecated conversion from string constant to ‘char*’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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 ims::AbstractMoleculeSequenceParser::sequence_type&)’:
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:55:65: warning: suggest parentheses around ‘&&’ within ‘||’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/include" -I"/loc/home/biocbuild/bbs-2.10-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
g++ -shared -L/usr/local/lib64 -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/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/lib -lRcppClassic -Wl,-rpath,/loc/home/biocbuild/bbs-2.10-bioc/R/library/RcppClassic/lib -L/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/Rdisop.Rcheck/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)