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Package 196/514HostnameOS / ArchBUILDCHECKBUILD BIN
GeneR 2.24.0
Y. d'Aubenton-Carafa
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GeneR
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  ERROR  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GeneR
Version: 2.24.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneR_2.24.0.tar.gz
StartedAt: 2012-03-24 01:16:49 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:17:48 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 59.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.24.0'
* 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 'GeneR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  CeCILL-2.0
Standardizable: TRUE
Standardized license specification:
  CeCILL-2
* 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 ... NOTE
and.segSet: possible error in as.segSet(deb, fin): unused argument(s)
  (fin)
relist: no visible global function definition for 'error'
setParam: no visible global function definition for 'seqSize'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'Xor.globalSeg':
  'Xor.globalSeg'

S3 methods shown with full name in documentation object 'Xor.segSet':
  'Xor.segSet'

S3 methods shown with full name in documentation object 'and.globalSeg':
  'and.globalSeg'

S3 methods shown with full name in documentation object 'and.segSet':
  'and.segSet'

S3 methods shown with full name in documentation object 'as.globalSeg':
  'as.matrix.globalSeg' 'range.globalSeg'

S3 methods shown with full name in documentation object 'as.segSet':
  'as.matrix.segSet' 'as.data.frame.segSet' 'plot.segSet'

S3 methods shown with full name in documentation object 'densityProfile':
  'plot.profile'

S3 methods shown with full name in documentation object 'not.globalSeg':
  'not.globalSeg'

S3 methods shown with full name in documentation object 'not.segSet':
  'not.segSet'

S3 methods shown with full name in documentation object 'or.globalSeg':
  'or.globalSeg'

S3 methods shown with full name in documentation object 'or.segSet':
  'or.segSet'

S3 methods shown with full name in documentation object 'plot.globalSeg':
  'plot.globalSeg'

S3 methods shown with full name in documentation object 'size.globalSeg':
  'size.globalSeg'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/i386/GeneR.so':
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
  Found '___stderrp', possibly from 'stderr' (C)
  Found '___stdoutp', possibly from 'stdout' (C)
  Found '_printf', possibly from 'printf' (C)
  Found '_puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... 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

GeneR.Rcheck/00install.out:

* installing *source* package 'GeneR' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c GeneR_glob.cc -o GeneR_glob.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c GeneR_seq.cc -o GeneR_seq.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c complementaire.cc -o complementaire.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c compoSeq.cc -o compoSeq.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c dnaRna.cc -o dnaRna.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c libIndex.cc -o libIndex.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c libStrings.cc -o libStrings.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c makeIndex.cc -o makeIndex.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c masked.cc -o masked.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c misc.cc -o misc.o
misc.cc: In function 'SEXPREC* str_to_nbstr(SEXPREC*, SEXPREC*)':
misc.cc:31: warning: 'multiple' may be used uninitialized in this function
misc.cc:30: warning: 'ans' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readEmblDescript.cc -o readEmblDescript.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readIndex.cc -o readIndex.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readLocation.cc -o readLocation.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readSeqFasta.cc -o readSeqFasta.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readSeqGbk.cc -o readSeqGbk.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c seqManip.cc -o seqManip.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c strcasestr.c -o strcasestr.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c translate.cc -o translate.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c upperSeq.cc -o upperSeq.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c vecteurs.cc -o vecteurs.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c writeFasta.cc -o writeFasta.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneR.so GeneR_glob.o GeneR_seq.o complementaire.o compoSeq.o dnaRna.o libIndex.o libStrings.o makeIndex.o masked.o misc.o readEmblDescript.o readIndex.o readLocation.o readSeqEmbl.o readSeqFasta.o readSeqGbk.o seqManip.o strcasestr.o translate.o upperSeq.o vecteurs.o writeFasta.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GeneR.Rnw' 
** testing if installed package can be loaded

* DONE (GeneR)

GeneR.Rcheck/GeneR-Ex.timings:

nameusersystemelapsed
01GeneR0.1130.0130.450
02globalSeg0.0810.0010.083
02globals0.0090.0020.023
Allorf0.0340.0000.034
AtoR0.0000.0010.001
Match0.0080.0020.010
Xor.globalSeg0.0990.0020.106
Xor.segSet0.0150.0020.019
and.globalSeg0.0570.0020.065
and.segSet0.0130.0030.020
appendSeq0.0000.0000.001
assemble0.0060.0010.007
bankDensityProfile0.1540.0230.220
bankSummary0.1340.0360.281
compos.seq0.0070.0020.009
concat0.0010.0000.002
deleteCR0.0040.0030.244
densityProfile0.1960.0100.209
dna.rna0.0020.0010.003
exact.word0.0030.0010.003
fasta.descript0.0040.0020.263
free.seq0.0230.0050.028
getseq0.0010.0010.002
insert0.0010.0000.000
lower0.0070.0000.008
makeIndex0.0040.0020.651
mask0.0010.0000.001
not.globalSeg0.1020.0020.105
not.segSet0.0130.0010.015
or.globalSeg0.0140.0010.015
or.segSet0.0060.0010.006
placestring0.0010.0010.001
plot.globalSeg0.0020.0010.003
posMaskedSeq0.0110.0030.023
randomSeq0.0190.0030.461
read.gbk.location000
readEmblDescript0.0000.0000.001
readseq0.0330.0080.314
relist0.0060.0010.008
revcomp0.0070.0010.007
seqSkew0.0070.0010.008
sequrl0.0020.0010.240
size.globalSeg0.0040.0000.004
sizeseq0.0060.0020.009
sizeseqfasta0.0350.0110.892
sliceSegment0.0030.0000.004
translation0.0070.0030.010
write.fasta0.0080.0010.009
writeEMBL0.0260.0020.031