Package: GeneR

Version: 2.24.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GeneR_2.24.0.tar.gz

StartedAt: 2012-03-24 00:31:51 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:32:27 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 35.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/GeneR.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 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 ‘GeneR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c GeneR_glob.cc -o GeneR_glob.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c GeneR_seq.cc -o GeneR_seq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c complementaire.cc -o complementaire.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c compoSeq.cc -o compoSeq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c dnaRna.cc -o dnaRna.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c libIndex.cc -o libIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c libStrings.cc -o libStrings.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c makeIndex.cc -o makeIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c masked.cc -o masked.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c misc.cc -o misc.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readEmblDescript.cc -o readEmblDescript.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readIndex.cc -o readIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readLocation.cc -o readLocation.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqFasta.cc -o readSeqFasta.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqGbk.cc -o readSeqGbk.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c seqManip.cc -o seqManip.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c strcasestr.c -o strcasestr.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c translate.cc -o translate.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c upperSeq.cc -o upperSeq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c vecteurs.cc -o vecteurs.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c writeFasta.cc -o writeFasta.o
g++ -shared -L/usr/local/lib64 -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 -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs
** 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)

name	user	system	elapsed
01GeneR	0.092	0.008	0.422
02globalSeg	0.088	0.000	0.088
02globals	0.012	0.004	0.010
Allorf	0.032	0.000	0.031
AtoR	0	0	0
Match	0.004	0.000	0.007
Xor.globalSeg	0.084	0.000	0.086
Xor.segSet	0.008	0.000	0.010
and.globalSeg	0.052	0.000	0.055
and.segSet	0.008	0.004	0.014
appendSeq	0	0	0
assemble	0.008	0.000	0.006
bankDensityProfile	0.108	0.000	0.112
bankSummary	0.060	0.004	0.068
compos.seq	0.004	0.004	0.006
concat	0.000	0.000	0.001
deleteCR	0.004	0.004	0.317
densityProfile	0.160	0.000	0.159
dna.rna	0.004	0.000	0.001
exact.word	0.004	0.000	0.002
fasta.descript	0.008	0.000	0.252
free.seq	0.020	0.004	0.022
getseq	0.000	0.004	0.001
insert	0	0	0
lower	0.008	0.000	0.005
makeIndex	0.008	0.000	0.317
mask	0.000	0.000	0.001
not.globalSeg	0.128	0.016	0.221
not.segSet	0.012	0.000	0.016
or.globalSeg	0.008	0.000	0.015
or.segSet	0.008	0.000	0.008
placestring	0.000	0.000	0.001
plot.globalSeg	0.004	0.000	0.002
posMaskedSeq	0.008	0.000	0.009
randomSeq	0.016	0.000	0.278
read.gbk.location	0	0	0
readEmblDescript	0.000	0.000	0.001
readseq	0.032	0.000	0.357
relist	0.004	0.000	0.010
revcomp	0.008	0.000	0.006
seqSkew	0.000	0.004	0.006
sequrl	0.004	0.000	0.415
size.globalSeg	0.004	0.000	0.004
sizeseq	0.008	0.000	0.006
sizeseqfasta	0.020	0.004	0.933
sliceSegment	0.000	0.000	0.002
translation	0.004	0.004	0.006
write.fasta	0.004	0.000	0.005
writeEMBL	0.020	0.004	0.022