Package: GeneR

Version: 2.25.1

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings GeneR_2.25.1.tar.gz

StartedAt: 2012-02-29 00:43:38 -0800 (Wed, 29 Feb 2012)

EndedAt: 2012-02-29 00:44:28 -0800 (Wed, 29 Feb 2012)

EllapsedTime: 49.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/GeneR.Rcheck’
* using R Under development (unstable) (2012-01-10 r58085)
* 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 ‘2.25.1’
* 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 ... 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 ... 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-2.10-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-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GeneR_glob.cc -o GeneR_glob.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GeneR_seq.cc -o GeneR_seq.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c complementaire.cc -o complementaire.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c compoSeq.cc -o compoSeq.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c dnaRna.cc -o dnaRna.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c libIndex.cc -o libIndex.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c libStrings.cc -o libStrings.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c makeIndex.cc -o makeIndex.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c masked.cc -o masked.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c misc.cc -o misc.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readEmblDescript.cc -o readEmblDescript.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readIndex.cc -o readIndex.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readLocation.cc -o readLocation.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readSeqFasta.cc -o readSeqFasta.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readSeqGbk.cc -o readSeqGbk.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c seqManip.cc -o seqManip.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c strcasestr.c -o strcasestr.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c translate.cc -o translate.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c upperSeq.cc -o upperSeq.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c vecteurs.cc -o vecteurs.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -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-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/GeneR.Rcheck/GeneR/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GeneR.Rnw’ 
** testing if installed package can be loaded

* DONE (GeneR)

name	user	system	elapsed
01GeneR	0.076	0.004	0.392
02globalSeg	0.060	0.000	0.127
02globals	0.000	0.004	0.022
Allorf	0.024	0.000	0.043
AtoR	0	0	0
Match	0.004	0.000	0.005
Xor.globalSeg	0.076	0.000	0.155
Xor.segSet	0.012	0.000	0.032
and.globalSeg	0.044	0.000	0.043
and.segSet	0.008	0.000	0.010
appendSeq	0.004	0.000	0.001
assemble	0.004	0.000	0.005
bankDensityProfile	0.112	0.000	0.141
bankSummary	0.048	0.004	0.109
compos.seq	0.004	0.000	0.005
concat	0.000	0.000	0.002
deleteCR	0.000	0.004	0.349
densityProfile	0.140	0.004	0.287
dna.rna	0.000	0.000	0.001
exact.word	0.004	0.000	0.002
fasta.descript	0.000	0.000	0.245
free.seq	0.016	0.000	0.021
getseq	0.000	0.000	0.001
insert	0	0	0
lower	0.004	0.000	0.003
makeIndex	0.004	0.004	0.371
mask	0.000	0.000	0.001
not.globalSeg	0.116	0.000	0.228
not.segSet	0.012	0.000	0.031
or.globalSeg	0.012	0.000	0.010
or.segSet	0.008	0.000	0.027
placestring	0.000	0.000	0.001
plot.globalSeg	0.004	0.000	0.002
posMaskedSeq	0.008	0.004	0.025
randomSeq	0.012	0.000	0.261
read.gbk.location	0	0	0
readEmblDescript	0	0	0
readseq	0.032	0.000	0.400
relist	0.004	0.000	0.005
revcomp	0.004	0.000	0.004
seqSkew	0.004	0.000	0.025
sequrl	0.000	0.004	0.382
size.globalSeg	0.004	0.000	0.003
sizeseq	0.008	0.000	0.005
sizeseqfasta	0.020	0.008	0.956
sliceSegment	0.004	0.000	0.015
translation	0.008	0.000	0.006
write.fasta	0.004	0.000	0.005
writeEMBL	0.020	0.000	0.037