Package: GeneR

Version: 2.21.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings GeneR_2.21.0.tar.gz

StartedAt: 2011-02-24 19:45:45 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:46:18 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 32.5 seconds

RetCode: 0

Status:  OK

CheckDir: GeneR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/GeneR.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘2.21.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘GeneR’ can be installed ... 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 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 ... 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 ... 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 use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘GeneR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c GeneR_glob.cc -o GeneR_glob.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c GeneR_seq.cc -o GeneR_seq.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c complementaire.cc -o complementaire.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c compoSeq.cc -o compoSeq.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c dnaRna.cc -o dnaRna.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c libIndex.cc -o libIndex.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c libStrings.cc -o libStrings.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c makeIndex.cc -o makeIndex.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c masked.cc -o masked.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c misc.cc -o misc.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readEmblDescript.cc -o readEmblDescript.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readIndex.cc -o readIndex.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readLocation.cc -o readLocation.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqFasta.cc -o readSeqFasta.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqGbk.cc -o readSeqGbk.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c seqManip.cc -o seqManip.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c strcasestr.c -o strcasestr.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c translate.cc -o translate.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c upperSeq.cc -o upperSeq.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c vecteurs.cc -o vecteurs.o
g++ -I/home/biocbuild/bbs-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/GeneR.Rcheck/GeneR/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneR)

name	user	system	elapsed
01GeneR	0.096	0.004	3.002
02globalSeg	0.068	0.000	0.126
02globals	0.008	0.000	0.008
Allorf	0.024	0.000	0.023
AtoR	0.004	0.000	0.000
Match	0.004	0.000	0.004
Xor.globalSeg	0.076	0.000	0.076
Xor.segSet	0.008	0.004	0.012
and.globalSeg	0.040	0.000	0.041
and.segSet	0.012	0.000	0.010
appendSeq	0	0	0
assemble	0.004	0.000	0.005
bankDensityProfile	0.116	0.020	0.142
bankSummary	0.096	0.012	0.111
compos.seq	0.004	0.000	0.006
concat	0.000	0.004	0.001
deleteCR	0	0	0
densityProfile	0.156	0.000	0.157
dna.rna	0.004	0.000	0.001
exact.word	0.004	0.000	0.004
fasta.descript	0	0	0
free.seq	0.012	0.008	0.017
getseq	0.000	0.000	0.001
insert	0	0	0
lower	0.004	0.004	0.005
makeIndex	0	0	0
mask	0.000	0.000	0.001
not.globalSeg	0.080	0.000	0.081
not.segSet	0.012	0.000	0.012
or.globalSeg	0.012	0.000	0.011
or.segSet	0.004	0.000	0.004
placestring	0.000	0.000	0.001
plot.globalSeg	0.000	0.000	0.002
posMaskedSeq	0.012	0.000	0.008
randomSeq	0.000	0.000	0.002
read.gbk.location	0.000	0.000	0.001
readEmblDescript	0	0	0
readseq	0.000	0.000	0.002
relist	0.004	0.004	0.005
revcomp	0.004	0.000	0.003
seqSkew	0.004	0.004	0.005
sequrl	0	0	0
size.globalSeg	0.004	0.000	0.003
sizeseq	0.004	0.000	0.005
sizeseqfasta	0.004	0.000	0.001
sliceSegment	0.004	0.000	0.003
translation	0.004	0.004	0.006
write.fasta	0.004	0.000	0.004
writeEMBL	0.020	0.000	0.019