Package: GeneR

Version: 2.23.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GeneR_2.23.0.tar.gz

StartedAt: 2011-05-09 12:34:11 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:34:43 -0700 (Mon, 09 May 2011)

EllapsedTime: 32.6 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 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘2.23.0’
* 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 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 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) and $(LAPACK_LIBS) ... 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

* installing *source* package ‘GeneR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -Wall -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 -Wall -c complementaire.cc -o complementaire.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c compoSeq.cc -o compoSeq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c dnaRna.cc -o dnaRna.o
dnaRna.cc: In function ‘void dna_rna(int*, int*, int*, int*, int*)’:
dnaRna.cc:62:15: warning: value computed is not used
dnaRna.cc:63:13: warning: value computed is not used
dnaRna.cc: In function ‘void rna_dna(int*, int*, int*, int*, int*)’:
dnaRna.cc:108:15: warning: value computed is not used
dnaRna.cc:109:13: warning: value computed is not used
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c libIndex.cc -o libIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c libStrings.cc -o libStrings.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c makeIndex.cc -o makeIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c masked.cc -o masked.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c misc.cc -o misc.o
misc.cc: In function ‘SEXPREC* str_to_nbstr(SEXPREC*, SEXPREC*)’:
misc.cc:31:18: warning: ‘multiple’ may be used uninitialized in this function
misc.cc:30:8: warning: ‘ans’ may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readEmblDescript.cc -o readEmblDescript.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readIndex.cc -o readIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readLocation.cc -o readLocation.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readSeqFasta.cc -o readSeqFasta.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readSeqGbk.cc -o readSeqGbk.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -Wall -c strcasestr.c -o strcasestr.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c translate.cc -o translate.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c upperSeq.cc -o upperSeq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c vecteurs.cc -o vecteurs.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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	0.112	0.008	0.294
02globalSeg	0.060	0.000	0.062
02globals	0.004	0.004	0.007
Allorf	0.024	0.000	0.025
AtoR	0.004	0.000	0.001
Match	0.004	0.000	0.004
Xor.globalSeg	0.080	0.000	0.082
Xor.segSet	0.008	0.000	0.010
and.globalSeg	0.040	0.000	0.042
and.segSet	0.012	0.000	0.011
appendSeq	0	0	0
assemble	0.004	0.000	0.005
bankDensityProfile	0.120	0.024	0.153
bankSummary	0.100	0.024	0.139
compos.seq	0.004	0.000	0.005
concat	0.000	0.000	0.001
deleteCR	0.004	0.000	0.259
densityProfile	0.152	0.000	0.150
dna.rna	0.000	0.000	0.001
exact.word	0.000	0.000	0.002
fasta.descript	0.004	0.000	0.178
free.seq	0.020	0.000	0.019
getseq	0.000	0.000	0.001
insert	0.000	0.000	0.001
lower	0.004	0.000	0.004
makeIndex	0.004	0.000	0.176
mask	0	0	0
not.globalSeg	0.076	0.000	0.076
not.segSet	0.004	0.004	0.009
or.globalSeg	0.008	0.000	0.009
or.segSet	0.004	0.000	0.004
placestring	0.000	0.000	0.001
plot.globalSeg	0.004	0.000	0.001
posMaskedSeq	0.04	0.00	0.04
randomSeq	0.012	0.000	0.188
read.gbk.location	0	0	0
readEmblDescript	0.004	0.000	0.000
readseq	0.020	0.008	0.299
relist	0.008	0.000	0.007
revcomp	0.004	0.000	0.003
seqSkew	0.004	0.000	0.004
sequrl	0.000	0.004	0.176
size.globalSeg	0.004	0.000	0.003
sizeseq	0.004	0.000	0.004
sizeseqfasta	0.020	0.004	0.829
sliceSegment	0.004	0.000	0.003
translation	0.004	0.000	0.005
write.fasta	0.008	0.000	0.005
writeEMBL	0.020	0.000	0.018