Package: GeneR

Version: 2.21.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneR_2.21.0.tar.gz

StartedAt: 2011-02-24 19:24:13 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:25:05 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 51.3 seconds

RetCode: 0

Status:  OK

CheckDir: GeneR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/GeneR.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-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
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-2.8-bioc/meat/GeneR.Rcheck/GeneR/libs/i386
** 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	0.160	0.022	2.686
02globalSeg	0.097	0.001	0.098
02globals	0.010	0.002	0.013
Allorf	0.040	0.001	0.042
AtoR	0.001	0.001	0.001
Match	0.007	0.001	0.009
Xor.globalSeg	0.118	0.001	0.120
Xor.segSet	0.019	0.001	0.020
and.globalSeg	0.065	0.001	0.066
and.segSet	0.016	0.001	0.017
appendSeq	0.001	0.000	0.001
assemble	0.008	0.000	0.008
bankDensityProfile	0.192	0.026	0.330
bankSummary	0.102	0.016	0.148
compos.seq	0.006	0.002	0.009
concat	0.002	0.000	0.002
deleteCR	0.000	0.000	0.001
densityProfile	0.224	0.007	0.231
dna.rna	0.002	0.000	0.002
exact.word	0.003	0.000	0.003
fasta.descript	0.001	0.000	0.001
free.seq	0.022	0.004	0.026
getseq	0.002	0.000	0.002
insert	0.001	0.000	0.001
lower	0.005	0.001	0.006
makeIndex	0.000	0.000	0.001
mask	0.003	0.000	0.003
not.globalSeg	0.115	0.001	0.117
not.segSet	0.016	0.001	0.016
or.globalSeg	0.014	0.001	0.015
or.segSet	0.006	0.001	0.007
placestring	0.001	0.001	0.001
plot.globalSeg	0.002	0.000	0.003
posMaskedSeq	0.014	0.004	0.033
randomSeq	0.004	0.001	0.004
read.gbk.location	0.000	0.000	0.001
readEmblDescript	0.000	0.001	0.001
readseq	0.009	0.000	0.009
relist	0.011	0.001	0.012
revcomp	0.006	0.000	0.006
seqSkew	0.008	0.001	0.008
sequrl	0.000	0.000	0.001
size.globalSeg	0.005	0.001	0.005
sizeseq	0.007	0.002	0.009
sizeseqfasta	0.002	0.000	0.003
sliceSegment	0.004	0.000	0.005
translation	0.010	0.003	0.013
write.fasta	0.006	0.001	0.015
writeEMBL	0.053	0.003	0.114