Package: GeneR

Version: 2.24.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GeneR_2.24.0.tar.gz

StartedAt: 2012-01-09 03:19:05 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 03:20:00 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 55.2 seconds

RetCode: 0

Status:  OK

CheckDir: GeneR.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GeneR.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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 'E:/biocbld/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/i386/GeneR.dll':
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (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"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c GeneR_glob.cc -o GeneR_glob.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c GeneR_seq.cc -o GeneR_seq.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c complementaire.cc -o complementaire.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c compoSeq.cc -o compoSeq.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -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"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c libIndex.cc -o libIndex.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c libStrings.cc -o libStrings.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c makeIndex.cc -o makeIndex.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c masked.cc -o masked.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -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"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c readEmblDescript.cc -o readEmblDescript.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c readIndex.cc -o readIndex.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c readLocation.cc -o readLocation.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c readSeqEmbl.cc -o readSeqEmbl.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c readSeqFasta.cc -o readSeqFasta.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c readSeqGbk.cc -o readSeqGbk.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c seqManip.cc -o seqManip.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c strcasestr.c -o strcasestr.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c translate.cc -o translate.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c upperSeq.cc -o upperSeq.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c vecteurs.cc -o vecteurs.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c writeFasta.cc -o writeFasta.o
g++ -shared -s -static-libgcc -o GeneR.dll tmp.def 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 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/i386
** 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	0.01	0.03	0.81
02globalSeg	0.05	0.00	0.05
02globals	0	0	0
Allorf	0.03	0.00	0.03
AtoR	0	0	0
Match	0	0	0
Xor.globalSeg	0.06	0.00	0.07
Xor.segSet	0	0	0
and.globalSeg	0.02	0.01	0.03
and.segSet	0.01	0.00	0.01
appendSeq	0	0	0
assemble	0	0	0
bankDensityProfile	0.13	0.02	0.53
bankSummary	0.09	0.05	0.60
compos.seq	0.02	0.00	0.01
concat	0	0	0
deleteCR	0.00	0.00	0.19
densityProfile	0.11	0.00	0.11
dna.rna	0	0	0
exact.word	0	0	0
fasta.descript	0.00	0.00	0.17
free.seq	0.03	0.00	0.03
getseq	0	0	0
insert	0	0	0
lower	0.01	0.00	0.01
makeIndex	0.00	0.00	0.19
mask	0	0	0
not.globalSeg	0.07	0.00	0.06
not.segSet	0.01	0.00	0.02
or.globalSeg	0	0	0
or.segSet	0	0	0
placestring	0	0	0
plot.globalSeg	0	0	0
posMaskedSeq	0.01	0.00	0.01
randomSeq	0.00	0.02	0.17
read.gbk.location	0	0	0
readEmblDescript	0	0	0
readseq	0.02	0.01	0.36
relist	0.02	0.00	0.02
revcomp	0	0	0
seqSkew	0	0	0
sequrl	0.00	0.02	1.09
size.globalSeg	0	0	0
sizeseq	0	0	0
sizeseqfasta	0.06	0.00	2.77
sliceSegment	0	0	0
translation	0.01	0.00	0.01
write.fasta	0	0	0
writeEMBL	0.02	0.00	0.02