GeneR 2.14.0
Y. d'Aubenton-Carafa
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/GeneR | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/GeneR.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.14.0'
* 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 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 name space can be loaded with stated dependencies ... 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 files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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
making DLL ...
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c GeneR_glob.cc -o GeneR_glob.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c GeneR_seq.cc -o GeneR_seq.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c complementaire.cc -o complementaire.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c compoSeq.cc -o compoSeq.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c dnaRna.cc -o dnaRna.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c libIndex.cc -o libIndex.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c libStrings.cc -o libStrings.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c makeIndex.cc -o makeIndex.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c masked.cc -o masked.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -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++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c readEmblDescript.cc -o readEmblDescript.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c readIndex.cc -o readIndex.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c readLocation.cc -o readLocation.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c readSeqFasta.cc -o readSeqFasta.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c readSeqGbk.cc -o readSeqGbk.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c seqManip.cc -o seqManip.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c strcasestr.c -o strcasestr.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c translate.cc -o translate.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c upperSeq.cc -o upperSeq.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c vecteurs.cc -o vecteurs.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c writeFasta.cc -o writeFasta.o
g++ -shared -s -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-2.4-bioc/R/bin -lR
... done
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> Building/Updating help pages for package 'GeneR'
Formats: text html latex example chm
01GeneR text html latex example chm
02globalSeg text html latex example chm
02globals text html latex example chm
Allorf text html latex example chm
AtoR text html latex example chm
Match text html latex example chm
Xor.globalSeg text html latex example chm
Xor.segSet text html latex example chm
and.globalSeg text html latex example chm
and.segSet text html latex example chm
appendSeq text html latex example chm
as.globalSeg text html latex chm
as.segSet text html latex chm
assemble text html latex example chm
bankDensityProfile text html latex example chm
bankSummary text html latex example chm
compos.seq text html latex example chm
concat text html latex example chm
deleteCR text html latex example chm
densityProfile text html latex example chm
dna.rna text html latex example chm
exact.word text html latex example chm
fasta.descript text html latex example chm
free.seq text html latex example chm
getAccn text html latex chm
getParam text html latex chm
getseq text html latex example chm
indexfasta text html latex chm
insert text html latex example chm
lower text html latex example chm
makeIndex text html latex example chm
mask text html latex example chm
not.globalSeg text html latex example chm
not.segSet text html latex example chm
or.globalSeg text html latex example chm
or.segSet text html latex example chm
placestring text html latex example chm
plot.globalSeg text html latex example chm
posMaskedSeq text html latex example chm
randomSeq text html latex example chm
read.gbk.location text html latex example chm
readEmblDescript text html latex example chm
readseq text html latex example chm
relist text html latex example chm
revcomp text html latex example chm
seqSkew text html latex example chm
sequrl text html latex example chm
setAccn text html latex chm
setParam text html latex chm
size.globalSeg text html latex example chm
sizeseq text html latex example chm
sizeseqfasta text html latex example chm
sliceSegment text html latex example chm
translation text html latex example chm
write.fasta text html latex example chm
writeEMBL text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\GENER~1.RCH\00_PKG~1\GeneR\chm\GeneR.chm
Compile time: 0 minutes, 1 second
57 Topics
329 Local links
0 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\GENER~1.RCH\00_PKG~1\GeneR\chm\GeneR.chm, 78,074 bytes
Compression decreased file by 112,642 bytes.
** building package indices ...
** MD5 sums
* DONE (GeneR)