GeneR 2.8.0
Y. d'Aubenton-Carafa
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/GeneR | | Last Changed Rev: 27709 / Revision: 30966 | | Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/GeneR.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.8.0'
* 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 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
* creating GeneR-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneR-manual.tex ... OK
* checking GeneR-manual.tex ... OK
installing R.css in D:/biocbld/bbs-2.1-bioc/meat/GeneR.Rcheck
---------- Making package GeneR ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making strcasestr.d from strcasestr.c
making GeneR_glob.d from GeneR_glob.cc
making GeneR_seq.d from GeneR_seq.cc
making complementaire.d from complementaire.cc
making compoSeq.d from compoSeq.cc
making dnaRna.d from dnaRna.cc
making libIndex.d from libIndex.cc
making libStrings.d from libStrings.cc
making makeIndex.d from makeIndex.cc
making masked.d from masked.cc
making misc.d from misc.cc
making readEmblDescript.d from readEmblDescript.cc
making readIndex.d from readIndex.cc
making readLocation.d from readLocation.cc
making readSeqEmbl.d from readSeqEmbl.cc
making readSeqFasta.d from readSeqFasta.cc
making readSeqGbk.d from readSeqGbk.cc
making seqManip.d from seqManip.cc
making translate.d from translate.cc
making upperSeq.d from upperSeq.cc
making vecteurs.d from vecteurs.cc
making writeFasta.d from writeFasta.cc
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c strcasestr.c -o strcasestr.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c GeneR_glob.cc -o GeneR_glob.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c GeneR_seq.cc -o GeneR_seq.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c complementaire.cc -o complementaire.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c compoSeq.cc -o compoSeq.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c dnaRna.cc -o dnaRna.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c libIndex.cc -o libIndex.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c libStrings.cc -o libStrings.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c makeIndex.cc -o makeIndex.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c masked.cc -o masked.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c misc.cc -o misc.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c readEmblDescript.cc -o readEmblDescript.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c readIndex.cc -o readIndex.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c readLocation.cc -o readLocation.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c readSeqEmbl.cc -o readSeqEmbl.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c readSeqFasta.cc -o readSeqFasta.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c readSeqGbk.cc -o readSeqGbk.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c seqManip.cc -o seqManip.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c translate.cc -o translate.o
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c upperSeq.cc -o upperSeq.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c vecteurs.cc -o vecteurs.o
g++-sjlj -Id:/biocbld/bbs-2.1-bioc/R/include -O2 -Wall -c writeFasta.cc -o writeFasta.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include -i GeneR_res.rc -o GeneR_res.o
g++-sjlj -shared -s -o GeneR.dll GeneR.def strcasestr.o 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 translate.o upperSeq.o vecteurs.o writeFasta.o GeneR_res.o -Ld:/biocbld/bbs-2.1-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing demos
installing inst files
installing man source files
installing indices
installing help
>>> 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
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\GeneR.Rcheck\00_pkg_src\GeneR\chm\GeneR.chm
HHC4016: Warning: Cannot open "\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
The following files were not compiled:
preparing package GeneR for lazy loading
adding MD5 sums
* DONE (GeneR)