GeneR 2.18.1
Y. d'Aubenton-Carafa
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/GeneR | | Last Changed Rev: 47904 / Revision: 49923 | | Last Changed Date: 2010-07-03 07:59:58 -0700 (Sat, 03 Jul 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ ERROR ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/GeneR.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.18.1'
* 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 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 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 ... ERROR
Running examples in 'GeneR-Ex.R' failed.
The error most likely occurred in:
> ### * bankSummary
>
> flush(stderr()); flush(stdout())
>
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bankSummary
> ### Title: Computes informations on all a bank file
> ### Aliases: bankSummary
> ### Keywords: utilities
>
> ### ** Examples
>
> for(i in 1:8)
+ {
+ s=randomSeq(n=100)
+ placeString(s,seqno=0)
+ writeFasta("toto_norm.fa",append=TRUE,name=i)
+ }
> bankSummary(file="toto_norm.fa")
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in fun() : error in the transformation of the limits
name T C A G X
1 1 0.2 0.27 0.32 0.21 0
2 1 0.2 0.27 0.32 0.21 0
3 10 0.2 0.27 0.32 0.21 0
4 2 0.2 0.27 0.32 0.21 0
5 2 0.2 0.27 0.32 0.21 0
6 3 0.2 0.27 0.32 0.21 0
7 3 0.2 0.27 0.32 0.21 0
8 4 0.2 0.27 0.32 0.21 0
9 4 0.2 0.27 0.32 0.21 0
10 5 0.2 0.27 0.32 0.21 0
11 5 0.2 0.27 0.32 0.21 0
12 6 0.2 0.27 0.32 0.21 0
13 6 0.2 0.27 0.32 0.21 0
14 7 0.2 0.27 0.32 0.21 0
15 7 0.2 0.27 0.32 0.21 0
16 8 0.2 0.27 0.32 0.21 0
17 8 0.2 0.27 0.32 0.21 0
18 9 0.2 0.27 0.32 0.21 0
> bankSummary(file="toto_norm.fa",fun=seqSkew)
[1] "<readseq paramFromIndex error>"
Warning in .transf.limites(seqno, limites) : NA in from or To
Warning in compoSeq(seqno = seqno, from = from, to = to, strand = strand, :
error in the transformation of the limits
Warning in is.na(compos[1]) :
is.na() applied to non-(list or vector) of type 'NULL'
Error in if (!is.na(compos[1])) { : argument is of length zero
Calls: bankSummary -> fun
Execution halted
* install options are ' --no-html'
* installing *source* package 'GeneR' ...
** libs
making DLL ...
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c GeneR_glob.cc -o GeneR_glob.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c GeneR_seq.cc -o GeneR_seq.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c complementaire.cc -o complementaire.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c compoSeq.cc -o compoSeq.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c dnaRna.cc -o dnaRna.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c libIndex.cc -o libIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c libStrings.cc -o libStrings.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c makeIndex.cc -o makeIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c masked.cc -o masked.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-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
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c readEmblDescript.cc -o readEmblDescript.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c readIndex.cc -o readIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c readLocation.cc -o readLocation.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c readSeqEmbl.cc -o readSeqEmbl.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c readSeqFasta.cc -o readSeqFasta.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c readSeqGbk.cc -o readSeqGbk.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c seqManip.cc -o seqManip.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c strcasestr.c -o strcasestr.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c translate.cc -o translate.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c upperSeq.cc -o upperSeq.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c vecteurs.cc -o vecteurs.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c writeFasta.cc -o writeFasta.o
x86_64-w64-mingw32-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 -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/GeneR.Rcheck/GeneR/libs/x64
... done
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (GeneR)