GeneR 2.24.0
Y. d'Aubenton-Carafa
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GeneR | | Last Changed Rev: 59920 / Revision: 61898 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ ERROR ] | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GeneR.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-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 'D:/biocbld/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/x64/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 ... ERROR
Running examples in 'GeneR-Ex.R' failed
The error most likely occurred in:
> 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
* installing *source* package 'GeneR' ...
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c GeneR_glob.cc -o GeneR_glob.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c GeneR_seq.cc -o GeneR_seq.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c complementaire.cc -o complementaire.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c compoSeq.cc -o compoSeq.o
x86_64-w64-mingw32-g++ -I"D:/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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c libIndex.cc -o libIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c libStrings.cc -o libStrings.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c makeIndex.cc -o makeIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c masked.cc -o masked.o
x86_64-w64-mingw32-g++ -I"D:/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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c readEmblDescript.cc -o readEmblDescript.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c readIndex.cc -o readIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c readLocation.cc -o readLocation.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c readSeqEmbl.cc -o readSeqEmbl.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c readSeqFasta.cc -o readSeqFasta.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c readSeqGbk.cc -o readSeqGbk.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c seqManip.cc -o seqManip.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -std=gnu99 -mtune=core2 -c strcasestr.c -o strcasestr.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c translate.cc -o translate.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c upperSeq.cc -o upperSeq.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -c vecteurs.cc -o vecteurs.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O2 -Wall -mtune=core2 -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˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/x64
** 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)