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Package 159/436HostnameOS / ArchBUILDCHECKBUILD BIN
GeneR 2.21.0
Y. d'Aubenton-Carafa
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneR
Last Changed Rev: 50295 / Revision: 53255
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / 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 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: GeneR
Version: 2.21.0
Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneR_2.21.0.tar.gz
StartedAt: 2011-02-24 19:48:36 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 19:49:13 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 36.8 seconds
RetCode: 1
Status:  ERROR  
CheckDir: GeneR.Rcheck
Warnings: NA

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/GeneR.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 '2.21.0'
* 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 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 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 ... OK
* 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

GeneR.Rcheck/00install.out:

* installing *source* package 'GeneR' ...
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c GeneR_glob.cc -o GeneR_glob.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c GeneR_seq.cc -o GeneR_seq.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c complementaire.cc -o complementaire.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c compoSeq.cc -o compoSeq.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -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˜1.8-B/R/include"          -O2 -Wall  -c libIndex.cc -o libIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c libStrings.cc -o libStrings.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c makeIndex.cc -o makeIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c masked.cc -o masked.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -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˜1.8-B/R/include"          -O2 -Wall  -c readEmblDescript.cc -o readEmblDescript.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c readIndex.cc -o readIndex.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c readLocation.cc -o readLocation.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c readSeqEmbl.cc -o readSeqEmbl.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c readSeqFasta.cc -o readSeqFasta.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c readSeqGbk.cc -o readSeqGbk.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c seqManip.cc -o seqManip.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c strcasestr.c -o strcasestr.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c translate.cc -o translate.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c upperSeq.cc -o upperSeq.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c vecteurs.cc -o vecteurs.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/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˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/GeneR.Rcheck/GeneR/libs/x64
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneR)

GeneR.Rcheck/GeneR-Ex.timings:

nameusersystemelapsed
01GeneR0.140.032.59
02globalSeg0.050.010.07
02globals0.020.000.01
Allorf0.010.000.02
AtoR000
Match000
Xor.globalSeg0.080.000.08
Xor.segSet0.010.000.02
and.globalSeg0.040.000.03
and.segSet0.010.000.01
appendSeq000
assemble0.020.000.02
bankDensityProfile0.060.020.53