Package: htSeqTools

Version: 0.99.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch htSeqTools_0.99.1.tar.gz

StartedAt: 2011-07-07 02:18:50 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:20:59 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 128.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: htSeqTools.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/htSeqTools.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'htSeqTools/DESCRIPTION' ... OK
* this is package 'htSeqTools' version '0.99.1'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: multicore
* checking if this is a source package ... OK
* checking whether package 'htSeqTools' 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 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'htSeqTools-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot-methods
> ### Title: Methods for Function plot in Package 'htSeq'
> ### Aliases: plot,cmdsFit-method plot,gridCover-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> d <- matrix(c(0,5,10,5,0,15,10,15,0),byrow=TRUE,ncol=3)
> rownames(d) <- colnames(d) <- letters[1:3]
> fit1 <- cmdsFit(d)
Warning in cmdscale(as.dist(d), k = k) :
  only 1 of the first 2 eigenvalues are > 0
> plot(fit1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' and 'y' lengths differ
Calls: plot -> plot -> plot -> plot -> plot.default -> xy.coords
Execution halted

* installing *source* package 'htSeqTools' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
Creating a generic function for "plot" from package "graphics" in package "htSeqTools"
Creating a generic function for "lines" from package "graphics" in package "htSeqTools"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'htSeqTools.Rnw' 
** testing if installed package can be loaded

* DONE (htSeqTools)

name	user	system	elapsed
alignPeaks	0.28	0.01	0.32
cmds	4.72	0.02	4.75
cmdsFit-class	0	0	0
cmdsFit	0	0	0
countHitsWindow	0.07	0.00	0.06
coverageDiff	0.14	0.00	0.14
enrichedChrRegions	1.68	0.00	1.70
enrichedPeaks	0.63	0.00	0.63
enrichedRegions	0.25	0.00	0.25
extendRanges	0.17	0.00	0.17
fdrEnrichedCounts	0.20	0.00	0.25
filterDuplReads	0.58	0.00	0.58
giniCoverage	0.39	0.00	0.39
gridCover-class	0	0	0
htSample	0.55	0.03	0.59
islandCounts	0.28	0.00	0.28
listOverlap	0	0	0
mergeRegions	0.06	0.00	0.06