Package: leeBamViews

Version: 0.99.16

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings leeBamViews_0.99.16.tar.gz

StartedAt: 2012-03-19 13:46:00 -0700 (Mon, 19 Mar 2012)

EndedAt: 2012-03-19 13:48:32 -0700 (Mon, 19 Mar 2012)

EllapsedTime: 151.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: leeBamViews.Rcheck

Warnings: NA

* using log directory ‘/loc/home/biocbuild/bbs-2.9-data-experiment/meat/leeBamViews.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leeBamViews/DESCRIPTION’ ... OK
* this is package ‘leeBamViews’ version ‘0.99.16’
* 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 ‘leeBamViews’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    bam  10.1Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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 ... 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 ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘lbvtest.R’
 ERROR
Running the tests in ‘tests/lbvtest.R’ failed.
Last 13 lines of output:
  +  grm = makeGeneRegion(start, end, chromosome=martchr,
  +        strand="-", biomart=mart, dp=DisplayPars(plotId=TRUE,
  +        idRotation=0, idColor="black"))
  +  covtrs[[length(covtrs)+1]] = gr
  +  covtrs[[length(covtrs)+1]] = makeGenomeAxis()
  +  covtrs[[length(covtrs)+1]] = grm
  +  gdPlot( covtrs, minBase=start[1], maxBase=end[1] )
  + }
  > 
  > 
  > NN = GRanges(IRanges(start=START,end=END), seqnames="Scchr13")
  > plotStrains(bs1, NN, 800000, 900000, LETTERS[1:8], mart, "XIII", seqname="Scchr13")
  Execution halted

* installing *source* package ‘leeBamViews’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘leeViews.Rnw’ 
** testing if installed package can be loaded

* DONE (leeBamViews)

name	user	system	elapsed
bs1	1.312	0.132	1.533
leeRPKM	0.056	0.004	0.061
leeUnn	0.144	0.008	0.161
tabulateReads	7.461	0.332	8.025
totalReadCounts	1.432	0.020	1.449