Package: GeneRegionScan

Version: 1.4.0

Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneRegionScan_1.4.0.tar.gz

StartedAt: 2010-10-04 16:55:34 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:00:44 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 310.4 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/GeneRegionScan.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneRegionScan/DESCRIPTION' ... OK
* this is package 'GeneRegionScan' version '1.4.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneRegionScan' 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 ... 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

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

Welcome to Bioconductor

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

Loading required package: IRanges

Attaching package: 'IRanges'

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

    updateObject

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

    Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
    rbind, rep.int, table

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneRegionScan)

name	user	system	elapsed
addSnpPdata	0	0	0
checkForFileInPath	0.05	0.00	0.34
doProbeLinear	3.54	0.00	3.55
doProbeTTest	0.63	0.00	0.63
exampleProbeLevelSet	0.03	0.01	0.04
excludeDoubleMatchingProbes	0	0	0
exonStructure	14.87	0.00	14.93
findSequenceInGenome	0	0	0
geneRegionScan	97.83	0.07	98.07
getLocalMetaprobeIntensities	0	0	0
getLocalProbeIntensities	0	0	0
getMetaprobesetsFromRegionOfInterest	0	0	0
getProbeLevelAnnotationForExonArrays	0	0	0
getProbesetsFromMetaprobeset	0	0	0
getProbesetsFromRegionOfInterest	0	0	0
getSequence	0.02	0.03	0.05
getServerProbeIntensities	0	0	0
plotCoexpression	70.33	3.62	74.08
plotOnGene	23.62	0.00	23.70
readGeneInput	0	0	0
translateSampleNames	0.11	0.00	0.11