Package: GeneRegionScan

Version: 1.10.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GeneRegionScan_1.10.0.tar.gz

StartedAt: 2012-03-24 00:32:28 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:37:18 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 290.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneRegionScan.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 ‘GeneRegionScan/DESCRIPTION’ ... OK
* this is package ‘GeneRegionScan’ version ‘1.10.0’
* 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 ‘GeneRegionScan’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.4Mb
  sub-directories of 1Mb or more:
    exec  19.7Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... 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 vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

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

* DONE (GeneRegionScan)

name	user	system	elapsed
addSnpPdata	0	0	0
checkForFileInPath	0.020	0.004	0.026
doProbeLinear	2.680	0.016	2.700
doProbeTTest	0.488	0.004	0.493
exampleProbeLevelSet	0.036	0.008	0.043
excludeDoubleMatchingProbes	0	0	0
exonStructure	10.477	0.032	10.637
findProbePositions	0.904	0.012	0.913
findSequenceInGenome	0	0	0
geneRegionScan	73.008	14.140	88.627
getLocalMetaprobeIntensities	0.000	0.000	0.001
getLocalProbeIntensities	0	0	0
getMetaprobesetsFromRegionOfInterest	0	0	0
getProbeLevelAnnotationForExonArrays	0	0	0
getProbesetsFromMetaprobeset	0	0	0
getProbesetsFromRegionOfInterest	0	0	0
getSequence	0.032	0.000	0.031
getServerProbeIntensities	0	0	0
plotCoexpression	51.283	12.029	63.976
plotOnGene	17.274	0.024	17.327
readGeneInput	0	0	0
translateSampleNames	0.064	0.000	0.065