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Package 214/553HostnameOS / ArchBUILDCHECKBUILD BIN
GeneRegionScan 1.12.0
Lasse Folkersen
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/GeneRegionScan
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GeneRegionScan
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.12.0.tar.gz
StartedAt: 2012-09-24 00:15:26 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:21:22 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 356.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneRegionScan.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/GeneRegionScan.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneRegionScan/DESCRIPTION' ... OK
* this is package 'GeneRegionScan' version '1.12.0'
* 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 ... NOTE
readGeneInput: warning in readFASTA(gene, strip.desc = FALSE): partial
  argument match of 'strip.desc' to 'strip.descs'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/GeneRegionScan.Rcheck/00check.log'
for details.

GeneRegionScan.Rcheck/00install.out:

* installing *source* package 'GeneRegionScan' ...
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GeneRegionScan.Rnw' 
** testing if installed package can be loaded

* DONE (GeneRegionScan)

GeneRegionScan.Rcheck/GeneRegionScan-Ex.timings:

nameusersystemelapsed
addSnpPdata0.0000.0010.000
checkForFileInPath0.0150.0080.094
doProbeLinear2.8230.0222.846
doProbeTTest0.5510.0040.557
exampleProbeLevelSet0.0280.0120.040
excludeDoubleMatchingProbes000
exonStructure10.548 0.02610.575
findProbePositions0.4300.0050.435
findSequenceInGenome000
geneRegionScan 90.692 22.654114.757
getLocalMetaprobeIntensities000
getLocalProbeIntensities000
getMetaprobesetsFromRegionOfInterest0.0000.0010.001
getProbeLevelAnnotationForExonArrays000
getProbesetsFromMetaprobeset000
getProbesetsFromRegionOfInterest000
getSequence0.0170.0070.025
getServerProbeIntensities000
plotCoexpression62.48820.84483.758
plotOnGene16.146 0.04716.239
readGeneInput000
translateSampleNames0.0680.0050.072