Package: GeneRegionScan

Version: 1.9.7

Command: mkdir GeneRegionScan.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneRegionScan.buildbin-libdir GeneRegionScan_1.9.7.tar.gz >GeneRegionScan-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=GeneRegionScan.buildbin-libdir --install="check:GeneRegionScan-install.out" --force-multiarch --no-vignettes --timings GeneRegionScan_1.9.7.tar.gz && mv GeneRegionScan.buildbin-libdir/* GeneRegionScan.Rcheck/ && rmdir GeneRegionScan.buildbin-libdir

StartedAt: 2011-07-07 05:03:04 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:11:41 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 516.5 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GeneRegionScan.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneRegionScan/DESCRIPTION' ... OK
* this is package 'GeneRegionScan' version '1.9.7'
* 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 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

install for i386

* installing *source* package 'GeneRegionScan' ...
** R
** data
** exec
** 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")'.

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

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GeneRegionScan.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'GeneRegionScan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneRegionScan' as GeneRegionScan_1.9.7.zip

* DONE (GeneRegionScan)

name	user	system	elapsed
addSnpPdata	0	0	0
checkForFileInPath	0.01	0.03	0.04
doProbeLinear	3.26	0.00	3.26
doProbeTTest	0.63	0.00	0.63
exampleProbeLevelSet	0.03	0.00	0.03
excludeDoubleMatchingProbes	0	0	0
exonStructure	12.48	0.00	12.48
findProbePositions	0.55	0.00	0.54
findSequenceInGenome	0	0	0
geneRegionScan	88.06	0.07	89.44
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	0.03	0.00	0.03
getServerProbeIntensities	0	0	0
plotCoexpression	62.37	0.43	62.92
plotOnGene	18.20	0.03	18.25
readGeneInput	0	0	0
translateSampleNames	0.08	0.00	0.08