Package: marray

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.30.0.tar.gz

StartedAt: 2011-10-20 15:51:23 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:53:43 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 139.7 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/marray.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'marray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc         5.8Mb
    swirldata   5.5Mb
* 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
findID: no visible binding for global variable 'gnames'
findID: no visible global function definition for 'phenoData'
htmlPage: no visible binding for global variable 'Gnames'
maTwoSamples: no visible global function definition for 'gpTools'
scale.na: no visible global function definition for 'applyy'
widget.TwoSamples: no visible global function definition for
  'widgetRender'
widget.mapGeneInfo: no visible global function definition for
  'widgetRender'
* checking Rd files ... NOTE
prepare_Rd: cbind.Rd:35-36: Dropping empty section \value
prepare_Rd: cbind.Rd:41-42: Dropping empty section \examples
prepare_Rd: maCompLayout.Rd:19-21: Dropping empty section \details
prepare_Rd: read.marrayInfo.Rd:30-32: Dropping empty section \details
prepare_Rd: read.marrayLayout.Rd:35: Dropping empty section \details
prepare_Rd: read.marrayLayout.Rd:42: Dropping empty section \note
prepare_Rd: read.marrayRaw.Rd:73-75: Dropping empty section \details
prepare_Rd: showLargeObject.Rd:26-27: Dropping empty section \examples
* 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 ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'marrayNorm.pdf' from 1539Kb to 346Kb
     compacted 'marrayPlots.pdf' from 3046Kb to 448Kb
  consider running tools::compactPDF() on these files
* 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 'marray' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (marray)

name	user	system	elapsed
boxplot	0.823	0.204	1.046
checkTargetInfo	0.190	0.034	0.225
dim	0.003	0.000	0.003
findID	0.165	0.024	0.191
htmlPage	0.162	0.045	0.210
image	0.089	0.004	0.094
ma2D	0.000	0.001	0.000
maBoxplot	0.000	0.000	0.001
maColorBar	0.019	0.001	0.020
maCompCoord	0.001	0.001	0.002
maCompInd	0.006	0.002	0.007
maCompLayout	0.011	0.000	0.012
maCompNormA	0	0	0
maCompPlate	0.015	0.004	0.019
maCoord2Ind	0.005	0.001	0.006
maDefaultPar	0.000	0.001	0.001
maDotsDefaults	0.002	0.000	0.002
maDotsMatch	0.002	0.000	0.002
maGenControls	0.332	0.020	0.353
maGeneTable	0.112	0.016	0.132
maImage	1.456	0.379	1.895
maImage.func	0	0	0
maInd2Coord	0.006	0.002	0.008
maLegendLines	0.000	0.001	0.000
maLoess	0.000	0.000	0.001
maLoessLines	0	0	0
maMAD	0.000	0.000	0.001
maMed	0.001	0.000	0.000
maNorm	4.049	0.322	4.425
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	27.010	1.171	28.434
maNormMed	0.000	0.000	0.001
maNormScale	0.566	0.243	0.822
maNum2Logic	0.000	0.000	0.001
maPalette	0.010	0.001	0.010
maPlot	4.222	0.407	4.680
maPlot.func	0	0	0
maSelectGnames	0.014	0.000	0.016
maText	0	0	0
maTop	0.000	0.000	0.001
mapGeneInfo	0.001	0.001	0.001
marrayInfo-class	0.000	0.000	0.001
marrayLayout-class	0.001	0.000	0.000
marrayNorm-class	0.544	0.219	0.781
marrayRaw-class	0.297	0.064	0.364
opVersionID	0.001	0.000	0.002
plotMA	3.845	0.279	4.181
read.Galfile	0.087	0.024	0.112
read.marrayInfo	0.105	0.011	0.115
read.marrayLayout	0.192	0.021	0.218
read.marrayRaw	3.556	0.266	3.851
rm.na	0.000	0.001	0.000
stat.confband.text	1.097	0.090	1.193
stat.gnames	0.625	0.067	0.699
write.list	0.215	0.068	0.287
write.marray	0.169	0.024	0.196
write.xls	0.145	0.036	0.187