Package: marray

Version: 1.31.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.31.0.tar.gz

StartedAt: 2011-07-07 01:17:55 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:19:31 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 95.9 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/marray.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.31.0’
* checking package name space 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  8.6Mb
  sub-directories of 1Mb or more:
    swirldata   5.5Mb
    doc         2.1Mb
* 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 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 ... 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 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 ...
*** tangling vignette sources ...
   ‘marray.Rnw’ 
   ‘marrayClasses.Rnw’ 
   ‘marrayClassesShort.Rnw’ 
   ‘marrayInput.Rnw’ 
   ‘marrayNorm.Rnw’ 
   ‘marrayPlots.Rnw’ 
** testing if installed package can be loaded

* DONE (marray)

name	user	system	elapsed
boxplot	0.980	0.024	1.005
checkTargetInfo	0.168	0.000	0.171
dim	0.000	0.000	0.003
findID	0.124	0.008	0.132
htmlPage	0.176	0.004	0.177
image	0.040	0.000	0.042
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.016	0.000	0.015
maCompCoord	0.000	0.000	0.001
maCompInd	0.004	0.000	0.004
maCompLayout	0.008	0.000	0.008
maCompNormA	0	0	0
maCompPlate	0.012	0.000	0.010
maCoord2Ind	0.000	0.000	0.003
maDefaultPar	0	0	0
maDotsDefaults	0.000	0.000	0.002
maDotsMatch	0.004	0.000	0.002
maGenControls	0.216	0.000	0.218
maGeneTable	0.124	0.000	0.122
maImage	1.436	0.012	1.446
maImage.func	0	0	0
maInd2Coord	0.004	0.000	0.004
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	2.888	0.008	2.892
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	17.501	0.008	17.613
maNormMed	0	0	0
maNormScale	0.528	0.008	0.534
maNum2Logic	0.000	0.000	0.001
maPalette	0.008	0.000	0.008
maPlot	2.828	0.012	2.845
maPlot.func	0	0	0
maSelectGnames	0.008	0.004	0.009
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0	0	0
marrayLayout-class	0	0	0
marrayNorm-class	0.476	0.004	0.481
marrayRaw-class	0.196	0.004	0.200
opVersionID	0.000	0.000	0.001
plotMA	2.520	0.004	2.523
read.Galfile	0.084	0.004	0.086
read.marrayInfo	0.048	0.000	0.048
read.marrayLayout	0.152	0.000	0.149
read.marrayRaw	3.093	0.032	3.135
rm.na	0	0	0
stat.confband.text	0.784	0.004	0.786
stat.gnames	0.484	0.000	0.486
write.list	0.128	0.000	0.129
write.marray	0.068	0.008	0.075
write.xls	0.092	0.000	0.093