Package: marray

Version: 1.26.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.26.0.tar.gz

StartedAt: 2010-10-04 18:31:53 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:33:10 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 77.5 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/marray.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.26.0'
* 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 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.mapGeneInfo: no visible global function definition for
  'widgetRender'
widget.TwoSamples: 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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	0.840	0.012	0.849
checkTargetInfo	0.132	0.008	0.138
dim	0.004	0.000	0.003
findID	0.116	0.000	0.117
htmlPage	0.152	0.000	0.152
image	0.04	0.00	0.04
ma2D	0	0	0
maBoxplot	0.000	0.000	0.001
maColorBar	0.012	0.000	0.014
maCompCoord	0.000	0.000	0.001
maCompInd	0.004	0.000	0.004
maCompLayout	0.008	0.000	0.009
maCompNormA	0	0	0
maCompPlate	0.008	0.000	0.011
maCoord2Ind	0.000	0.000	0.003
maDefaultPar	0	0	0
maDotsDefaults	0.000	0.000	0.001
maDotsMatch	0.004	0.000	0.001
maGenControls	0.108	0.004	0.113
maGeneTable	0.104	0.004	0.105
maImage	1.288	0.028	1.316
maImage.func	0	0	0
maInd2Coord	0.004	0.000	0.004
maLegendLines	0.000	0.000	0.001
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	2.856	0.008	2.864
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	17.937	0.012	17.996
maNormMed	0	0	0
maNormScale	0.552	0.004	0.557
maNum2Logic	0	0	0
maPalette	0.008	0.000	0.007
maPlot	2.844	0.008	2.854
maPlot.func	0	0	0
maSelectGnames	0.008	0.000	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	0.488	0.000	0.485
marrayRaw-class	0.128	0.004	0.133
opVersionID	0.004	0.000	0.002
plotMA	2.640	0.004	2.646
read.Galfile	0.048	0.000	0.049
read.marrayInfo	0.12	0.00	0.12
read.marrayLayout	0.200	0.004	0.203
read.marrayRaw	2.585	0.020	2.604
rm.na	0	0	0
stat.confband.text	0.776	0.016	0.801
stat.gnames	0.420	0.008	0.441
write.list	0.148	0.004	0.148
write.marray	0.124	0.000	0.124
write.xls	0.076	0.000	0.078