Package: marray

Version: 1.29.1

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings marray_1.29.1.tar.gz

StartedAt: 2011-02-24 18:46:32 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:48:02 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 90.0 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/marray.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.29.1'
* 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 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'
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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... 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	0.64	0.02	0.66
checkTargetInfo	0.22	0.00	0.21
dim	0	0	0
findID	0.09	0.00	0.10
htmlPage	0.19	0.01	0.20
image	0.06	0.00	0.06
ma2D	0	0	0
maBoxplot	0.02	0.00	0.02
maColorBar	0.01	0.00	0.02
maCompCoord	0	0	0
maCompInd	0	0	0
maCompLayout	0	0	0
maCompNormA	0	0	0
maCompPlate	0.02	0.00	0.02
maCoord2Ind	0	0	0
maDefaultPar	0	0	0
maDotsDefaults	0	0	0
maDotsMatch	0.01	0.00	0.01
maGenControls	0.22	0.00	0.22
maGeneTable	0.08	0.00	0.08
maImage	1.45	0.00	1.47
maImage.func	0	0	0
maInd2Coord	0	0	0
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	2.96	0.00	2.96
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	19.62	0.00	19.64
maNormMed	0	0	0
maNormScale	0.56	0.00	0.56
maNum2Logic	0	0	0
maPalette	0	0	0
maPlot	3.21	0.01	3.22
maPlot.func	0	0	0
maSelectGnames	0	0	0
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0	0	0
marrayLayout-class	0	0	0
marrayNorm-class	0.45	0.00	0.46
marrayRaw-class	0.21	0.00	0.20
opVersionID	0.01	0.00	0.02
plotMA	2.96	0.00	2.95
read.Galfile	0.07	0.00	0.08
read.marrayInfo	0.07	0.00	0.06
read.marrayLayout	0.12	0.02	0.14
read.marrayRaw	3.42	0.03	3.45
rm.na	0	0	0
stat.confband.text	0.82	0.00	0.82
stat.gnames	0.40	0.01	0.42
write.list	0.20	0.00	0.21
write.marray	0.10	0.00	0.09
write.xls	0.10	0.00	0.11