BioC 2.8: CHECK report for marray on lamb2

Package: marray

Version: 1.29.1

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.29.1.tar.gz

StartedAt: 2011-02-24 21:06:11 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:07:24 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 73.6 seconds

RetCode: 0

Status: OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/marray.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.29.1’
* 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 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 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	0.660	0.008	0.666
checkTargetInfo	0.176	0.000	0.177
dim	0.000	0.000	0.003
findID	0.108	0.000	0.108
htmlPage	0.096	0.000	0.098
image	0.040	0.000	0.039
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.012	0.000	0.015
maCompCoord	0	0	0
maCompInd	0.004	0.000	0.003
maCompLayout	0.008	0.000	0.007
maCompNormA	0	0	0
maCompPlate	0.012	0.000	0.009
maCoord2Ind	0.004	0.000	0.003
maDefaultPar	0	0	0
maDotsDefaults	0.000	0.000	0.002
maDotsMatch	0.004	0.000	0.002
maGenControls	0.192	0.000	0.194
maGeneTable	0.100	0.000	0.097
maImage	1.304	0.004	1.306
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	2.688	0.004	2.695
maNorm2D	0.000	0.000	0.001
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	17.361	0.004	17.371
maNormMed	0	0	0
maNormScale	0.448	0.000	0.450
maNum2Logic	0.000	0.004	0.000
maPalette	0.008	0.000	0.007
maPlot	2.844	0.000	2.846
maPlot.func	0.000	0.000	0.001
maSelectGnames	0.008	0.000	0.012
maText	0	0	0
maTop	0.000	0.000	0.001
mapGeneInfo	0.000	0.000	0.001
marrayInfo-class	0.000	0.000	0.001
marrayLayout-class	0.000	0.000	0.001
marrayNorm-class	0.444	0.000	0.444
marrayRaw-class	0.168	0.004	0.173
opVersionID	0.000	0.004	0.001
plotMA	2.672	0.000	2.670
read.Galfile	0.072	0.000	0.072
read.marrayInfo	0.06	0.00	0.06
read.marrayLayout	0.112	0.000	0.112
read.marrayRaw	2.621	0.020	2.643
rm.na	0.000	0.000	0.001
stat.confband.text	0.728	0.008	0.736
stat.gnames	0.392	0.012	0.404
write.list	0.176	0.004	0.178
write.marray	0.060	0.000	0.061
write.xls	0.076	0.004	0.079

Summary

Command output