BioC 2.8: CHECK report for marray on pelham

Package: marray

Version: 1.29.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.29.1.tar.gz

StartedAt: 2011-02-24 20:09:33 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:11:33 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 119.8 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 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-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	0.922	0.207	1.140
checkTargetInfo	0.205	0.035	0.241
dim	0.004	0.000	0.004
findID	0.173	0.023	0.197
htmlPage	0.208	0.043	0.254
image	0.094	0.005	0.100
ma2D	0.000	0.000	0.001
maBoxplot	0.001	0.000	0.001
maColorBar	0.022	0.002	0.023
maCompCoord	0.001	0.001	0.002
maCompInd	0.007	0.001	0.007
maCompLayout	0.012	0.000	0.013
maCompNormA	0	0	0
maCompPlate	0.017	0.004	0.021
maCoord2Ind	0.005	0.001	0.006
maDefaultPar	0.001	0.000	0.001
maDotsDefaults	0.002	0.000	0.003
maDotsMatch	0.003	0.000	0.003
maGenControls	0.369	0.021	0.391
maGeneTable	0.156	0.017	0.174
maImage	1.609	0.373	2.120
maImage.func	0.000	0.000	0.001
maInd2Coord	0.010	0.004	0.013
maLegendLines	0.000	0.001	0.000
maLoess	0	0	0
maLoessLines	0.000	0.001	0.000
maMAD	0	0	0
maMed	0	0	0
maNorm	4.099	0.326	4.438
maNorm2D	0	0	0
maNormLoess	0.001	0.000	0.001
maNormMAD	0.000	0.000	0.001
maNormMain	26.948	1.029	28.012
maNormMed	0.000	0.000	0.001
maNormScale	0.611	0.195	0.808
maNum2Logic	0.001	0.000	0.001
maPalette	0.012	0.001	0.012
maPlot	4.200	0.303	4.505
maPlot.func	0	0	0
maSelectGnames	0.015	0.001	0.016
maText	0	0	0
maTop	0.001	0.000	0.000
mapGeneInfo	0.001	0.000	0.001
marrayInfo-class	0.000	0.001	0.001
marrayLayout-class	0.000	0.000	0.001
marrayNorm-class	0.584	0.198	0.784
marrayRaw-class	0.256	0.058	0.315
opVersionID	0.002	0.001	0.002
plotMA	3.909	0.264	4.178
read.Galfile	0.210	0.021	0.233
read.marrayInfo	0.103	0.010	0.113
read.marrayLayout	0.179	0.017	0.197
read.marrayRaw	3.599	0.238	3.840
rm.na	0.001	0.001	0.001
stat.confband.text	1.082	0.080	1.163
stat.gnames	0.611	0.056	0.668
write.list	0.240	0.062	0.303
write.marray	0.136	0.020	0.158
write.xls	0.146	0.034	0.181

Summary

Command output