BioC 2.8: CHECK report for marray on petty

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 16:09:59 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:11:20 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 80.7 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: ASCII
* 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	0.593	0.024	0.616
checkTargetInfo	0.134	0.007	0.141
dim	0.002	0.000	0.003
findID	0.116	0.006	0.123
htmlPage	0.143	0.016	0.159
image	0.065	0.002	0.067
ma2D	0	0	0
maBoxplot	0.001	0.000	0.001
maColorBar	0.015	0.001	0.015
maCompCoord	0.001	0.001	0.001
maCompInd	0.004	0.000	0.004
maCompLayout	0.010	0.000	0.009
maCompNormA	0.001	0.000	0.000
maCompPlate	0.012	0.001	0.013
maCoord2Ind	0.003	0.001	0.004
maDefaultPar	0.000	0.000	0.001
maDotsDefaults	0.001	0.000	0.001
maDotsMatch	0.002	0.000	0.002
maGenControls	0.210	0.004	0.213
maGeneTable	0.107	0.002	0.109
maImage	1.047	0.022	1.069
maImage.func	0	0	0
maInd2Coord	0.006	0.000	0.006
maLegendLines	0	0	0
maLoess	0.000	0.000	0.001
maLoessLines	0	0	0
maMAD	0.001	0.000	0.000
maMed	0	0	0
maNorm	2.586	0.018	2.604
maNorm2D	0	0	0
maNormLoess	0.001	0.000	0.000
maNormMAD	0	0	0
maNormMain	17.071	0.085	17.156
maNormMed	0	0	0
maNormScale	0.391	0.016	0.408
maNum2Logic	0.001	0.000	0.000
maPalette	0.008	0.000	0.008
maPlot	2.623	0.027	2.651
maPlot.func	0.001	0.000	0.000
maSelectGnames	0.011	0.001	0.011
maText	0.001	0.000	0.000
maTop	0	0	0
mapGeneInfo	0.001	0.001	0.001
marrayInfo-class	0.001	0.000	0.000
marrayLayout-class	0.001	0.001	0.001
marrayNorm-class	0.350	0.019	0.368
marrayRaw-class	0.153	0.007	0.161
opVersionID	0.001	0.000	0.001
plotMA	2.417	0.008	2.426
read.Galfile	0.064	0.002	0.067
read.marrayInfo	0.085	0.001	0.086
read.marrayLayout	0.157	0.001	0.159
read.marrayRaw	3.091	0.040	3.131
rm.na	0	0	0
stat.confband.text	0.786	0.029	0.815
stat.gnames	0.422	0.017	0.440
write.list	0.160	0.019	0.179
write.marray	0.086	0.005	0.090
write.xls	0.096	0.014	0.110

Summary

Command output