BioC 2.9: CHECK report for marray on pelham

Package: marray

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.31.0.tar.gz

StartedAt: 2011-06-22 03:57:15 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 03:59:37 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 141.6 seconds

RetCode: 0

Status: OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/marray.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* 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 ‘1.31.0’
* 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 installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc         1.8Mb
    swirldata   5.5Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 ...
*** tangling vignette sources ...
   ‘marray.Rnw’ 
   ‘marrayClasses.Rnw’ 
   ‘marrayClassesShort.Rnw’ 
   ‘marrayInput.Rnw’ 
   ‘marrayNorm.Rnw’ 
   ‘marrayPlots.Rnw’ 
** testing if installed package can be loaded

* DONE (marray)

name	user	system	elapsed
boxplot	0.810	0.207	1.077
checkTargetInfo	0.187	0.038	0.231
dim	0.004	0.000	0.004
findID	0.170	0.025	0.206
htmlPage	0.212	0.047	0.273
image	0.091	0.006	0.100
ma2D	0.001	0.000	0.000
maBoxplot	0.000	0.000	0.001
maColorBar	0.02	0.00	0.02
maCompCoord	0.001	0.000	0.002
maCompInd	0.005	0.002	0.007
maCompLayout	0.011	0.000	0.012
maCompNormA	0.001	0.000	0.001
maCompPlate	0.017	0.005	0.023
maCoord2Ind	0.005	0.001	0.006
maDefaultPar	0.001	0.000	0.000
maDotsDefaults	0.002	0.001	0.002
maDotsMatch	0.002	0.000	0.003
maGenControls	0.399	0.024	0.435
maGeneTable	0.103	0.012	0.120
maImage	1.319	0.377	1.728
maImage.func	0.001	0.000	0.000
maInd2Coord	0.006	0.001	0.008
maLegendLines	0.001	0.000	0.001
maLoess	0.000	0.000	0.001
maLoessLines	0.001	0.000	0.001
maMAD	0.000	0.000	0.001
maMed	0.000	0.001	0.001
maNorm	3.989	0.317	4.343
maNorm2D	0.000	0.000	0.001
maNormLoess	0.000	0.001	0.001
maNormMAD	0	0	0
maNormMain	27.099	1.186	28.669
maNormMed	0.001	0.000	0.001
maNormScale	0.677	0.240	0.938
maNum2Logic	0.001	0.000	0.000
maPalette	0.013	0.000	0.013
maPlot	4.314	0.388	4.739
maPlot.func	0.000	0.001	0.000
maSelectGnames	0.015	0.001	0.016
maText	0.000	0.000	0.001
maTop	0.000	0.000	0.001
mapGeneInfo	0.001	0.000	0.002
marrayInfo-class	0.001	0.001	0.001
marrayLayout-class	0	0	0
marrayNorm-class	0.590	0.208	0.816
marrayRaw-class	0.258	0.061	0.323
opVersionID	0.002	0.000	0.002
plotMA	3.875	0.272	4.192
read.Galfile	0.219	0.023	0.244
read.marrayInfo	0.153	0.012	0.167
read.marrayLayout	0.195	0.020	0.216
read.marrayRaw	3.971	0.253	4.259
rm.na	0.001	0.001	0.000
stat.confband.text	1.136	0.095	1.269
stat.gnames	0.633	0.067	0.705
write.list	0.259	0.070	0.334
write.marray	0.128	0.023	0.151
write.xls	0.156	0.041	0.199

Summary

Command output