BioC 2.9: CHECK report for marray on gewurz

Package: marray

Version: 1.32.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch marray_1.32.0.tar.gz

StartedAt: 2012-01-09 04:05:11 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:06:46 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 94.5 seconds

RetCode: 0

Status: OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/marray.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.32.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'marray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    swirldata   5.5Mb
* 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... OK
* 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 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	0.75	0.00	0.75
checkTargetInfo	0.19	0.00	0.19
dim	0	0	0
findID	0.15	0.00	0.16
htmlPage	0.19	0.00	0.18
image	0.09	0.00	0.10
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.03	0.00	0.03
maCompCoord	0	0	0
maCompInd	0	0	0
maCompLayout	0	0	0
maCompNormA	0	0	0
maCompPlate	0.06	0.00	0.06
maCoord2Ind	0	0	0
maDefaultPar	0	0	0
maDotsDefaults	0.02	0.00	0.02
maDotsMatch	0	0	0
maGenControls	0.19	0.00	0.18
maGeneTable	0.11	0.00	0.11
maImage	1.33	0.03	1.38
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	2.26	0.00	2.27
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	14.74	0.02	14.75
maNormMed	0	0	0
maNormScale	0.5	0.0	0.5
maNum2Logic	0	0	0
maPalette	0.03	0.00	0.03
maPlot	2.54	0.03	2.58
maPlot.func	0	0	0
maSelectGnames	0.02	0.00	0.01
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0	0	0
marrayLayout-class	0	0	0
marrayNorm-class	0.66	0.02	0.68
marrayRaw-class	0.23	0.01	0.25
opVersionID	0	0	0
plotMA	2.42	0.02	2.43
read.Galfile	0.06	0.01	0.08
read.marrayInfo	0.06	0.00	0.06
read.marrayLayout	0.16	0.00	0.16
read.marrayRaw	4.26	0.02	4.28
rm.na	0	0	0
stat.confband.text	0.82	0.01	0.89
stat.gnames	0.43	0.00	0.44
write.list	0.19	0.00	0.18
write.marray	0.13	0.02	0.14
write.xls	0.23	0.00	0.24

Summary

Command output