BioC 2.9: CHECK report for marray on pitt

Package: marray

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.32.0.tar.gz

StartedAt: 2012-03-24 02:18:21 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:20:40 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 139.1 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 2.14.2 (2012-02-29)
* 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 '1.32.0'
* 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  7.9Mb
  sub-directories of 1Mb or more:
    doc         1.6Mb
    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 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'
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 ... 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 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	0.903	0.219	1.139
checkTargetInfo	0.281	0.039	0.357
dim	0.002	0.001	0.004
findID	0.255	0.030	0.287
htmlPage	0.288	0.050	0.356
image	0.165	0.011	0.178
ma2D	0.001	0.000	0.001
maBoxplot	0	0	0
maColorBar	0.021	0.003	0.025
maCompCoord	0.001	0.001	0.002
maCompInd	0.005	0.001	0.007
maCompLayout	0.010	0.001	0.011
maCompNormA	0.000	0.000	0.001
maCompPlate	0.013	0.003	0.015
maCoord2Ind	0.004	0.002	0.006
maDefaultPar	0.001	0.000	0.000
maDotsDefaults	0.004	0.002	0.005
maDotsMatch	0.002	0.001	0.003
maGenControls	0.361	0.031	0.395
maGeneTable	0.230	0.021	0.254
maImage	1.757	0.404	2.233
maImage.func	0	0	0
maInd2Coord	0.005	0.003	0.008
maLegendLines	0	0	0
maLoess	0.000	0.001	0.001
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0.000	0.000	0.001
maNorm	4.400	0.319	4.768
maNorm2D	0.001	0.000	0.000
maNormLoess	0.001	0.000	0.000
maNormMAD	0.001	0.001	0.001
maNormMain	28.974	1.194	30.410
maNormMed	0.000	0.000	0.001
maNormScale	0.757	0.242	1.010
maNum2Logic	0.000	0.000	0.001
maPalette	0.043	0.005	0.048
maPlot	4.729	0.424	5.255
maPlot.func	0	0	0
maSelectGnames	0.010	0.000	0.011
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0.001	0.000	0.001
marrayInfo-class	0.000	0.001	0.000
marrayLayout-class	0.001	0.000	0.001
marrayNorm-class	0.701	0.226	0.940
marrayRaw-class	0.328	0.069	0.403
opVersionID	0.002	0.000	0.002
plotMA	4.228	0.300	4.605
read.Galfile	0.084	0.024	0.114
read.marrayInfo	0.107	0.010	0.116
read.marrayLayout	0.189	0.018	0.212
read.marrayRaw	3.334	0.254	3.652
rm.na	0.001	0.000	0.001
stat.confband.text	1.084	0.092	1.181
stat.gnames	0.598	0.064	0.692
write.list	0.298	0.078	0.416
write.marray	0.269	0.029	0.362
write.xls	0.215	0.040	0.261

Summary

Command output