Package: marray

Version: 1.31.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.31.0.tar.gz

StartedAt: 2011-05-09 13:08:50 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:10:29 -0700 (Mon, 09 May 2011)

EllapsedTime: 99.3 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/marray.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-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 12.3Mb
  sub-directories of 1Mb or more:
    swirldata   5.5Mb
    doc         5.8Mb
* 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 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	0.908	0.016	0.925
checkTargetInfo	0.244	0.000	0.245
dim	0.004	0.000	0.003
findID	0.140	0.004	0.143
htmlPage	0.188	0.000	0.186
image	0.048	0.000	0.047
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.016	0.000	0.018
maCompCoord	0.004	0.000	0.001
maCompInd	0.004	0.004	0.009
maCompLayout	0.012	0.000	0.009
maCompNormA	0	0	0
maCompPlate	0.008	0.000	0.009
maCoord2Ind	0.000	0.000	0.003
maDefaultPar	0.000	0.000	0.001
maDotsDefaults	0.000	0.000	0.001
maDotsMatch	0.000	0.000	0.002
maGenControls	0.168	0.004	0.175
maGeneTable	0.132	0.000	0.133
maImage	1.620	0.020	1.642
maImage.func	0	0	0
maInd2Coord	0.004	0.000	0.004
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0.004	0.000	0.000
maNorm	2.980	0.004	2.983
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	18.277	0.008	18.297
maNormMed	0	0	0
maNormScale	0.688	0.000	0.724
maNum2Logic	0	0	0
maPalette	0.008	0.000	0.009
maPlot	3.128	0.004	3.199
maPlot.func	0	0	0
maSelectGnames	0.008	0.000	0.012
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0.000	0.000	0.001
marrayLayout-class	0	0	0
marrayNorm-class	0.792	0.004	0.796
marrayRaw-class	0.300	0.000	0.297
opVersionID	0.000	0.000	0.002
plotMA	2.897	0.000	2.900
read.Galfile	0.100	0.000	0.101
read.marrayInfo	0.052	0.004	0.054
read.marrayLayout	0.168	0.000	0.170
read.marrayRaw	3.492	0.024	3.516
rm.na	0.000	0.000	0.001
stat.confband.text	0.936	0.012	0.945
stat.gnames	0.440	0.004	0.447
write.list	0.152	0.000	0.154
write.marray	0.080	0.000	0.082
write.xls	0.124	0.000	0.125