Package: marray

Version: 1.30.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.30.0.tar.gz

StartedAt: 2011-10-20 13:24:45 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:26:24 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 99.4 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/marray.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘1.30.0’
* checking package namespace 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 12.4Mb
  sub-directories of 1Mb or more:
    swirldata   5.5Mb
    doc         5.9Mb
* 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 ... 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 ...
** testing if installed package can be loaded

* DONE (marray)

name	user	system	elapsed
boxplot	1.000	0.004	1.012
checkTargetInfo	0.172	0.004	0.176
dim	0.000	0.000	0.003
findID	0.148	0.000	0.149
htmlPage	0.204	0.000	0.202
image	0.044	0.000	0.045
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.016	0.000	0.016
maCompCoord	0.000	0.004	0.001
maCompInd	0.004	0.000	0.006
maCompLayout	0.012	0.000	0.013
maCompNormA	0	0	0
maCompPlate	0.008	0.000	0.010
maCoord2Ind	0.004	0.000	0.004
maDefaultPar	0	0	0
maDotsDefaults	0.000	0.000	0.001
maDotsMatch	0.004	0.000	0.002
maGenControls	0.24	0.00	0.24
maGeneTable	0.148	0.000	0.145
maImage	1.636	0.008	1.647
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	0	0
maNorm	3.048	0.008	3.137
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	18.133	0.012	18.442
maNormMed	0	0	0
maNormScale	0.708	0.008	0.721
maNum2Logic	0	0	0
maPalette	0.008	0.004	0.010
maPlot	3.056	0.004	3.080
maPlot.func	0	0	0
maSelectGnames	0.012	0.000	0.011
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0	0	0
marrayLayout-class	0.000	0.000	0.001
marrayNorm-class	0.580	0.004	0.638
marrayRaw-class	0.196	0.000	0.205
opVersionID	0.004	0.000	0.002
plotMA	2.709	0.012	2.841
read.Galfile	0.076	0.000	0.148
read.marrayInfo	0.056	0.000	0.073
read.marrayLayout	0.108	0.000	0.117
read.marrayRaw	3.744	0.036	3.833
rm.na	0	0	0
stat.confband.text	0.872	0.008	0.915
stat.gnames	0.484	0.004	0.485
write.list	0.240	0.000	0.243
write.marray	0.076	0.000	0.078
write.xls	0.100	0.000	0.102