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: 2011-05-09 15:32:29 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:34:50 -0700 (Mon, 09 May 2011)

EllapsedTime: 140.9 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) (2011-04-24 r55634)
* 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 12.0Mb
  sub-directories of 1Mb or more:
    doc         5.6Mb
    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 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘marrayNorm.pdf’ from 1498Kb to 279Kb
     compacted ‘marrayPlots.pdf’ from 3006Kb to 382Kb
  consider running tools::compactPDF() on these files
* 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	0.771	0.207	1.020
checkTargetInfo	0.230	0.036	0.282
dim	0.003	0.001	0.004
findID	0.127	0.021	0.154
htmlPage	0.199	0.046	0.258
image	0.095	0.006	0.105
ma2D	0.001	0.000	0.000
maBoxplot	0.000	0.000	0.001
maColorBar	0.021	0.001	0.023
maCompCoord	0.001	0.001	0.002
maCompInd	0.006	0.001	0.007
maCompLayout	0.012	0.000	0.013
maCompNormA	0	0	0
maCompPlate	0.018	0.005	0.023
maCoord2Ind	0.005	0.001	0.006
maDefaultPar	0.001	0.001	0.000
maDotsDefaults	0.002	0.000	0.003
maDotsMatch	0.002	0.001	0.003
maGenControls	0.341	0.023	0.370
maGeneTable	0.143	0.014	0.158
maImage	1.353	0.374	1.761
maImage.func	0.000	0.000	0.001
maInd2Coord	0.008	0.002	0.011
maLegendLines	0	0	0
maLoess	0.000	0.000	0.001
maLoessLines	0.000	0.001	0.000
maMAD	0	0	0
maMed	0	0	0
maNorm	3.969	0.323	4.343
maNorm2D	0	0	0
maNormLoess	0.000	0.001	0.000
maNormMAD	0	0	0
maNormMain	26.693	1.154	28.123
maNormMed	0.000	0.000	0.001
maNormScale	0.591	0.242	0.846
maNum2Logic	0.001	0.000	0.001
maPalette	0.012	0.001	0.013
maPlot	4.156	0.391	4.574
maPlot.func	0.000	0.000	0.001
maSelectGnames	0.016	0.001	0.017
maText	0.000	0.001	0.001
maTop	0.000	0.000	0.001
mapGeneInfo	0.002	0.001	0.002
marrayInfo-class	0.001	0.000	0.000
marrayLayout-class	0.000	0.001	0.000
marrayNorm-class	0.553	0.220	0.783
marrayRaw-class	0.250	0.054	0.305
opVersionID	0.002	0.000	0.002
plotMA	3.825	0.270	4.121
read.Galfile	0.205	0.021	0.226
read.marrayInfo	0.103	0.009	0.112
read.marrayLayout	0.187	0.019	0.207
read.marrayRaw	3.727	0.260	4.018
rm.na	0.001	0.000	0.001
stat.confband.text	1.135	0.089	1.233
stat.gnames	0.661	0.059	0.727
write.list	0.203	0.065	0.271
write.marray	0.143	0.024	0.169
write.xls	0.150	0.040	0.192