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: 2011-07-07 04:13:39 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:16:08 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 149.6 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) (2011-06-22 r56208)
* 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 '1.31.0'
* 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  8.6Mb
  sub-directories of 1Mb or more:
    doc         2.1Mb
    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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
              old_size new_size compress
  swirl.RData    455Kb    284Kb       xz
* 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	0.758	0.207	0.994
checkTargetInfo	0.197	0.035	0.235
dim	0.003	0.000	0.004
findID	0.176	0.026	0.204
htmlPage	0.217	0.048	0.280
image	0.094	0.006	0.101
ma2D	0.000	0.001	0.001
maBoxplot	0.001	0.000	0.000
maColorBar	0.022	0.001	0.023
maCompCoord	0.001	0.001	0.002
maCompInd	0.006	0.002	0.008
maCompLayout	0.012	0.001	0.012
maCompNormA	0	0	0
maCompPlate	0.017	0.003	0.021
maCoord2Ind	0.004	0.001	0.006
maDefaultPar	0	0	0
maDotsDefaults	0.002	0.000	0.003
maDotsMatch	0.002	0.001	0.002
maGenControls	0.341	0.023	0.367
maGeneTable	0.113	0.015	0.128
maImage	1.569	0.386	2.025
maImage.func	0	0	0
maInd2Coord	0.006	0.002	0.008
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	4.027	0.323	4.391
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	26.820	1.216	28.395
maNormMed	0	0	0
maNormScale	0.638	0.235	0.895
maNum2Logic	0.000	0.000	0.001
maPalette	0.011	0.000	0.011
maPlot	4.219	0.401	4.670
maPlot.func	0.001	0.001	0.000
maSelectGnames	0.015	0.001	0.016
maText	0.001	0.000	0.000
maTop	0.000	0.000	0.001
mapGeneInfo	0.001	0.000	0.001
marrayInfo-class	0.000	0.000	0.001
marrayLayout-class	0	0	0
marrayNorm-class	0.598	0.219	0.832
marrayRaw-class	0.215	0.058	0.279
opVersionID	0.002	0.000	0.002
plotMA	3.860	0.269	4.191
read.Galfile	0.082	0.021	0.105
read.marrayInfo	0.112	0.010	0.123
read.marrayLayout	0.246	0.022	0.270
read.marrayRaw	3.325	0.267	3.660
rm.na	0.001	0.001	0.001
stat.confband.text	1.151	0.091	1.260
stat.gnames	0.654	0.065	0.730
write.list	0.269	0.069	0.343
write.marray	0.130	0.023	0.155
write.xls	0.158	0.041	0.201