Package: marray

Version: 1.29.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.29.1.tar.gz

StartedAt: 2011-03-17 16:47:46 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:49:16 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 89.6 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/marray.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.29.1'
* 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:
    doc         5.8Mb
    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 examples ... OK
* checking package vignettes in 'inst/doc' ... 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	0.478	0.018	0.496
checkTargetInfo	0.144	0.005	0.150
dim	0.003	0.000	0.003
findID	0.078	0.002	0.079
htmlPage	0.126	0.011	0.137
image	0.059	0.002	0.061
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.013	0.000	0.014
maCompCoord	0.000	0.001	0.001
maCompInd	0.005	0.001	0.006
maCompLayout	0.008	0.001	0.008
maCompNormA	0	0	0
maCompPlate	0.008	0.001	0.008
maCoord2Ind	0.003	0.000	0.004
maDefaultPar	0	0	0
maDotsDefaults	0.001	0.000	0.001
maDotsMatch	0.001	0.001	0.002
maGenControls	0.182	0.002	0.184
maGeneTable	0.068	0.002	0.070
maImage	0.841	0.020	0.862
maImage.func	0.000	0.000	0.001
maInd2Coord	0.004	0.000	0.004
maLegendLines	0.001	0.000	0.000
maLoess	0	0	0
maLoessLines	0.000	0.000	0.001
maMAD	0	0	0
maMed	0	0	0
maNorm	2.526	0.011	2.537
maNorm2D	0.001	0.000	0.001
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	16.947	0.057	17.004
maNormMed	0	0	0
maNormScale	0.338	0.014	0.352
maNum2Logic	0	0	0
maPalette	0.008	0.000	0.009
maPlot	2.721	0.021	2.742
maPlot.func	0	0	0
maSelectGnames	0.011	0.000	0.011
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0.001	0.001	0.001
marrayInfo-class	0	0	0
marrayLayout-class	0.000	0.000	0.001
marrayNorm-class	0.416	0.013	0.429
marrayRaw-class	0.167	0.007	0.174
opVersionID	0.001	0.000	0.001
plotMA	2.470	0.007	2.477
read.Galfile	0.067	0.002	0.069
read.marrayInfo	0.087	0.002	0.088
read.marrayLayout	0.161	0.001	0.163
read.marrayRaw	3.238	0.031	3.270
rm.na	0	0	0
stat.confband.text	0.750	0.028	0.778
stat.gnames	0.432	0.022	0.454
write.list	0.134	0.014	0.148
write.marray	0.080	0.004	0.084
write.xls	0.102	0.013	0.115