Package: marray

Version: 1.35.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.35.0.tar.gz

StartedAt: 2012-06-21 01:26:23 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:28:41 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 138.2 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/marray.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.35.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'marray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc         1.6Mb
    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 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
maImage: warning in layout(matrix(c(1, 2), 1, 2), width = c(8, 2)):
  partial argument match of 'width' to 'widths'
widget.marrayInfo : inputInfo: warning in assign(newname, newInfo, env
  = .GlobalEnv): partial argument match of 'env' to 'envir'
widget.marrayLayout : inputLayout: warning in assign(newname,
  newLayout, env = .GlobalEnv): partial argument match of 'env' to
  'envir'
widget.marrayRaw : inputRaw: warning in assign(newname, newRaw, env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
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 ... OK
* 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' ... OK
* checking installed files from '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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/marray.Rcheck/00check.log'
for details.

* installing *source* package 'marray' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   '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	0.913	0.216	1.172
checkTargetInfo	0.221	0.036	0.259
dim	0.003	0.000	0.003
findID	0.189	0.024	0.216
htmlPage	0.231	0.048	0.285
image	0.106	0.006	0.114
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.022	0.003	0.025
maCompCoord	0.001	0.001	0.001
maCompInd	0.008	0.002	0.010
maCompLayout	0.01	0.00	0.01
maCompNormA	0.001	0.001	0.000
maCompPlate	0.012	0.002	0.015
maCoord2Ind	0.004	0.001	0.006
maDefaultPar	0	0	0
maDotsDefaults	0.003	0.002	0.005
maDotsMatch	0.002	0.001	0.002
maGenControls	0.287	0.023	0.311
maGeneTable	0.128	0.019	0.152
maImage	1.578	0.402	2.051
maImage.func	0	0	0
maInd2Coord	0.006	0.002	0.008
maLegendLines	0	0	0
maLoess	0.000	0.000	0.001
maLoessLines	0	0	0
maMAD	0.000	0.000	0.001
maMed	0.000	0.000	0.001
maNorm	4.093	0.326	4.458
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	26.687	1.109	28.273
maNormMed	0.001	0.000	0.000
maNormScale	0.599	0.234	0.845
maNum2Logic	0.000	0.000	0.001
maPalette	0.042	0.005	0.047
maPlot	4.321	0.397	4.842
maPlot.func	0.000	0.001	0.000
maSelectGnames	0.010	0.001	0.011
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0.001	0.000	0.001
marrayInfo-class	0	0	0
marrayLayout-class	0.000	0.001	0.000
marrayNorm-class	0.641	0.218	0.885
marrayRaw-class	0.204	0.056	0.265
opVersionID	0.001	0.000	0.001
plotMA	3.888	0.289	4.265
read.Galfile	0.080	0.022	0.107
read.marrayInfo	0.100	0.010	0.115
read.marrayLayout	0.189	0.020	0.227
read.marrayRaw	3.298	0.274	3.663
rm.na	0.001	0.000	0.001
stat.confband.text	1.001	0.099	1.114
stat.gnames	0.564	0.070	0.648
write.list	0.289	0.075	0.442
write.marray	0.142	0.028	0.172
write.xls	0.161	0.042	0.208