Package: marray

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.34.0.tar.gz

StartedAt: 2012-09-24 00:49:28 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:51:21 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 112.1 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/marray.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.34.0'
* 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-2.10-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	0.603	0.130	0.738
checkTargetInfo	0.161	0.025	0.187
dim	0.002	0.000	0.002
findID	0.142	0.015	0.158
htmlPage	0.174	0.033	0.207
image	0.083	0.006	0.090
ma2D	0	0	0
maBoxplot	0.000	0.001	0.000
maColorBar	0.017	0.002	0.020
maCompCoord	0.001	0.000	0.001
maCompInd	0.006	0.002	0.008
maCompLayout	0.007	0.001	0.008
maCompNormA	0	0	0
maCompPlate	0.010	0.002	0.011
maCoord2Ind	0.003	0.001	0.004
maDefaultPar	0	0	0
maDotsDefaults	0.003	0.001	0.004
maDotsMatch	0.002	0.001	0.002
maGenControls	0.205	0.016	0.221
maGeneTable	0.099	0.012	0.112
maImage	1.463	0.314	1.838
maImage.func	0	0	0
maInd2Coord	0.008	0.003	0.011
maLegendLines	0.001	0.000	0.000
maLoess	0.001	0.000	0.000
maLoessLines	0.001	0.000	0.000
maMAD	0.000	0.001	0.001
maMed	0	0	0
maNorm	3.447	0.259	3.723
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0.001	0.000	0.000
maNormMain	19.087	0.841	19.973
maNormMed	0	0	0
maNormScale	0.553	0.192	0.759
maNum2Logic	0.000	0.001	0.001
maPalette	0.041	0.003	0.045
maPlot	3.481	0.271	3.768
maPlot.func	0.000	0.000	0.001
maSelectGnames	0.007	0.001	0.008
maText	0	0	0
maTop	0.000	0.001	0.000
mapGeneInfo	0.000	0.000	0.001
marrayInfo-class	0.000	0.001	0.001
marrayLayout-class	0.001	0.000	0.001
marrayNorm-class	0.640	0.192	0.849
marrayRaw-class	0.192	0.045	0.242
opVersionID	0.001	0.000	0.001
plotMA	3.138	0.224	3.376
read.Galfile	0.082	0.019	0.102
read.marrayInfo	0.101	0.010	0.111
read.marrayLayout	0.179	0.016	0.197
read.marrayRaw	2.620	0.190	2.823
rm.na	0.001	0.000	0.001
stat.confband.text	0.684	0.064	0.754
stat.gnames	0.420	0.038	0.460
write.list	0.169	0.045	0.216
write.marray	0.108	0.015	0.124
write.xls	0.124	0.025	0.152