Package: marray

Version: 1.34.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.34.0.tar.gz

StartedAt: 2012-04-01 01:59:53 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:01:02 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 68.5 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/marray.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* 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  8.1Mb
  sub-directories of 1Mb or more:
    doc         1.7Mb
    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
findID: no visible binding for global variable 'gnames'
findID: no visible global function definition for 'phenoData'
htmlPage: no visible binding for global variable 'Gnames'
maImage: warning in layout(matrix(c(1, 2), 1, 2), width = c(8, 2)):
  partial argument match of 'width' to 'widths'
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'
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'
* 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 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
  '/loc/home/hpages/test-puck5/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	0.520	0.012	0.536
checkTargetInfo	0.132	0.004	0.146
dim	0.000	0.000	0.002
findID	0.112	0.008	0.119
htmlPage	0.096	0.000	0.102
image	0.060	0.000	0.064
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.016	0.000	0.014
maCompCoord	0.000	0.000	0.001
maCompInd	0.004	0.000	0.004
maCompLayout	0.008	0.000	0.006
maCompNormA	0	0	0
maCompPlate	0.008	0.000	0.007
maCoord2Ind	0.004	0.000	0.003
maDefaultPar	0	0	0
maDotsDefaults	0.004	0.000	0.002
maDotsMatch	0.000	0.000	0.001
maGenControls	0.164	0.000	0.172
maGeneTable	0.064	0.000	0.068
maImage	1.000	0.016	1.020
maImage.func	0	0	0
maInd2Coord	0.004	0.000	0.004
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	2.048	0.000	2.053
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0.000	0.000	0.001
maNormMain	12.989	0.000	13.000
maNormMed	0	0	0
maNormScale	0.364	0.000	0.366
maNum2Logic	0	0	0
maPalette	0.02	0.00	0.02
maPlot	2.352	0.008	2.365
maPlot.func	0	0	0
maSelectGnames	0.008	0.000	0.005
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0.000	0.000	0.001
marrayInfo-class	0.004	0.000	0.000
marrayLayout-class	0	0	0
marrayNorm-class	0.316	0.004	0.327
marrayRaw-class	0.140	0.008	0.149
opVersionID	0.000	0.000	0.001
plotMA	1.840	0.004	1.851
read.Galfile	0.076	0.000	0.085
read.marrayInfo	0.040	0.000	0.046
read.marrayLayout	0.080	0.000	0.082
read.marrayRaw	1.660	0.000	1.669
rm.na	0.004	0.000	0.001
stat.confband.text	0.592	0.008	0.608
stat.gnames	0.304	0.000	0.309
write.list	0.120	0.000	0.124
write.marray	0.080	0.000	0.081
write.xls	0.088	0.000	0.092