Package: marray

Version: 1.30.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch marray_1.30.0.tar.gz

StartedAt: 2011-10-20 15:15:32 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:17:02 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 89.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: marray.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/marray.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.30.0'
* checking package namespace 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  7.2Mb
  sub-directories of 1Mb or more:
    swirldata   5.5Mb
* checking package directory ... OK
* checking for portable file names ... 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'
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 for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   marray.Rnw
   marrayClasses.Rnw
   marrayClassesShort.Rnw
   marrayInput.Rnw
   marrayNorm.Rnw
   marrayPlots.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-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 ...
** testing if installed package can be loaded

* DONE (marray)

name	user	system	elapsed
boxplot	0.77	0.00	0.77
checkTargetInfo	0.14	0.00	0.14
dim	0	0	0
findID	0.11	0.02	0.13
htmlPage	0.15	0.00	0.15
image	0.05	0.00	0.05
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.02	0.00	0.01
maCompCoord	0	0	0
maCompInd	0	0	0
maCompLayout	0	0	0
maCompNormA	0	0	0
maCompPlate	0.01	0.00	0.02
maCoord2Ind	0	0	0
maDefaultPar	0	0	0
maDotsDefaults	0	0	0
maDotsMatch	0	0	0
maGenControls	0.21	0.00	0.20
maGeneTable	0.09	0.00	0.09
maImage	1.25	0.00	1.27
maImage.func	0	0	0
maInd2Coord	0	0	0
maLegendLines	0	0	0
maLoess	0	0	0
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	2.29	0.00	2.29
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	14.68	0.00	14.68
maNormMed	0	0	0
maNormScale	0.52	0.00	0.52
maNum2Logic	0	0	0
maPalette	0.01	0.00	0.01
maPlot	2.60	0.04	2.63
maPlot.func	0	0	0
maSelectGnames	0.01	0.00	0.01
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0	0	0
marrayLayout-class	0	0	0
marrayNorm-class	0.44	0.00	0.44
marrayRaw-class	0.14	0.00	0.14
opVersionID	0	0	0
plotMA	2.25	0.00	2.27
read.Galfile	0.14	0.00	0.14
read.marrayInfo	0.08	0.00	0.08
read.marrayLayout	0.14	0.00	0.14
read.marrayRaw	3.97	0.00	3.97
rm.na	0	0	0
stat.confband.text	0.80	0.01	0.81
stat.gnames	0.42	0.00	0.42
write.list	0.2	0.0	0.2
write.marray	0.08	0.02	0.10
write.xls	0.08	0.00	0.08