Package: marray

Version: 1.28.0

Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings marray_1.28.0.tar.gz

StartedAt: 2011-04-07 11:33:52 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 11:36:18 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 146.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: marray.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/marray.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.28.0'
* checking package name space information ...Warning: unknown namespace directive: function(lib, pkg) require(methods)
 OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'marray' can be installed ... WARNING
Found the following significant warnings:
  Warning: unknown namespace directive: function(lib, pkg) require(methods)
  Warning: unknown namespace directive: function(lib, pkg) require(methods)
See 'D:/biocbld/bbs-2.7-bioc/meat/marray.Rcheck/00install.out' for details.
* 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 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'
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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.7-bioc/meat/marray.Rcheck/00check.log'
for details

* installing *source* package 'marray' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: unknown namespace directive: function(lib, pkg) require(methods)
** help
*** installing help indices
** building package indices ...
Warning: unknown namespace directive: function(lib, pkg) require(methods)
** testing if installed package can be loaded

* DONE (marray)

name	user	system	elapsed
boxplot	0.81	0.00	0.81
checkTargetInfo	0.22	0.00	0.22
dim	0	0	0
findID	0.14	0.00	0.14
htmlPage	0.16	0.00	0.17
image	0.04	0.00	0.05
ma2D	0.02	0.00	0.01
maBoxplot	0	0	0
maColorBar	0.02	0.00	0.02
maCompCoord	0	0	0
maCompInd	0	0	0
maCompLayout	0.01	0.00	0.01
maCompNormA	0	0	0
maCompPlate	0.02	0.00	0.02
maCoord2Ind	0	0	0
maDefaultPar	0	0	0
maDotsDefaults	0	0	0
maDotsMatch	0	0	0
maGenControls	0.20	0.02	0.22
maGeneTable	0.12	0.00	0.12
maImage	1.52	0.01	1.55
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	2.26	0.00	2.26
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	13.61	0.00	13.64
maNormMed	0.00	0.02	0.02
maNormScale	0.56	0.01	0.58
maNum2Logic	0	0	0
maPalette	0	0	0
maPlot	2.28	0.00	2.28
maPlot.func	0	0	0
maSelectGnames	0	0	0
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0	0	0
marrayInfo-class	0	0	0
marrayLayout-class	0	0	0
marrayNorm-class	0.42	0.00	0.43
marrayRaw-class	0.18	0.02	0.18
opVersionID	0	0	0
plotMA	2.06	0.01	2.08
read.Galfile	0.08	0.00	0.08
read.marrayInfo	0.06	0.00	0.06
read.marrayLayout	0.14	0.02	0.16
read.marrayRaw	3.62	0.03	3.65
rm.na	0	0	0
stat.confband.text	0.83	0.00	0.83
stat.gnames	0.41	0.00	0.40
write.list	0.20	0.00	0.21
write.marray	0.08	0.00	0.08
write.xls	0.11	0.00	0.11