Package: marray

Version: 1.28.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.28.0.tar.gz

StartedAt: 2011-04-07 07:31:58 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 07:33:22 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 83.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: marray.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/marray.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/marray.Rcheck/00install.out’ for details.
* 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 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’
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 ... 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
  ‘/loc/home/biocbuild/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	0.652	0.016	0.668
checkTargetInfo	0.180	0.004	0.183
dim	0.004	0.000	0.002
findID	0.108	0.004	0.113
htmlPage	0.140	0.004	0.144
image	0.036	0.000	0.038
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.012	0.000	0.013
maCompCoord	0.004	0.000	0.001
maCompInd	0.004	0.000	0.004
maCompLayout	0.008	0.000	0.008
maCompNormA	0	0	0
maCompPlate	0.008	0.000	0.007
maCoord2Ind	0.004	0.004	0.006
maDefaultPar	0	0	0
maDotsDefaults	0.000	0.000	0.001
maDotsMatch	0.004	0.000	0.001
maGenControls	0.188	0.004	0.193
maGeneTable	0.108	0.000	0.106
maImage	1.188	0.012	1.198
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	0.000	0.000	0.001
maNorm	2.732	0.000	2.730
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0	0	0
maNormMain	17.469	0.012	17.482
maNormMed	0	0	0
maNormScale	0.504	0.000	0.503
maNum2Logic	0	0	0
maPalette	0.008	0.000	0.007
maPlot	2.768	0.008	2.779
maPlot.func	0	0	0
maSelectGnames	0.008	0.000	0.009
maText	0	0	0
maTop	0	0	0
mapGeneInfo	0.000	0.000	0.001
marrayInfo-class	0	0	0
marrayLayout-class	0.000	0.000	0.001
marrayNorm-class	0.396	0.004	0.398
marrayRaw-class	0.164	0.004	0.169
opVersionID	0.004	0.000	0.002
plotMA	2.528	0.000	2.545
read.Galfile	0.076	0.000	0.075
read.marrayInfo	0.056	0.004	0.059
read.marrayLayout	0.112	0.000	0.111
read.marrayRaw	2.617	0.000	2.617
rm.na	0	0	0
stat.confband.text	0.728	0.020	0.750
stat.gnames	0.416	0.000	0.417
write.list	0.184	0.000	0.183
write.marray	0.072	0.000	0.069
write.xls	0.076	0.000	0.078