Package: marray

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.28.0.tar.gz

StartedAt: 2011-03-31 06:40:04 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 06:42:24 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 139.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: marray.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/marray.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘/Users/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
  ‘/Users/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	0.813	0.186	1.016
checkTargetInfo	0.184	0.029	0.216
dim	0.004	0.001	0.004
findID	0.170	0.022	0.195
htmlPage	0.203	0.042	0.247
image	0.089	0.005	0.095
ma2D	0	0	0
maBoxplot	0	0	0
maColorBar	0.019	0.000	0.020
maCompCoord	0.001	0.000	0.002
maCompInd	0.006	0.001	0.007
maCompLayout	0.011	0.000	0.012
maCompNormA	0	0	0
maCompPlate	0.012	0.002	0.015
maCoord2Ind	0.007	0.002	0.009
maDefaultPar	0	0	0
maDotsDefaults	0.002	0.000	0.003
maDotsMatch	0.002	0.000	0.002
maGenControls	0.406	0.022	0.432
maGeneTable	0.108	0.014	0.124
maImage	1.363	0.345	1.790
maImage.func	0.000	0.000	0.001
maInd2Coord	0.007	0.002	0.011
maLegendLines	0	0	0
maLoess	0.000	0.001	0.000
maLoessLines	0	0	0
maMAD	0	0	0
maMed	0	0	0
maNorm	3.977	0.277	4.332
maNorm2D	0	0	0
maNormLoess	0	0	0
maNormMAD	0.000	0.000	0.001
maNormMain	26.714	1.083	28.401
maNormMed	0.001	0.000	0.000
maNormScale	0.570	0.228	0.978
maNum2Logic	0.000	0.000	0.001
maPalette	0.012	0.001	0.013
maPlot	4.405	0.365	4.958
maPlot.func	0	0	0
maSelectGnames	0.014	0.001	0.015
maText	0.000	0.001	0.000
maTop	0	0	0
mapGeneInfo	0.001	0.000	0.002
marrayInfo-class	0	0	0
marrayLayout-class	0.001	0.001	0.000
marrayNorm-class	0.579	0.198	0.798
marrayRaw-class	0.245	0.052	0.304
opVersionID	0.002	0.000	0.003
plotMA	3.856	0.248	4.201
read.Galfile	0.214	0.022	0.260
read.marrayInfo	0.111	0.010	0.132
read.marrayLayout	0.183	0.017	0.203
read.marrayRaw	3.822	0.261	4.282
rm.na	0.001	0.000	0.001
stat.confband.text	1.127	0.085	1.304
stat.gnames	0.650	0.060	0.724
write.list	0.251	0.064	0.337
write.marray	0.124	0.021	0.164
write.xls	0.152	0.039	0.229