Package: ArrayTools

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.18.0.tar.gz

StartedAt: 2013-03-24 22:35:33 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:37:06 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 93.1 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ArrayTools.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ArrayTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ArrayTools' version '1.18.0'
* 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 'ArrayTools' can be installed ... OK
* checking installed package size ... OK
* 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 for left-over 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
qa3prime : emptyPlot: warning in png(file = figureName): partial
  argument match of 'file' to 'filename'
qa3prime: warning in png(file = figure2): partial argument match of
  'file' to 'filename'
qa3prime: warning in png(file = figure6): partial argument match of
  'file' to 'filename'
qa3prime: warning in plotAffyRNAdeg(deg, col = rainbow(nchip)): partial
  argument match of 'col' to 'cols'
qa3prime: warning in png(file = figure8): partial argument match of
  'file' to 'filename'
qa3prime: warning in png(file = figure9): partial argument match of
  'file' to 'filename'
preProcessGeneST: no visible binding for global variable
  'hugene10stCONTROL'
preProcessGeneST: no visible binding for global variable
  'mogene10stCONTROL'
regress: no visible global function definition for 'permute.1'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
preProcess3prime 5.675  0.244   5.979
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/ArrayTools.Rcheck/00check.log'
for details.

* installing *source* package 'ArrayTools' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'ArrayTools'
** help
*** installing help indices
** building package indices
** installing vignettes
   'ArrayTools.Rnw' 
** testing if installed package can be loaded

* DONE (ArrayTools)

name	user	system	elapsed
Output2HTML	0.229	0.016	0.246
QC	0.002	0.001	0.002
Sort	0.096	0.008	0.104
contrastMatrix-class	0.044	0.002	0.047
createExpressionSet	0.099	0.002	0.103
createGSEAFiles	0.005	0.001	0.005
createIndex	0.350	0.012	0.364
createIngenuityFile	0.088	0.004	0.093
designMatrix-class	0.015	0.002	0.017
eSetExample	0.004	0.001	0.006
exprsExample	0.003	0.000	0.004
geneFilter	4.074	0.129	4.212
interactionResult-class	0.457	0.018	0.478
pDataExample	0.001	0.001	0.002
postInteraction	0.267	0.009	0.277
preProcess3prime	5.675	0.244	5.979
preProcessGeneST	0.014	0.002	0.015
qa3prime	0	0	0
qaGeneST	0.012	0.002	0.014
regress	0.330	0.010	0.341
regressResult-class	0.083	0.003	0.087
selectSigGene	0.092	0.004	0.096
selectSigGeneInt	0.283	0.025	0.308