Package: ArrayTools

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.19.0.tar.gz

StartedAt: 2013-03-25 01:14:46 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:16:51 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 125.1 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ArrayTools.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.19.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'ArrayTools' can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
preProcess3prime 6.933  0.258   7.200
geneFilter       5.035  0.148   5.189
* 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-2.12-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	0.223	0.030	0.262
QC	0.012	0.007	0.020
Sort	0.164	0.017	0.182
contrastMatrix-class	0.092	0.026	0.123
createExpressionSet	0.109	0.008	0.117
createGSEAFiles	0.070	0.006	0.076
createIndex	0.587	0.033	0.621
createIngenuityFile	0.159	0.014	0.175
designMatrix-class	0.054	0.018	0.071
eSetExample	0.014	0.007	0.022
exprsExample	0.013	0.009	0.027
geneFilter	5.035	0.148	5.189
interactionResult-class	0.357	0.029	0.386
pDataExample	0.011	0.006	0.018
postInteraction	0.581	0.026	0.608
preProcess3prime	6.933	0.258	7.200
preProcessGeneST	0.023	0.008	0.031
qa3prime	0.012	0.007	0.019
qaGeneST	0.030	0.013	0.043
regress	0.152	0.014	0.167
regressResult-class	0.160	0.019	0.179
selectSigGene	0.161	0.016	0.181
selectSigGeneInt	0.469	0.025	0.494