BioC 2.12: CHECK report for ArrayTools on george2

Package: ArrayTools

Version: 1.20.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ArrayTools_1.20.0.tar.gz

StartedAt: 2013-10-09 00:12:54 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:15:15 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 141.3 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ArrayTools.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ArrayTools’ version ‘1.20.0’
* 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 ... [10s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
preProcess3prime 10.925  0.216  11.383
geneFilter        6.496  0.132   6.694
* 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
  ‘/home/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
** testing if installed package can be loaded
* DONE (ArrayTools)

name	user	system	elapsed
Output2HTML	0.236	0.008	0.244
QC	0.024	0.004	0.026
Sort	0.140	0.000	0.142
contrastMatrix-class	0.164	0.008	0.172
createExpressionSet	0.244	0.004	0.250
createGSEAFiles	0.032	0.000	0.031
createIndex	0.824	0.004	0.827
createIngenuityFile	0.136	0.004	0.139
designMatrix-class	0.064	0.000	0.065
eSetExample	0.024	0.000	0.022
exprsExample	0.016	0.004	0.019
geneFilter	6.496	0.132	6.694
interactionResult-class	0.400	0.004	0.405
pDataExample	0.004	0.008	0.014
postInteraction	0.400	0.008	0.405
preProcess3prime	10.925	0.216	11.383
preProcessGeneST	0.024	0.000	0.026
qa3prime	0.068	0.000	0.065
qaGeneST	0.064	0.000	0.065
regress	0.212	0.000	0.214
regressResult-class	0.292	0.000	0.293
selectSigGene	0.224	0.000	0.225
selectSigGeneInt	0.472	0.000	0.490