BioC 2.13: CHECK report for ArrayTools on perceval

Package: ArrayTools

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.22.0.tar.gz

StartedAt: 2014-04-04 23:30:18 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:32:19 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 121.5 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ArrayTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.22.0’
* 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 ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’ ‘Biobase’ ‘methods’
A package should be listed in only one of these fields.
* 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 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
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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ArrayTools.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
preProcess3prime 7.81  0.156   7.979
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.174	0.009	0.183
QC	0.007	0.001	0.007
Sort	0.213	0.006	0.219
contrastMatrix-class	0.069	0.003	0.072
createExpressionSet	0.101	0.001	0.102
createGSEAFiles	0.008	0.000	0.009
createIndex	0.346	0.005	0.351
createIngenuityFile	0.092	0.001	0.093
designMatrix-class	0.029	0.001	0.031
eSetExample	0.008	0.001	0.009
exprsExample	0.009	0.001	0.010
geneFilter	4.269	0.086	4.355
interactionResult-class	0.871	0.024	0.895
pDataExample	0.011	0.001	0.013
postInteraction	0.301	0.005	0.307
preProcess3prime	7.810	0.156	7.979
preProcessGeneST	0.043	0.012	0.055
qa3prime	0.030	0.004	0.035
qaGeneST	0.039	0.006	0.045
regress	0.161	0.008	0.169
regressResult-class	0.142	0.014	0.156
selectSigGene	0.152	0.011	0.165
selectSigGeneInt	0.382	0.016	0.399