BioC 2.13: CHECK report for ArrayTools on zin1

Package: ArrayTools

Version: 1.22.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ArrayTools_1.22.0.tar.gz

StartedAt: 2014-04-04 23:38:13 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:39:19 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 66.6 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ArrayTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.22.0’
* 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 ... [4s/4s] 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 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 ... [12s/12s] OK
* 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
  ‘/home/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	0.116	0.008	0.122
QC	0.004	0.000	0.004
Sort	0.124	0.004	0.131
contrastMatrix-class	0.040	0.004	0.047
createExpressionSet	0.080	0.000	0.082
createGSEAFiles	0.004	0.000	0.007
createIndex	0.272	0.004	0.274
createIngenuityFile	0.068	0.000	0.068
designMatrix-class	0.016	0.004	0.021
eSetExample	0.008	0.000	0.006
exprsExample	0.000	0.004	0.005
geneFilter	2.772	0.012	2.787
interactionResult-class	0.332	0.000	0.334
pDataExample	0.004	0.000	0.004
postInteraction	0.212	0.004	0.216
preProcess3prime	4.576	0.072	4.653
preProcessGeneST	0.024	0.000	0.023
qa3prime	0.000	0.000	0.001
qaGeneST	0.02	0.00	0.02
regress	0.092	0.000	0.095
regressResult-class	0.108	0.000	0.111
selectSigGene	0.104	0.000	0.104
selectSigGeneInt	0.268	0.000	0.268