BioC 2.14: CHECK report for EDASeq on petty

Package: EDASeq

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EDASeq_1.10.0.tar.gz

StartedAt: 2014-10-07 21:47:53 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:55:24 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 450.7 seconds

RetCode: 0

Status:  OK

CheckDir: EDASeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EDASeq_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/EDASeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EDASeq/DESCRIPTION’ ... OK
* this is package ‘EDASeq’ version ‘1.10.0’
* 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 ‘EDASeq’ can be installed ... [44s/45s] 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:
  ‘BiocGenerics’ ‘DESeq’
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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [27s/28s] 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/EDASeq.Rcheck/00check.log’
for details.

* installing *source* package ‘EDASeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘barplot’ from package ‘graphics’ in package ‘EDASeq’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘EDASeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EDASeq)

name	user	system	elapsed
MDPlot-methods	1.071	0.036	1.123
SeqExpressionSet-class	0.195	0.004	0.203
betweenLaneNormalization-methods	0.331	0.008	0.338
biasBoxplot-methods	0.280	0.006	0.302
biasPlot-methods	0.529	0.010	0.559
newSeqExpressionSet	0.079	0.000	0.080
plotRLE-methods	2.141	0.033	2.191
withinLaneNormalization-methods	0.537	0.008	0.547