BioC 3.2: CHECK report for EDASeq on oaxaca

Package: EDASeq

Version: 2.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EDASeq_2.4.0.tar.gz

StartedAt: 2015-10-27 03:17:36 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:21:38 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 242.1 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 EDASeq_2.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/EDASeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EDASeq/DESCRIPTION’ ... OK
* this is package ‘EDASeq’ version ‘2.4.0’
* 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 ... [21s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.isAvailable: no visible global function definition for ‘biocLite’
barplot,BamFileList : .local: no visible global function definition for
  ‘countBam’
plot,BamFileList-FastqFileList : .local: no visible global function
  definition for ‘elementMetadata’
plot,BamFileList-FastqFileList : .local: no visible global function
  definition for ‘countBam’
plotQuality,BamFile : .local: no visible global function definition for
  ‘path’
plotQuality,BamFile : .local: no visible global function definition for
  ‘narrow’
plotQuality,BamFileList : .local : <anonymous>: no visible global
  function definition for ‘path’
plotQuality,BamFileList : .local : <anonymous>: no visible global
  function definition for ‘narrow’
plotQuality,FastqFileList : .local : <anonymous>: no visible global
  function definition for ‘quality’
plotQuality,FastqFileList : .local : <anonymous>: no visible global
  function definition for ‘path’
plotQuality,FastqFileList : .local : <anonymous>: no visible global
  function definition for ‘narrow’
* 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 ... [13s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘plotPCA.R’ [10s/11s]
 [11s/11s] 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EDASeq)

name	user	system	elapsed
MDPlot-methods	0.284	0.017	0.845
SeqExpressionSet-class	0.095	0.002	0.113
betweenLaneNormalization-methods	0.143	0.006	0.151
biasBoxplot-methods	0.083	0.002	0.114
biasPlot-methods	0.183	0.005	0.367
getGeneLengthAndGCContent	0.988	0.010	4.539
newSeqExpressionSet	0.027	0.000	0.027
plotPCA-methods	0.654	0.012	0.687
plotRLE-methods	0.802	0.011	2.263
withinLaneNormalization-methods	0.225	0.013	0.239