BioC 3.3: CHECK report for EDASeq on linux2.bioconductor.org

Package: EDASeq

Version: 2.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings EDASeq_2.5.0.tar.gz

StartedAt: 2015-10-27 03:33:43 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:36:35 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 172.0 seconds

RetCode: 0

Status:  OK

CheckDir: EDASeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings EDASeq_2.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/EDASeq.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EDASeq/DESCRIPTION’ ... OK
* this is package ‘EDASeq’ version ‘2.5.0’
* 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 ... [15s/15s] 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: no visible global function definition for
  ‘countBam’
plot,BamFileList-FastqFileList: no visible global function definition
  for ‘elementMetadata’
plot,BamFileList-FastqFileList: no visible global function definition
  for ‘countBam’
plotQuality,BamFile: no visible global function definition for ‘path’
plotQuality,BamFile: no visible global function definition for ‘narrow’
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for ‘path’
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for ‘narrow’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘quality’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘path’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘narrow’
Undefined global functions or variables:
  biocLite countBam elementMetadata narrow path quality
* 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 files in ‘vignettes’ ... OK
* checking examples ... [10s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘plotPCA.R’ [8s/8s]
 [9s/9s] 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
  ‘/home/biocbuild/bbs-3.3-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	0.295	0.007	0.305
SeqExpressionSet-class	0.101	0.004	0.104
betweenLaneNormalization-methods	0.138	0.000	0.138
biasBoxplot-methods	0.117	0.000	0.117
biasPlot-methods	0.29	0.00	0.29
getGeneLengthAndGCContent	0.734	0.000	1.400
newSeqExpressionSet	0.02	0.00	0.02
plotPCA-methods	0.535	0.008	0.543
plotRLE-methods	0.702	0.004	0.710
withinLaneNormalization-methods	0.134	0.007	0.141