BioC 3.3: CHECK report for DEXSeq on morelia

Package: DEXSeq

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.17.0.tar.gz

StartedAt: 2015-10-22 05:23:42 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 05:26:58 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 196.6 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.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 DEXSeq_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/DEXSeq.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.17.0’
* 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 ‘DEXSeq’ can be installed ... [13s/13s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEXSeqDataSet: no visible global function definition for ‘DataFrame’
estimateExonFoldChanges: no visible global function definition for
  ‘DataFrame’
show.DEXSeqResults: no visible global function definition for
  ‘DataFrame’
show,DEXSeqResults: no visible global function definition for
  ‘DataFrame’
Undefined global functions or variables:
  DataFrame
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [75s/74s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
estimateExonFoldChanges 25.015  0.549  25.219
DEXSeq                  23.777  0.537  24.021
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘DEXSeq’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEXSeq)

name	user	system	elapsed
DEXSeq	23.777	0.537	24.021
DEXSeqDataSet	0.001	0.000	0.002
DEXSeqHTML	0.001	0.000	0.001
DEXSeqResults	3.827	0.061	3.888
accessors	0.086	0.002	0.089
counts	0.013	0.001	0.015
estimateDispersions	3.414	0.012	3.427
estimateExonFoldChanges	25.015	0.549	25.219
methods-gr	3.524	0.037	3.560
perGeneQValue	3.928	0.018	3.949
plotDEXSeq	0.001	0.000	0.001
plotMA	0.001	0.000	0.001
testForDEU	4.076	0.016	4.102