BioC 3.0: CHECK report for DEXSeq on oaxaca

Package: DEXSeq

Version: 1.12.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEXSeq_1.12.2.tar.gz

StartedAt: 2015-04-09 22:56:53 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:01:51 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 298.1 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 --no-multiarch DEXSeq_1.12.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/DEXSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.12.2’
* 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 ... [25s/26s] 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’
* 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 ... [59s/59s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DEXSeq                  9.635  0.070   9.775
estimateExonFoldChanges 8.294  0.022   8.414
methods-gr              6.331  0.014   6.389
testForDEU              5.773  0.012   5.820
perGeneQValue           5.640  0.010   5.701
DEXSeqResults           5.590  0.012   5.640
estimateDispersions     5.024  0.014   5.174
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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	9.635	0.070	9.775
DEXSeqDataSet	0.004	0.001	0.004
DEXSeqHTML	0.001	0.000	0.000
DEXSeqResults	5.590	0.012	5.640
accessors	0.080	0.001	0.081
counts	0.011	0.001	0.013
estimateDispersions	5.024	0.014	5.174
estimateExonFoldChanges	8.294	0.022	8.414
methods-gr	6.331	0.014	6.389
perGeneQValue	5.640	0.010	5.701
plotDEXSeq	0.001	0.000	0.000
plotMA	0.001	0.000	0.001
testForDEU	5.773	0.012	5.820