BioC 3.2: CHECK report for DEXSeq on perceval

Package: DEXSeq

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.16.1.tar.gz

StartedAt: 2015-11-10 04:09:07 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 04:14:27 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 320.0 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_1.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DEXSeq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.16.1’
* 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 ... [20s/22s] 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 ... [122s/121s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DEXSeq                  39.691  0.870  40.135
estimateExonFoldChanges 39.142  0.875  39.570
DEXSeqResults            6.547  0.129   6.677
methods-gr               6.327  0.087   6.414
testForDEU               6.273  0.083   6.357
perGeneQValue            6.137  0.023   6.161
estimateDispersions      5.178  0.015   5.193
* 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-3.2-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	39.691	0.870	40.135
DEXSeqDataSet	0.002	0.000	0.003
DEXSeqHTML	0.001	0.001	0.001
DEXSeqResults	6.547	0.129	6.677
accessors	0.090	0.009	0.100
counts	0.016	0.008	0.025
estimateDispersions	5.178	0.015	5.193
estimateExonFoldChanges	39.142	0.875	39.570
methods-gr	6.327	0.087	6.414
perGeneQValue	6.137	0.023	6.161
plotDEXSeq	0.000	0.000	0.001
plotMA	0.000	0.000	0.001
testForDEU	6.273	0.083	6.357