BioC 3.1: CHECK report for DEXSeq on zin2

Package: DEXSeq

Version: 1.14.2

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.14.2.tar.gz

StartedAt: 2015-10-09 00:30:52 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:35:38 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 286.0 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.14.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/DEXSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.14.2’
* 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 ... [12s/19s] 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 ... [78s/112s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DEXSeq                  26.125  0.231  38.249
estimateExonFoldChanges 25.688  0.187  35.126
methods-gr               4.166  0.016   6.544
testForDEU               4.114  0.010   6.278
DEXSeqResults            4.086  0.009   5.881
perGeneQValue            4.059  0.000   5.566
estimateDispersions      3.672  0.029   5.077
* 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘DEXSeq’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (DEXSeq)

name	user	system	elapsed
DEXSeq	26.125	0.231	38.249
DEXSeqDataSet	0.002	0.000	0.002
DEXSeqHTML	0.000	0.000	0.001
DEXSeqResults	4.086	0.009	5.881
accessors	0.058	0.004	0.061
counts	0.005	0.003	0.009
estimateDispersions	3.672	0.029	5.077
estimateExonFoldChanges	25.688	0.187	35.126
methods-gr	4.166	0.016	6.544
perGeneQValue	4.059	0.000	5.566
plotDEXSeq	0.001	0.000	0.001
plotMA	0.001	0.000	0.000
testForDEU	4.114	0.010	6.278