BioC 3.2: CHECK report for DEXSeq on zin1

Package: DEXSeq

Version: 1.16.10

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.16.10.tar.gz

StartedAt: 2016-04-23 00:02:53 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:06:20 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 207.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DEXSeq.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.16.10.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/DEXSeq.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.16.10’
* 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 ... [16s/16s] 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'DEXSeqDataSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [44s/45s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
estimateExonFoldChanges 7.127  0.000   7.151
DEXSeqResults           6.538  0.020   6.564
methods-gr              6.010  0.000   6.007
perGeneQValue           5.834  0.003   5.833
testForDEU              5.694  0.004   5.900
* 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 WARNING, 1 NOTE
See
  ‘/home/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	0	0	0
DEXSeqDataSet	0.002	0.000	0.003
DEXSeqHTML	0	0	0
DEXSeqResults	6.538	0.020	6.564
accessors	0.069	0.000	0.069
counts	0.013	0.000	0.013
estimateDispersions	4.808	0.037	4.840
estimateExonFoldChanges	7.127	0.000	7.151
methods-gr	6.010	0.000	6.007
perGeneQValue	5.834	0.003	5.833
plotDEXSeq	0	0	0
plotMA	0.001	0.000	0.001
testForDEU	5.694	0.004	5.900