BioC 3.3: CHECK report for DEXSeq on morelia

Package: DEXSeq

Version: 1.17.32

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.17.32.tar.gz

StartedAt: 2016-04-21 01:36:01 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 01:40:38 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 277.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DEXSeq.Rcheck

Warnings: 1

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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_1.17.32.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/DEXSeq.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.17.32’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocParallel’ ‘Biobase’ ‘SummarizedExperiment’ ‘IRanges’
  ‘GenomicRanges’ ‘DESeq2’ ‘AnnotationDbi’ ‘RColorBrewer’ ‘S4Vectors’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [23s/23s] 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 ... OK
* 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 ... [60s/62s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
estimateExonFoldChanges 10.137  0.084  10.660
DEXSeqResults            8.251  0.073   8.424
methods-gr               8.200  0.037   8.355
perGeneQValue            8.047  0.030   8.197
testForDEU               7.468  0.037   7.546
estimateDispersions      6.216  0.023   6.333
* 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
  ‘/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	0.001	0.000	0.000
DEXSeqDataSet	0.003	0.001	0.004
DEXSeqHTML	0.001	0.000	0.000
DEXSeqResults	8.251	0.073	8.424
accessors	0.116	0.002	0.123
counts	0.017	0.002	0.021
estimateDispersions	6.216	0.023	6.333
estimateExonFoldChanges	10.137	0.084	10.660
methods-gr	8.200	0.037	8.355
perGeneQValue	8.047	0.030	8.197
plotDEXSeq	0.001	0.000	0.001
plotMA	0.001	0.000	0.001
testForDEU	7.468	0.037	7.546