BioC 3.5: CHECK report for DEXSeq on veracruz2

Package: DEXSeq

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.22.0.tar.gz

StartedAt: 2017-08-16 01:59:09 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:03:02 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 233.5 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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DEXSeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.22.0’
* 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 ... 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DEXSeqResults           8.530  0.084   8.869
estimateExonFoldChanges 7.286  0.040   7.521
perGeneQValue           6.676  0.031   6.860
methods-gr              6.661  0.024   6.868
estimateDispersions     5.921  0.036   6.082
testForDEU              5.523  0.038   5.717
* 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-3.5-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	0.000	0.000	0.001
DEXSeqDataSet	0.002	0.000	0.002
DEXSeqHTML	0.001	0.000	0.000
DEXSeqResults	8.530	0.084	8.869
accessors	0.081	0.002	0.089
counts	0.016	0.002	0.018
estimateDispersions	5.921	0.036	6.082
estimateExonFoldChanges	7.286	0.040	7.521
methods-gr	6.661	0.024	6.868
perGeneQValue	6.676	0.031	6.860
plotDEXSeq	0	0	0
plotMA	0.001	0.000	0.001
testForDEU	5.523	0.038	5.717