Package: DEXSeq

Version: 1.24.4

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.24.4.tar.gz

StartedAt: 2018-04-11 22:54:42 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:57:59 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 197.4 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.24.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DEXSeq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.24.4’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
estimateExonFoldChanges 6.892  0.024   6.920
DEXSeqResults           6.716  0.024   6.903
methods-gr              5.648  0.016   5.671
perGeneQValue           5.284  0.012   5.309
estimateDispersions     5.040  0.020   5.062
* 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-3.6-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	0.000	0.000	0.002
DEXSeqHTML	0.000	0.000	0.001
DEXSeqResults	6.716	0.024	6.903
accessors	0.072	0.000	0.070
counts	0.012	0.000	0.012
estimateDispersions	5.040	0.020	5.062
estimateExonFoldChanges	6.892	0.024	6.920
methods-gr	5.648	0.016	5.671
perGeneQValue	5.284	0.012	5.309
plotDEXSeq	0	0	0
plotMA	0.000	0.000	0.001
testForDEU	4.768	0.008	4.776