Package: DEXSeq

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEXSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEXSeq_1.30.0.tar.gz

StartedAt: 2019-10-16 02:10:41 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:16:53 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 371.7 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 --install=check:DEXSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEXSeq_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DEXSeq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.30.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
estimateExonFoldChanges 14.453  0.192  14.688
DEXSeqResults           14.266  0.329  14.630
methods-gr              12.676  0.089  13.372
perGeneQValue           12.498  0.065  12.641
testForDEU              10.588  0.061  10.686
estimateDispersions      8.520  0.049   8.581
* 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-3.9-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DEXSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DEXSeq’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DEXSeq)

name	user	system	elapsed
DEXSeq	0.001	0.000	0.000
DEXSeqDataSet	0.001	0.001	0.001
DEXSeqHTML	0.001	0.000	0.000
DEXSeqResults	14.266	0.329	14.630
accessors	0.254	0.005	0.260
counts	0.021	0.005	0.027
estimateDispersions	8.520	0.049	8.581
estimateExonFoldChanges	14.453	0.192	14.688
methods-gr	12.676	0.089	13.372
perGeneQValue	12.498	0.065	12.641
plotDEXSeq	0.000	0.000	0.001
plotMA	0.001	0.001	0.001
testForDEU	10.588	0.061	10.686