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CHECK report for DEXSeq on veracruz1

This page was generated on 2018-04-12 13:34:22 -0400 (Thu, 12 Apr 2018).

Package 360/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEXSeq 1.24.4
Alejandro Reyes
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/DEXSeq
Branch: RELEASE_3_6
Last Commit: 59bc2b3
Last Changed Date: 2018-03-28 16:56:28 -0400 (Wed, 28 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DEXSeq
Version: 1.24.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.24.4.tar.gz
StartedAt: 2018-04-12 02:50:39 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:54:35 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 236.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DEXSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.24.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DEXSeq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.24.4’
* 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 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           8.725  0.089   8.976
estimateExonFoldChanges 8.722  0.043   8.911
methods-gr              7.843  0.062   8.040
perGeneQValue           6.576  0.042   6.713
testForDEU              6.233  0.032   6.370
estimateDispersions     5.970  0.027   6.129
* 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-3.6-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.



Installation output

DEXSeq.Rcheck/00install.out

* 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)

Tests output


Example timings

DEXSeq.Rcheck/DEXSeq-Ex.timings

nameusersystemelapsed
DEXSeq0.0000.0000.001
DEXSeqDataSet0.0030.0010.004
DEXSeqHTML0.0010.0000.001
DEXSeqResults8.7250.0898.976
accessors0.0810.0020.087
counts0.0170.0030.020
estimateDispersions5.9700.0276.129
estimateExonFoldChanges8.7220.0438.911
methods-gr7.8430.0628.040
perGeneQValue6.5760.0426.713
plotDEXSeq0.0000.0000.001
plotMA0.0010.0000.001
testForDEU6.2330.0326.370