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BioC 3.5: CHECK report for DEXSeq on oaxaca

This page was generated on 2017-03-04 16:41:17 -0500 (Sat, 04 Mar 2017).

Package 328/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEXSeq 1.21.1
Alejandro Reyes
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEXSeq
Last Changed Rev: 124561 / Revision: 127142
Last Changed Date: 2016-11-29 09:04:25 -0500 (Tue, 29 Nov 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: DEXSeq
Version: 1.21.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.21.1.tar.gz
StartedAt: 2017-03-04 01:49:25 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 01:53:23 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 238.1 seconds
RetCode: 0
Status:  OK 
CheckDir: DEXSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEXSeq_1.21.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DEXSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.21.1’
* 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
estimateExonFoldChanges 9.640  0.071   9.716
DEXSeqResults           9.003  0.067   9.121
methods-gr              7.830  0.036   7.869
perGeneQValue           6.862  0.033   6.903
testForDEU              5.885  0.025   5.911
estimateDispersions     5.620  0.064   5.686
* 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.


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)

DEXSeq.Rcheck/DEXSeq-Ex.timings:

nameusersystemelapsed
DEXSeq0.0000.0000.001
DEXSeqDataSet0.0020.0000.002
DEXSeqHTML0.0010.0000.000
DEXSeqResults9.0030.0679.121
accessors0.0730.0080.082
counts0.0140.0090.023
estimateDispersions5.6200.0645.686
estimateExonFoldChanges9.6400.0719.716
methods-gr7.8300.0367.869
perGeneQValue6.8620.0336.903
plotDEXSeq0.0000.0010.001
plotMA0.0010.0000.001
testForDEU5.8850.0255.911