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CHECK report for baySeq on malbec2

This page was generated on 2018-01-19 07:05:33 -0500 (Fri, 19 Jan 2018).

Package 98/1482HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.13.0
Thomas J. Hardcastle
Snapshot Date: 2018-01-18 17:01:21 -0500 (Thu, 18 Jan 2018)
URL: https://git.bioconductor.org/packages/baySeq
Branch: master
Last Commit: f1008f2
Last Changed Date: 2017-10-30 12:52:09 -0500 (Mon, 30 Oct 2017)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: baySeq
Version: 2.13.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_2.13.0.tar.gz
StartedAt: 2018-01-18 21:30:40 -0500 (Thu, 18 Jan 2018)
EndedAt: 2018-01-18 21:33:01 -0500 (Thu, 18 Jan 2018)
EllapsedTime: 141.7 seconds
RetCode: 0
Status:  OK 
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_2.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/baySeq.Rcheck’
* using R Under development (unstable) (2017-12-05 r73840)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘baySeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘baySeq’ version ‘2.13.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘baySeq’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
baySeq-package 36.808  0.044  36.875
getPriors      25.108  0.000  25.127
getLikelihoods 11.600  0.012  11.618
* 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: OK


Installation output

baySeq.Rcheck/00install.out

* installing *source* package ‘baySeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (baySeq)

Tests output


Example timings

baySeq.Rcheck/baySeq-Ex.timings

nameusersystemelapsed
allModels0.3840.0000.384
baySeq-classes0.1400.0000.141
baySeq-package36.808 0.04436.875
bimodalSep0.0040.0000.001
densityFunction0.0000.0000.001
getLibsizes0.0080.0000.006
getLikelihoods11.600 0.01211.618
getPosteriors0.020.000.02
getPriors25.108 0.00025.127
getTPs0.0240.0000.024
makeOrderings0.0400.0040.042
marginaliseEqual0.3440.0000.346
marginalisePairwise0.3040.0000.303
plotMA.CD0.0120.0000.010
plotPosteriors0.0200.0000.021
plotPriors0.0040.0040.010
selectTop0.0840.0000.084
summarisePosteriors0.0120.0000.014
topCounts0.0600.0120.070