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CHECK report for baySeq on veracruz1

This page was generated on 2018-04-12 13:33:22 -0400 (Thu, 12 Apr 2018).

Package 98/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.12.0
Thomas J. Hardcastle
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/baySeq
Branch: RELEASE_3_6
Last Commit: 740d041
Last Changed Date: 2017-10-30 12:39:27 -0400 (Mon, 30 Oct 2017)
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  OK  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: baySeq
Version: 2.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.12.0.tar.gz
StartedAt: 2018-04-12 00:46:00 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:49:45 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 224.8 seconds
RetCode: 0
Status:  OK 
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/baySeq.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 ‘baySeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘baySeq’ version ‘2.12.0’
* 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 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
baySeq-package 57.084  0.266  59.227
getPriors      40.907  0.089  41.874
getLikelihoods 10.499  0.107  10.830
* 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
allModels0.7360.0210.789
baySeq-classes0.1940.0040.213
baySeq-package57.084 0.26659.227
bimodalSep0.0010.0000.002
densityFunction0.0010.0010.002
getLibsizes0.0060.0010.007
getLikelihoods10.499 0.10710.830
getPosteriors0.0270.0010.029
getPriors40.907 0.08941.874
getTPs0.0310.0040.036
makeOrderings0.0540.0040.059
marginaliseEqual0.4900.0050.504
marginalisePairwise0.4810.0020.499
plotMA.CD0.0130.0020.015
plotPosteriors0.0240.0010.026
plotPriors0.0110.0010.020
selectTop0.1190.0030.122
summarisePosteriors0.0210.0010.022
topCounts0.0890.0030.093