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CHECK report for baySeq on merida1

This page was generated on 2020-10-24 11:07:49 -0400 (Sat, 24 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE baySeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 128/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.23.0
Thomas J. Hardcastle
Snapshot Date: 2020-10-23 14:40:36 -0400 (Fri, 23 Oct 2020)
URL: https://git.bioconductor.org/packages/baySeq
Branch: master
Last Commit: 2ea28df
Last Changed Date: 2020-04-27 14:20:16 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: baySeq
Version: 2.23.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:baySeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings baySeq_2.23.0.tar.gz
StartedAt: 2020-10-23 23:31:02 -0400 (Fri, 23 Oct 2020)
EndedAt: 2020-10-23 23:36:11 -0400 (Fri, 23 Oct 2020)
EllapsedTime: 308.8 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 --install=check:baySeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings baySeq_2.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/baySeq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.23.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
baySeq-package 66.920  0.736  67.778
getPriors      57.620  0.146  57.857
getLikelihoods 13.189  0.357  13.576
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL baySeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘baySeq’ ...
** using staged installation
** R
** data
** 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 (baySeq)

Tests output


Example timings

baySeq.Rcheck/baySeq-Ex.timings

nameusersystemelapsed
allModels0.6960.0310.727
baySeq-classes0.1760.0050.180
baySeq-package66.920 0.73667.778
bimodalSep0.0010.0000.001
densityFunction0.0010.0000.002
getLibsizes0.0120.0130.026
getLikelihoods13.189 0.35713.576
getPosteriors0.0070.0010.007
getPriors57.620 0.14657.857
getTPs0.0120.0120.024
makeOrderings0.0800.0060.085
marginaliseEqual0.6560.0040.661
marginalisePairwise0.7360.0080.748
plotMA.CD0.0250.0040.030
plotPosteriors0.0740.0080.084
plotPriors0.0460.0040.070
selectTop0.0280.0070.035
summarisePosteriors0.0110.0030.014
topCounts0.0380.0080.047