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CHECK report for baySeq on malbec1

This page was generated on 2020-04-15 12:05:41 -0400 (Wed, 15 Apr 2020).

Package 121/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.20.0
Thomas J. Hardcastle
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/baySeq
Branch: RELEASE_3_10
Last Commit: f4f56a9
Last Changed Date: 2019-10-29 13:08:09 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: baySeq
Version: 2.20.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:baySeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings baySeq_2.20.0.tar.gz
StartedAt: 2020-04-15 00:42:12 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:45:55 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 223.3 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-3.10-bioc/R/bin/R CMD check --install=check:baySeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings baySeq_2.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/baySeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.20.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 52.092  0.056  52.308
getPriors      36.100  0.008  36.190
getLikelihoods 15.400  0.004  15.445
* 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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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL baySeq
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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
allModels0.6160.0200.635
baySeq-classes0.2000.0000.197
baySeq-package52.092 0.05652.308
bimodalSep0.0000.0000.001
densityFunction0.0000.0000.001
getLibsizes0.0080.0000.005
getLikelihoods15.400 0.00415.445
getPosteriors0.0120.0000.009
getPriors36.100 0.00836.190
getTPs0.0000.0080.010
makeOrderings0.0560.0040.059
marginaliseEqual0.5440.0000.547
marginalisePairwise0.5840.0040.589
plotMA.CD0.0080.0040.013
plotPosteriors0.0200.0000.022
plotPriors0.0120.0000.010
selectTop0.0160.0000.014
summarisePosteriors0.0040.0000.006
topCounts0.020.000.02