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CHECK report for baySeq on malbec1

This page was generated on 2021-05-06 12:26:57 -0400 (Thu, 06 May 2021).

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 2.24.0  (landing page)
Thomas J. Hardcastle
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/baySeq
Branch: RELEASE_3_12
Last Commit: 4221784
Last Changed Date: 2020-10-27 10:36:38 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: baySeq
Version: 2.24.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:baySeq.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings baySeq_2.24.0.tar.gz
StartedAt: 2021-05-05 23:16:38 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:20:46 -0400 (Wed, 05 May 2021)
EllapsedTime: 248.4 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-3.12-bioc/R/bin/R CMD check --install=check:baySeq.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings baySeq_2.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/baySeq.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.24.0’
* 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 (user + system) or elapsed time > 5s
                 user system elapsed
baySeq-package 58.752  0.044  58.916
getPriors      40.688  0.008  40.772
getLikelihoods 15.304  0.004  15.347
* 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-3.12-bioc/R/bin/R CMD INSTALL baySeq
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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
allModels0.6240.0240.649
baySeq-classes0.1960.0000.199
baySeq-package58.752 0.04458.916
bimodalSep0.0040.0000.002
densityFunction0.0000.0000.001
getLibsizes0.0040.0040.010
getLikelihoods15.304 0.00415.347
getPosteriors0.0080.0000.007
getPriors40.688 0.00840.772
getTPs0.0000.0040.007
makeOrderings0.0360.0040.041
marginaliseEqual0.3640.0040.369
marginalisePairwise0.440.000.44
plotMA.CD0.0400.0000.039
plotPosteriors0.0640.0040.071
plotPriors0.0320.0000.031
selectTop0.0160.0000.017
summarisePosteriors0.0080.0000.005
topCounts0.0160.0040.021