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CHECK report for baySeq on malbec2

This page was generated on 2018-07-19 10:32:02 -0400 (Thu, 19 Jul 2018).

Package 100/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.14.0
Thomas J. Hardcastle
Snapshot Date: 2018-07-18 16:45:10 -0400 (Wed, 18 Jul 2018)
URL: https://git.bioconductor.org/packages/baySeq
Branch: RELEASE_3_7
Last Commit: 850f7f8
Last Changed Date: 2018-04-30 10:35:12 -0400 (Mon, 30 Apr 2018)
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: 2.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:baySeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings baySeq_2.14.0.tar.gz
StartedAt: 2018-07-18 22:35:08 -0400 (Wed, 18 Jul 2018)
EndedAt: 2018-07-18 22:37:37 -0400 (Wed, 18 Jul 2018)
EllapsedTime: 149.1 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 --install=check:baySeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings baySeq_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/baySeq.Rcheck’
* using R version 3.5.1 RC (2018-06-24 r74929)
* 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 ‘2.14.0’
* 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 35.992  0.040  36.054
getPriors      28.508  0.008  28.544
getLikelihoods 11.452  0.016  11.473
* 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-3.7-bioc/R/bin/R CMD INSTALL baySeq
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘baySeq’ ...
** 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
* DONE (baySeq)

Tests output


Example timings

baySeq.Rcheck/baySeq-Ex.timings

nameusersystemelapsed
allModels0.3560.0080.363
baySeq-classes0.1000.0000.102
baySeq-package35.992 0.04036.054
bimodalSep0.0000.0000.002
densityFunction0.0000.0000.001
getLibsizes0.0080.0000.006
getLikelihoods11.452 0.01611.473
getPosteriors0.0040.0040.008
getPriors28.508 0.00828.544
getTPs0.0080.0000.008
makeOrderings0.0440.0040.045
marginaliseEqual0.3080.0000.307
marginalisePairwise0.3000.0000.299
plotMA.CD0.0120.0000.011
plotPosteriors0.0240.0000.023
plotPriors0.0120.0000.011
selectTop0.020.000.02
summarisePosteriors0.0080.0040.010
topCounts0.0320.0000.032