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

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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

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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)

name	user	system	elapsed
allModels	0.616	0.020	0.635
baySeq-classes	0.200	0.000	0.197
baySeq-package	52.092	0.056	52.308
bimodalSep	0.000	0.000	0.001
densityFunction	0.000	0.000	0.001
getLibsizes	0.008	0.000	0.005
getLikelihoods	15.400	0.004	15.445
getPosteriors	0.012	0.000	0.009
getPriors	36.100	0.008	36.190
getTPs	0.000	0.008	0.010
makeOrderings	0.056	0.004	0.059
marginaliseEqual	0.544	0.000	0.547
marginalisePairwise	0.584	0.004	0.589
plotMA.CD	0.008	0.004	0.013
plotPosteriors	0.020	0.000	0.022
plotPriors	0.012	0.000	0.010
selectTop	0.016	0.000	0.014
summarisePosteriors	0.004	0.000	0.006
topCounts	0.02	0.00	0.02