Package: baySeq

Version: 2.17.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:baySeq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings baySeq_2.17.0.tar.gz

StartedAt: 2019-04-08 22:55:14 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 22:58:52 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 217.3 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:baySeq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings baySeq_2.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/baySeq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.17.0’
* 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 47.955  0.039  48.006
getPriors      34.597  0.000  34.606
getLikelihoods 14.834  0.016  14.851
* 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-3.9-bioc/R/bin/R CMD INSTALL baySeq
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* installing to library ‘/home/biocbuild/bbs-3.9-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	0.584	0.012	0.596
baySeq-classes	0.193	0.000	0.193
baySeq-package	47.955	0.039	48.006
bimodalSep	0.002	0.000	0.001
densityFunction	0.001	0.000	0.001
getLibsizes	0.008	0.000	0.008
getLikelihoods	14.834	0.016	14.851
getPosteriors	0.009	0.000	0.009
getPriors	34.597	0.000	34.606
getTPs	0.003	0.004	0.008
makeOrderings	0.033	0.004	0.037
marginaliseEqual	0.318	0.004	0.321
marginalisePairwise	0.451	0.004	0.455
plotMA.CD	0.017	0.000	0.017
plotPosteriors	0.034	0.000	0.034
plotPriors	0.016	0.000	0.016
selectTop	0.019	0.004	0.023
summarisePosteriors	0.009	0.000	0.008
topCounts	0.031	0.000	0.032