BioC 3.5: CHECK report for baySeq on malbec2

Package: baySeq

Version: 2.10.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_2.10.0.tar.gz

StartedAt: 2017-10-17 21:23:45 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:26:40 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 174.7 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_2.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/baySeq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.10.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 44.080  0.044  44.233
getPriors      27.996  0.004  28.021
getLikelihoods 13.888  0.020  13.921
* 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

* installing *source* package ‘baySeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (baySeq)

name	user	system	elapsed
allModels	0.368	0.004	0.374
baySeq-classes	0.136	0.000	0.137
baySeq-package	44.080	0.044	44.233
bimodalSep	0.000	0.000	0.001
densityFunction	0.004	0.000	0.001
getLibsizes	0.004	0.000	0.005
getLikelihoods	13.888	0.020	13.921
getPosteriors	0.024	0.000	0.023
getPriors	27.996	0.004	28.021
getTPs	0.024	0.000	0.025
makeOrderings	0.040	0.000	0.041
marginaliseEqual	0.344	0.000	0.343
marginalisePairwise	0.316	0.000	0.318
plotMA.CD	0.008	0.000	0.010
plotPosteriors	0.02	0.00	0.02
plotPriors	0.008	0.000	0.010
selectTop	0.092	0.000	0.089
summarisePosteriors	0.012	0.000	0.014
topCounts	0.060	0.000	0.062