BioC 3.5: CHECK report for baySeq on veracruz2

Package: baySeq

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.10.0.tar.gz

StartedAt: 2017-08-16 00:04:45 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:08:52 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 246.6 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/baySeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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 53.909  0.170  55.639
getPriors      41.628  0.076  45.689
getLikelihoods 16.194  0.059  16.739
* 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	0.420	0.006	0.443
baySeq-classes	0.155	0.003	0.159
baySeq-package	53.909	0.170	55.639
bimodalSep	0.001	0.000	0.002
densityFunction	0.001	0.001	0.002
getLibsizes	0.006	0.001	0.007
getLikelihoods	16.194	0.059	16.739
getPosteriors	0.010	0.002	0.012
getPriors	41.628	0.076	45.689
getTPs	0.035	0.004	0.038
makeOrderings	0.065	0.003	0.102
marginaliseEqual	0.550	0.004	0.574
marginalisePairwise	0.499	0.002	0.525
plotMA.CD	0.013	0.001	0.015
plotPosteriors	0.025	0.001	0.027
plotPriors	0.013	0.002	0.015
selectTop	0.104	0.003	0.107
summarisePosteriors	0.019	0.002	0.020
topCounts	0.097	0.002	0.099