BioC 3.5: CHECK report for baySeq on oaxaca

Package: baySeq

Version: 2.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.9.1.tar.gz

StartedAt: 2017-03-03 23:26:58 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:31:14 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 255.9 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_2.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/baySeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.9.1’
* 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 70.483  0.262  70.837
getPriors      52.940  0.081  53.058
getLikelihoods 17.474  0.057  17.541
* 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	0.642	0.007	0.650
baySeq-classes	0.223	0.003	0.227
baySeq-package	70.483	0.262	70.837
bimodalSep	0.001	0.000	0.001
densityFunction	0.002	0.000	0.002
getLibsizes	0.009	0.002	0.009
getLikelihoods	17.474	0.057	17.541
getPosteriors	0.009	0.001	0.009
getPriors	52.940	0.081	53.058
getTPs	0.039	0.004	0.043
makeOrderings	0.071	0.003	0.073
marginaliseEqual	0.605	0.002	0.608
marginalisePairwise	0.551	0.002	0.555
plotMA.CD	0.015	0.001	0.017
plotPosteriors	0.035	0.002	0.037
plotPriors	0.018	0.002	0.019
selectTop	0.157	0.003	0.160
summarisePosteriors	0.025	0.002	0.027
topCounts	0.120	0.003	0.123