BioC 3.4: CHECK report for roar on morelia

Package: roar

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings roar_1.9.1.tar.gz

StartedAt: 2016-09-20 12:29:54 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:32:08 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 133.9 seconds

RetCode: 0

Status:  OK

CheckDir: roar.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 roar_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/roar.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘roar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘roar’ version ‘1.9.1’
* 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 ‘roar’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ‘roar’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (roar)

name	user	system	elapsed
RoarDataset-class	0.002	0.000	0.003
RoarDataset-constructor	0.232	0.010	0.241
RoarDatasetFromFiles-constructor	0	0	0
RoarDatasetMultipleAPA-class	0.001	0.000	0.001
RoarDatasetMultipleAPA-constructor	0.199	0.006	0.205
RoarDatasetMultipleAPAFromFiles-constructor	0.000	0.000	0.001
computePairedPvals-method	0.583	0.008	0.591
computePvals-method	0.342	0.006	0.348
computeRoars-method	0.357	0.005	0.362
countPrePost-method	0.337	0.005	0.342
countResults-method	0.363	0.005	0.368
fpkmResults-method	0.352	0.005	0.357
pvalueCorrectFilter-method	0.355	0.005	0.360
pvalueFilter-method	0.392	0.006	0.397
standardFilter-method	0.379	0.005	0.383
totalResults-method	0.349	0.005	0.354