Package: LOLA

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LOLA_1.8.0.tar.gz

StartedAt: 2018-04-12 05:39:57 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:41:47 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 109.5 seconds

RetCode: 0

Status:  OK

CheckDir: LOLA.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 LOLA_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/LOLA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LOLA/DESCRIPTION’ ... OK
* this is package ‘LOLA’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘simpleCache’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘LOLA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Nathan Sheffield [aut, cre]
  Christoph Bock [cre]
Authors@R field gives no person with maintainer role, valid email
address and non-empty name.
* 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
extractEnrichmentOverlaps 4.755   0.26   4.051
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/LOLA.Rcheck/00check.log’
for details.

* installing *source* package ‘LOLA’ ...
** 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 (LOLA)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(LOLA)
> 
> test_check("LOLA")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 51 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.657   0.705  10.830 

name	user	system	elapsed
buildRestrictedUniverse	0.509	0.011	0.530
checkUniverseAppropriateness	0.412	0.003	0.418
extractEnrichmentOverlaps	4.755	0.260	4.051
getRegionFile	2.356	0.250	1.814
getRegionSet	2.222	0.236	1.564
listRegionSets	0.103	0.038	0.049
loadRegionDB	0.510	0.082	0.293
mergeRegionDBs	0.497	0.023	0.384
plotTopLOLAEnrichments	2.206	0.151	1.483
readBed	0.036	0.009	0.015
readCollection	0.322	0.068	0.160
readCollectionAnnotation	0.008	0.002	0.006
readCollectionFiles	0.011	0.001	0.012
readRegionGRL	0.380	0.027	0.301
readRegionSetAnnotation	0.040	0.015	0.049
redefineUserSets	2.010	0.120	1.786
runLOLA	1.977	0.108	1.957
setSharedDataDir	0.001	0.000	0.000
splitFileIntoCollection	0.015	0.004	0.011
userSets	0.002	0.000	0.001
writeCombinedEnrichment	2.252	0.214	1.661