Multiple platform build/check report for BioC 3.7 - CHECK report for LOLA on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LOLA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LOLA_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/LOLA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 ... OK
* 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 ... 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/LOLA.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL LOLA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘LOLA’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LOLA)

Tests output


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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 
 13.530   0.844  10.434

Example timings

name	user	system	elapsed
buildRestrictedUniverse	0.352	0.046	0.398
checkUniverseAppropriateness	0.125	0.005	0.130
extractEnrichmentOverlaps	4.072	0.275	2.558
getRegionFile	3.124	0.224	1.707
getRegionSet	3.035	0.269	1.674
listRegionSets	0.262	0.043	0.080
loadRegionDB	0.760	0.054	0.437
mergeRegionDBs	0.591	0.040	0.479
plotTopLOLAEnrichments	2.800	0.219	1.759
readBed	0.056	0.014	0.020
readCollection	0.586	0.078	0.274
readCollectionAnnotation	0.007	0.001	0.008
readCollectionFiles	0.017	0.001	0.018
readRegionGRL	0.528	0.054	0.437
readRegionSetAnnotation	0.085	0.033	0.071
redefineUserSets	2.865	0.348	1.950
runLOLA	3.390	0.218	1.887
setSharedDataDir	0.004	0.000	0.001
splitFileIntoCollection	0.041	0.012	0.015
userSets	0.005	0.002	0.002
writeCombinedEnrichment	3.101	0.250	1.774

CHECK report for LOLA on merida2

Summary

Command output

Installation output

Tests output

Example timings