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CHECK report for LOLA on merida1

This page was generated on 2019-04-16 11:58:56 -0400 (Tue, 16 Apr 2019).

Package 846/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOLA 1.12.0
Nathan Sheffield
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/LOLA
Branch: RELEASE_3_8
Last Commit: 5841496
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: LOLA
Version: 1.12.0
Command: /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_1.12.0.tar.gz
StartedAt: 2019-04-16 00:55:16 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:57:11 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 114.5 seconds
RetCode: 0
Status:  OK 
CheckDir: LOLA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/LOLA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.0’
* 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
Examples with CPU or elapsed time > 5s
                           user system elapsed
extractEnrichmentOverlaps 9.455  7.482   3.088
redefineUserSets          5.949  6.586   2.161
getRegionFile             5.550  6.000   1.988
writeCombinedEnrichment   6.470  5.069   1.928
getRegionSet              5.717  5.706   1.998
plotTopLOLAEnrichments    5.732  5.644   1.954
runLOLA                   5.788  5.509   1.937
* 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-3.8-bioc/meat/LOLA.Rcheck/00check.log’
for details.



Installation output

LOLA.Rcheck/00install.out

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###
### Running command:
###
###   /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

LOLA.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 
  23.30   19.27   11.53 

Example timings

LOLA.Rcheck/LOLA-Ex.timings

nameusersystemelapsed
buildRestrictedUniverse0.4350.0470.482
checkUniverseAppropriateness0.1240.0050.133
extractEnrichmentOverlaps9.4557.4823.088
getRegionFile5.5506.0001.988
getRegionSet5.7175.7061.998
listRegionSets0.5440.2120.082
loadRegionDB1.0601.3500.455
mergeRegionDBs1.0991.3340.486
plotTopLOLAEnrichments5.7325.6441.954
readBed0.0700.0970.022
readCollection0.6850.8600.276
readCollectionAnnotation0.0070.0020.005
readCollectionFiles0.0690.0760.019
readRegionGRL1.1561.2290.462
readRegionSetAnnotation0.3110.5460.112
redefineUserSets5.9496.5862.161
runLOLA5.7885.5091.937
setSharedDataDir0.0010.0030.000
splitFileIntoCollection0.0450.0590.014
userSets0.0010.0020.000
writeCombinedEnrichment6.4705.0691.928