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CHECK report for LOLA on veracruz1

This page was generated on 2018-04-12 13:41:32 -0400 (Thu, 12 Apr 2018).

Package 757/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOLA 1.8.0
Nathan Sheffield
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/LOLA
Branch: RELEASE_3_6
Last Commit: 0e9367e
Last Changed Date: 2017-10-30 12:40:54 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: LOLA
Version: 1.8.0
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

Command output

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


* 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.



Installation output

LOLA.Rcheck/00install.out

* 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)

Tests output

LOLA.Rcheck/tests/testthat.Rout


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 

Example timings

LOLA.Rcheck/LOLA-Ex.timings

nameusersystemelapsed
buildRestrictedUniverse0.5090.0110.530
checkUniverseAppropriateness0.4120.0030.418
extractEnrichmentOverlaps4.7550.2604.051
getRegionFile2.3560.2501.814
getRegionSet2.2220.2361.564
listRegionSets0.1030.0380.049
loadRegionDB0.5100.0820.293
mergeRegionDBs0.4970.0230.384
plotTopLOLAEnrichments2.2060.1511.483
readBed0.0360.0090.015
readCollection0.3220.0680.160
readCollectionAnnotation0.0080.0020.006
readCollectionFiles0.0110.0010.012
readRegionGRL0.3800.0270.301
readRegionSetAnnotation0.0400.0150.049
redefineUserSets2.0100.1201.786
runLOLA1.9770.1081.957
setSharedDataDir0.0010.0000.000
splitFileIntoCollection0.0150.0040.011
userSets0.0020.0000.001
writeCombinedEnrichment2.2520.2141.661