Nathan Sheffield
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/LOLA |
| Branch: RELEASE_3_9 |
| Last Commit: 3e4dc7c |
| Last Changed Date: 2019-05-02 11:53:57 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:56:17 -0400 (Wed, 16 Oct 2019).
| Package 885/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| LOLA 1.14.0 Nathan Sheffield
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: LOLA |
| Version: 1.14.0 |
| 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_1.14.0.tar.gz |
| StartedAt: 2019-10-16 04:08:16 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:11:06 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 170.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LOLA.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/LOLA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.0’
* 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 7.726 2.155 4.326
getRegionFile 5.801 2.795 2.727
runLOLA 6.022 2.110 2.531
getRegionSet 5.658 1.592 2.908
plotTopLOLAEnrichments 4.646 1.287 2.701
* 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-3.9-bioc/meat/LOLA.Rcheck/00check.log’
for details.
LOLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL LOLA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘LOLA’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (LOLA)
LOLA.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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: 34 | SKIPPED: 0 | WARNINGS: 17 | FAILED: 0 ]
>
> proc.time()
user system elapsed
25.119 6.090 16.819
LOLA.Rcheck/LOLA-Ex.timings
| name | user | system | elapsed | |
| buildRestrictedUniverse | 0.605 | 0.092 | 0.697 | |
| checkUniverseAppropriateness | 0.217 | 0.023 | 0.240 | |
| extractEnrichmentOverlaps | 7.726 | 2.155 | 4.326 | |
| getRegionFile | 5.801 | 2.795 | 2.727 | |
| getRegionSet | 5.658 | 1.592 | 2.908 | |
| listRegionSets | 0.256 | 0.235 | 0.123 | |
| loadRegionDB | 1.348 | 0.639 | 0.815 | |
| mergeRegionDBs | 1.080 | 0.344 | 0.916 | |
| plotTopLOLAEnrichments | 4.646 | 1.287 | 2.701 | |
| readBed | 0.078 | 0.053 | 0.026 | |
| readCollection | 0.661 | 0.306 | 0.335 | |
| readCollectionAnnotation | 0.007 | 0.002 | 0.006 | |
| readCollectionFiles | 0.060 | 0.037 | 0.022 | |
| readRegionGRL | 1.229 | 0.641 | 0.826 | |
| readRegionSetAnnotation | 1.087 | 0.047 | 0.127 | |
| redefineUserSets | 3.756 | 0.856 | 3.276 | |
| runLOLA | 6.022 | 2.110 | 2.531 | |
| setSharedDataDir | 0.002 | 0.001 | 0.000 | |
| splitFileIntoCollection | 0.043 | 0.030 | 0.016 | |
| userSets | 0.002 | 0.002 | 0.001 | |
| writeCombinedEnrichment | 3.209 | 0.951 | 2.808 | |