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This page was generated on 2023-05-10 10:04:34 -0000 (Wed, 10 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6211
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CHECK results for LOLA on kunpeng1


To the developers/maintainers of the LOLA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LOLA.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1063/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOLA 1.31.0  (landing page)
Nathan Sheffield
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 May 2023)
git_url: https://git.bioconductor.org/packages/LOLA
git_branch: devel
git_last_commit: 66575cd
git_last_commit_date: 2023-04-25 14:41:21 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: LOLA
Version: 1.31.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:LOLA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings LOLA_1.31.0.tar.gz
StartedAt: 2023-05-09 19:55:06 -0000 (Tue, 09 May 2023)
EndedAt: 2023-05-09 19:57:12 -0000 (Tue, 09 May 2023)
EllapsedTime: 126.2 seconds
RetCode: 0
Status:   OK  
CheckDir: LOLA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:LOLA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings LOLA_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/LOLA.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘LOLA/DESCRIPTION’ ... OK
* this is package ‘LOLA’ version ‘1.31.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ...
  ‘choosingUniverse.Rmd’ using ‘UTF-8’... OK
  ‘gettingStarted.Rmd’ using ‘UTF-8’... OK
  ‘usingLOLACore.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

LOLA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL LOLA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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)

Tests output

LOLA.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  8.770   0.434   9.190 

Example timings

LOLA.Rcheck/LOLA-Ex.timings

nameusersystemelapsed
buildRestrictedUniverse0.4090.0040.412
checkUniverseAppropriateness0.1420.0030.145
extractEnrichmentOverlaps2.5590.0992.668
getRegionFile1.4310.0001.431
getRegionSet1.4370.0321.469
listRegionSets0.0070.0000.007
loadRegionDB0.0550.0000.055
mergeRegionDBs0.0840.0040.088
plotTopLOLAEnrichments1.4350.0081.444
readBed0.020.000.02
readCollection0.2390.0000.239
readCollectionAnnotation0.0040.0000.005
readCollectionFiles0.0110.0000.011
readRegionGRL0.3600.0040.364
readRegionSetAnnotation0.0020.0000.003
redefineUserSets1.4290.0321.461
runLOLA1.7650.0401.805
setSharedDataDir000
splitFileIntoCollection0.0040.0040.009
userSets000
writeCombinedEnrichment1.3820.0281.411