Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

This page was generated on 2025-04-17 11:47 -0400 (Thu, 17 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4667
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1141/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOLA 1.38.0  (landing page)
Nathan Sheffield
Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025)
git_url: https://git.bioconductor.org/packages/LOLA
git_branch: RELEASE_3_21
git_last_commit: 7bc2706
git_last_commit_date: 2025-04-15 10:53:20 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for LOLA on kunpeng2

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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: LOLA
Version: 1.38.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:LOLA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings LOLA_1.38.0.tar.gz
StartedAt: 2025-04-17 08:10:43 -0000 (Thu, 17 Apr 2025)
EndedAt: 2025-04-17 08:12:47 -0000 (Thu, 17 Apr 2025)
EllapsedTime: 123.3 seconds
RetCode: 0
Status:   OK  
CheckDir: LOLA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:LOLA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings LOLA_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/LOLA.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LOLA/DESCRIPTION’ ... OK
* this is package ‘LOLA’ version ‘1.38.0’
* 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 code 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 loading without being on the library search path ... 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

LOLA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL LOLA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘LOLA’ ...
** this is package ‘LOLA’ version ‘1.38.0’
** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 15 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 10.310   0.919  11.246 

Example timings

LOLA.Rcheck/LOLA-Ex.timings

nameusersystemelapsed
buildRestrictedUniverse0.4250.0390.466
checkUniverseAppropriateness0.1550.0040.159
extractEnrichmentOverlaps2.2250.4042.642
getRegionFile1.9930.0302.032
getRegionSet1.9600.0652.029
listRegionSets0.0270.0080.034
loadRegionDB0.4320.0030.434
mergeRegionDBs0.4650.0030.470
plotTopLOLAEnrichments1.9920.0312.027
readBed0.0230.0000.024
readCollection0.2690.0200.289
readCollectionAnnotation0.0050.0000.005
readCollectionFiles0.0130.0000.014
readRegionGRL0.4290.0270.456
readRegionSetAnnotation0.0290.0050.034
redefineUserSets2.0180.0902.110
runLOLA2.2820.1742.463
setSharedDataDir0.0010.0000.000
splitFileIntoCollection0.0110.0000.010
userSets000
writeCombinedEnrichment1.9460.0632.017