Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1093/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LOLA 1.35.0 (landing page) Nathan Sheffield
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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. |
Package: LOLA |
Version: 1.35.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LOLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LOLA_1.35.0.tar.gz |
StartedAt: 2024-06-10 05:32:28 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 05:36:25 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 236.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LOLA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LOLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LOLA_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/LOLA.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘LOLA/DESCRIPTION’ ... OK * this is package ‘LOLA’ version ‘1.35.0’ * 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 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 (user + system) or elapsed time > 5s user system elapsed extractEnrichmentOverlaps 4.508 0.181 8.151 * 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
LOLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LOLA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 14.958 0.755 18.006
LOLA.Rcheck/LOLA-Ex.timings
name | user | system | elapsed | |
buildRestrictedUniverse | 0.795 | 0.073 | 1.006 | |
checkUniverseAppropriateness | 0.270 | 0.008 | 0.289 | |
extractEnrichmentOverlaps | 4.508 | 0.181 | 8.151 | |
getRegionFile | 2.574 | 0.050 | 2.891 | |
getRegionSet | 2.609 | 0.047 | 2.951 | |
listRegionSets | 0.009 | 0.002 | 0.012 | |
loadRegionDB | 0.088 | 0.003 | 0.090 | |
mergeRegionDBs | 0.150 | 0.005 | 0.164 | |
plotTopLOLAEnrichments | 2.669 | 0.034 | 2.955 | |
readBed | 0.035 | 0.001 | 0.037 | |
readCollection | 0.467 | 0.003 | 0.514 | |
readCollectionAnnotation | 0.007 | 0.002 | 0.009 | |
readCollectionFiles | 0.020 | 0.002 | 0.025 | |
readRegionGRL | 0.673 | 0.007 | 0.750 | |
readRegionSetAnnotation | 0.004 | 0.002 | 0.007 | |
redefineUserSets | 2.994 | 0.046 | 3.308 | |
runLOLA | 2.605 | 0.035 | 2.918 | |
setSharedDataDir | 0.001 | 0.000 | 0.001 | |
splitFileIntoCollection | 0.015 | 0.003 | 0.018 | |
userSets | 0.000 | 0.000 | 0.001 | |
writeCombinedEnrichment | 2.647 | 0.032 | 2.980 | |