Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:04 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 1502/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.3.11 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the ontoProc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ontoProc.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: ontoProc |
Version: 2.3.11 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ontoProc_2.3.11.tar.gz |
StartedAt: 2025-10-10 23:50:03 -0400 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-11 00:26:32 -0400 (Sat, 11 Oct 2025) |
EllapsedTime: 2188.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ontoProc_2.3.11.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ontoProc.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘2.3.11’ * package encoding: UTF-8 * 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 ‘ontoProc’ can be installed ... OK * checking installed package size ... INFO installed size is 11.5Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb owl 3.8Mb * 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 ... NOTE ':::' call which should be '::': ‘ontologyPlot:::remove_uninformative_terms’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CLfeat : prupdate: no visible binding for global variable ‘PROSYM’ CLfeat : prupdate: no visible binding for global variable ‘PRID’ CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’ ctmarks : server: no visible binding for global variable ‘text’ ctmarks : server: no visible binding for global variable ‘packDesc2022’ ctmarks : server: no visible binding for global variable ‘packDesc2021’ ctmarks: no visible binding for global variable ‘cumu’ dropStop: no visible binding for global variable ‘stopWords’ getOnto: no visible binding for global variable ‘rdatadateadded’ getOnto: no visible binding for global variable ‘title’ getOnto: no visible binding for global variable ‘description’ ldfToTerm: no visible binding for global variable ‘PROSYM’ sym2CellOnto: no visible binding for global variable ‘PROSYM’ sym2CellOnto: no visible binding for global variable ‘SYMBOL’ Undefined global functions or variables: PRID PROSYM SYMBOL cumu description packDesc2021 packDesc2022 rdatadateadded stopWords text title Consider adding importFrom("graphics", "text", "title") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: findCommonAncestors.Rd: graph, DataFrame-class, List-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'plot.owlents.Rd': ‘plot.owlents’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 sym2CellOnto 226.891 2.562 231.220 siblings_TAG 130.706 1.880 137.316 cleanCLOnames 104.768 3.150 142.364 nomenCheckup 96.613 0.895 98.645 CLfeats 76.613 2.802 105.248 fastGrep 65.301 1.395 67.477 getLeavesFromTerm 60.668 1.067 68.974 common_classes 49.746 2.198 53.649 TermSet-class 42.428 6.474 90.510 mapOneNaive 47.085 0.889 48.630 selectFromMap 46.982 0.844 48.638 liberalMap 46.491 0.893 48.157 findCommonAncestors 45.838 0.880 47.213 getOnto 45.657 0.671 46.719 make_graphNEL_from_ontology_plot 45.361 0.786 46.660 secLevGen 44.928 0.603 46.153 onto_plot2 42.205 0.692 43.254 ontoDiff 13.113 1.030 15.057 graph2paths 9.993 0.063 11.850 plot.owlents 6.127 0.803 96.320 cellTypeToGO 2.234 0.598 7.162 search_labels 0.471 0.030 18.863 bioregistry_ols_resources 0.049 0.027 43.363 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ontoProc’ ... ** this is package ‘ontoProc’ version ‘2.3.11’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (ontoProc)
ontoProc.Rcheck/tests/test.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 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(ontoProc) Loading required package: ontologyIndex > library(testthat) > > test_check("ontoProc") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ] > > > proc.time() user system elapsed 300.556 5.446 313.025
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 76.613 | 2.802 | 105.248 | |
PROSYM | 0.268 | 0.011 | 0.406 | |
TermSet-class | 42.428 | 6.474 | 90.510 | |
allGOterms | 0.122 | 0.005 | 0.244 | |
ancestors | 0.456 | 0.398 | 1.561 | |
ancestors_names | 0.008 | 0.017 | 0.025 | |
bioregistry_ols_resources | 0.049 | 0.027 | 43.363 | |
cellTypeToGO | 2.234 | 0.598 | 7.162 | |
children_names | 0.008 | 0.012 | 0.108 | |
cleanCLOnames | 104.768 | 3.150 | 142.364 | |
common_classes | 49.746 | 2.198 | 53.649 | |
ctmarks | 0.000 | 0.000 | 0.001 | |
cyclicSigset | 0.007 | 0.001 | 0.008 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.004 | 0.003 | 0.008 | |
fastGrep | 65.301 | 1.395 | 67.477 | |
findCommonAncestors | 45.838 | 0.880 | 47.213 | |
formalize | 0.000 | 0.000 | 0.001 | |
getLeavesFromTerm | 60.668 | 1.067 | 68.974 | |
getOnto | 45.657 | 0.671 | 46.719 | |
graph2paths | 9.993 | 0.063 | 11.850 | |
humrna | 0.005 | 0.001 | 0.008 | |
jowl2classgraph | 0.293 | 0.003 | 0.319 | |
jowl2classgraph_nio | 0.781 | 0.023 | 1.072 | |
labels.owlents | 0 | 0 | 0 | |
ldfToTerms | 2.702 | 0.075 | 3.082 | |
liberalMap | 46.491 | 0.893 | 48.157 | |
makeSelectInput | 0.000 | 0.001 | 0.001 | |
make_graphNEL_from_ontology_plot | 45.361 | 0.786 | 46.660 | |
mapOneNaive | 47.085 | 0.889 | 48.630 | |
minicorpus | 0.002 | 0.002 | 0.004 | |
nomenCheckup | 96.613 | 0.895 | 98.645 | |
ontoDiff | 13.113 | 1.030 | 15.057 | |
onto_plot2 | 42.205 | 0.692 | 43.254 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 0.023 | 0.005 | 0.029 | |
packDesc2019 | 0.004 | 0.003 | 0.007 | |
packDesc2021 | 0.002 | 0.001 | 0.004 | |
packDesc2022 | 0.002 | 0.001 | 0.004 | |
packDesc2023 | 0.002 | 0.013 | 0.016 | |
parents | 0.004 | 0.001 | 0.005 | |
plot.owlents | 6.127 | 0.803 | 96.320 | |
quickOnto | 0.421 | 0.033 | 0.462 | |
recognizedPredicates | 0 | 0 | 0 | |
search_labels | 0.471 | 0.030 | 18.863 | |
secLevGen | 44.928 | 0.603 | 46.153 | |
selectFromMap | 46.982 | 0.844 | 48.638 | |
setup_entities | 0.005 | 0.001 | 0.006 | |
setup_entities2 | 0.379 | 0.011 | 0.393 | |
seur3kTab | 0.004 | 0.002 | 0.007 | |
siblings_TAG | 130.706 | 1.880 | 137.316 | |
stopWords | 0.001 | 0.002 | 0.003 | |
subclasses | 0.006 | 0.002 | 0.007 | |
sym2CellOnto | 226.891 | 2.562 | 231.220 | |
valid_ontonames | 0.001 | 0.000 | 0.001 | |