Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-28 12:04 -0400 (Thu, 28 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4613 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4556 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 1483/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.3.9 (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 | OK | TIMEOUT | ||||||||||
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: 2.3.9 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ontoProc_2.3.9.tar.gz |
StartedAt: 2025-08-28 01:34:33 -0400 (Thu, 28 Aug 2025) |
EndedAt: 2025-08-28 02:09:24 -0400 (Thu, 28 Aug 2025) |
EllapsedTime: 2090.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ontoProc_2.3.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ontoProc.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘2.3.9’ * 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 loading without being on the library search path ... 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 203.803 6.819 211.186 cleanCLOnames 132.987 3.559 159.956 siblings_TAG 114.708 4.658 120.223 nomenCheckup 86.568 1.974 88.840 fastGrep 84.450 3.794 100.634 common_classes 77.340 3.641 102.091 CLfeats 69.929 4.968 75.940 getLeavesFromTerm 60.241 1.728 62.462 getOnto 55.580 3.603 60.678 findCommonAncestors 53.143 1.986 63.950 liberalMap 43.981 2.793 49.012 make_graphNEL_from_ontology_plot 42.836 1.599 44.727 selectFromMap 42.169 1.587 44.025 onto_plot2 41.302 1.835 43.369 mapOneNaive 40.519 1.536 42.320 TermSet-class 39.511 2.360 42.132 secLevGen 38.357 2.223 40.901 ontoDiff 12.026 2.325 14.846 graph2paths 12.597 0.099 14.987 search_labels 0.437 0.035 14.866 bioregistry_ols_resources 0.070 0.009 12.605 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ontoProc’ ... ** this is package ‘ontoProc’ version ‘2.3.9’ ** 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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-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(ontoProc) Loading required package: ontologyIndex > library(testthat) > > test_check("ontoProc") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ] > > > proc.time() user system elapsed 265.593 9.534 276.817
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 69.929 | 4.968 | 75.940 | |
PROSYM | 0.237 | 0.009 | 0.246 | |
TermSet-class | 39.511 | 2.360 | 42.132 | |
allGOterms | 0.098 | 0.003 | 0.101 | |
ancestors | 0.628 | 0.136 | 0.714 | |
ancestors_names | 0.013 | 0.001 | 0.007 | |
bioregistry_ols_resources | 0.070 | 0.009 | 12.605 | |
cellTypeToGO | 1.550 | 0.077 | 1.627 | |
children_names | 0.005 | 0.000 | 0.005 | |
cleanCLOnames | 132.987 | 3.559 | 159.956 | |
common_classes | 77.340 | 3.641 | 102.091 | |
ctmarks | 0.001 | 0.000 | 0.000 | |
cyclicSigset | 0.019 | 0.001 | 0.041 | |
demoApp | 0.001 | 0.000 | 0.000 | |
dropStop | 0.011 | 0.001 | 0.026 | |
fastGrep | 84.450 | 3.794 | 100.634 | |
findCommonAncestors | 53.143 | 1.986 | 63.950 | |
formalize | 0.001 | 0.000 | 0.001 | |
getLeavesFromTerm | 60.241 | 1.728 | 62.462 | |
getOnto | 55.580 | 3.603 | 60.678 | |
graph2paths | 12.597 | 0.099 | 14.987 | |
humrna | 0.006 | 0.002 | 0.009 | |
jowl2classgraph | 0.395 | 0.004 | 0.402 | |
jowl2classgraph_nio | 0.914 | 0.005 | 0.957 | |
labels.owlents | 0.235 | 0.002 | 0.237 | |
ldfToTerms | 4.585 | 0.047 | 4.903 | |
liberalMap | 43.981 | 2.793 | 49.012 | |
makeSelectInput | 0 | 0 | 0 | |
make_graphNEL_from_ontology_plot | 42.836 | 1.599 | 44.727 | |
mapOneNaive | 40.519 | 1.536 | 42.320 | |
minicorpus | 0.000 | 0.001 | 0.001 | |
nomenCheckup | 86.568 | 1.974 | 88.840 | |
ontoDiff | 12.026 | 2.325 | 14.846 | |
onto_plot2 | 41.302 | 1.835 | 43.369 | |
onto_roots | 0 | 0 | 0 | |
owl2cache | 0.022 | 0.003 | 0.026 | |
packDesc2019 | 0.002 | 0.001 | 0.003 | |
packDesc2021 | 0.002 | 0.000 | 0.003 | |
packDesc2022 | 0.001 | 0.001 | 0.002 | |
packDesc2023 | 0.003 | 0.000 | 0.002 | |
parents | 0.004 | 0.001 | 0.005 | |
plot.owlents | 0.220 | 0.004 | 0.223 | |
quickOnto | 0.333 | 0.007 | 0.342 | |
recognizedPredicates | 0 | 0 | 0 | |
search_labels | 0.437 | 0.035 | 14.866 | |
secLevGen | 38.357 | 2.223 | 40.901 | |
selectFromMap | 42.169 | 1.587 | 44.025 | |
setup_entities | 0.006 | 0.000 | 0.006 | |
setup_entities2 | 0.343 | 0.015 | 0.358 | |
seur3kTab | 0.003 | 0.000 | 0.003 | |
siblings_TAG | 114.708 | 4.658 | 120.223 | |
stopWords | 0.001 | 0.001 | 0.001 | |
subclasses | 0.006 | 0.000 | 0.006 | |
sym2CellOnto | 203.803 | 6.819 | 211.186 | |
valid_ontonames | 0.000 | 0.000 | 0.001 | |