Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-06 13:52 -0400 (Wed, 06 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4813 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 1479/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.3.8 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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: 2.3.8 |
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_2.3.8.tar.gz |
StartedAt: 2025-08-06 01:02:44 -0400 (Wed, 06 Aug 2025) |
EndedAt: 2025-08-06 01:38:36 -0400 (Wed, 06 Aug 2025) |
EllapsedTime: 2151.5 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_2.3.8.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 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘2.3.8’ * 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 202.754 6.106 209.343 cleanCLOnames 152.754 6.643 182.321 siblings_TAG 113.974 5.312 120.039 nomenCheckup 87.414 1.275 88.926 fastGrep 81.053 2.601 90.433 CLfeats 69.481 4.240 74.565 common_classes 70.360 3.188 83.735 findCommonAncestors 57.407 2.518 67.821 getLeavesFromTerm 57.542 1.847 59.647 getOnto 56.773 2.334 60.144 make_graphNEL_from_ontology_plot 42.363 1.817 44.464 selectFromMap 42.164 1.631 44.018 liberalMap 43.011 0.617 43.909 mapOneNaive 41.495 1.651 43.376 onto_plot2 41.156 1.644 43.033 secLevGen 40.397 1.707 42.330 TermSet-class 38.156 1.517 39.895 labels.owlents 20.448 0.747 20.156 owl2cache 15.261 1.119 11.916 graph2paths 13.256 0.300 14.980 ontoDiff 11.321 0.893 12.644 ancestors 10.012 0.356 10.981 search_labels 0.454 0.014 14.014 bioregistry_ols_resources 0.042 0.014 12.632 * 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 ‘2.3.8’ ** 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 266.659 13.253 281.315
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 69.481 | 4.240 | 74.565 | |
PROSYM | 0.236 | 0.003 | 0.240 | |
TermSet-class | 38.156 | 1.517 | 39.895 | |
allGOterms | 0.092 | 0.005 | 0.096 | |
ancestors | 10.012 | 0.356 | 10.981 | |
ancestors_names | 3.814 | 0.101 | 3.915 | |
bioregistry_ols_resources | 0.042 | 0.014 | 12.632 | |
cellTypeToGO | 1.673 | 0.220 | 1.893 | |
children_names | 3.746 | 0.196 | 3.943 | |
cleanCLOnames | 152.754 | 6.643 | 182.321 | |
common_classes | 70.360 | 3.188 | 83.735 | |
ctmarks | 0 | 0 | 0 | |
cyclicSigset | 0.011 | 0.002 | 0.013 | |
demoApp | 0.001 | 0.000 | 0.001 | |
dropStop | 0.007 | 0.002 | 0.009 | |
fastGrep | 81.053 | 2.601 | 90.433 | |
findCommonAncestors | 57.407 | 2.518 | 67.821 | |
formalize | 0.001 | 0.000 | 0.001 | |
getLeavesFromTerm | 57.542 | 1.847 | 59.647 | |
getOnto | 56.773 | 2.334 | 60.144 | |
graph2paths | 13.256 | 0.300 | 14.980 | |
humrna | 0.013 | 0.000 | 0.026 | |
jowl2classgraph | 0.653 | 0.004 | 0.660 | |
jowl2classgraph_nio | 1.300 | 0.026 | 1.368 | |
labels.owlents | 20.448 | 0.747 | 20.156 | |
ldfToTerms | 2.539 | 0.042 | 2.592 | |
liberalMap | 43.011 | 0.617 | 43.909 | |
makeSelectInput | 0.001 | 0.000 | 0.000 | |
make_graphNEL_from_ontology_plot | 42.363 | 1.817 | 44.464 | |
mapOneNaive | 41.495 | 1.651 | 43.376 | |
minicorpus | 0.002 | 0.000 | 0.002 | |
nomenCheckup | 87.414 | 1.275 | 88.926 | |
ontoDiff | 11.321 | 0.893 | 12.644 | |
onto_plot2 | 41.156 | 1.644 | 43.033 | |
onto_roots | 0.001 | 0.000 | 0.000 | |
owl2cache | 15.261 | 1.119 | 11.916 | |
packDesc2019 | 0.003 | 0.001 | 0.004 | |
packDesc2021 | 0.002 | 0.000 | 0.002 | |
packDesc2022 | 0.001 | 0.002 | 0.002 | |
packDesc2023 | 0.002 | 0.000 | 0.002 | |
parents | 3.892 | 0.152 | 4.045 | |
plot.owlents | 4.677 | 0.086 | 4.763 | |
quickOnto | 0.353 | 0.010 | 0.363 | |
recognizedPredicates | 0.001 | 0.000 | 0.000 | |
search_labels | 0.454 | 0.014 | 14.014 | |
secLevGen | 40.397 | 1.707 | 42.330 | |
selectFromMap | 42.164 | 1.631 | 44.018 | |
setup_entities | 3.566 | 0.021 | 3.587 | |
setup_entities2 | 0.368 | 0.024 | 0.392 | |
seur3kTab | 0.002 | 0.001 | 0.004 | |
siblings_TAG | 113.974 | 5.312 | 120.039 | |
stopWords | 0.001 | 0.000 | 0.002 | |
subclasses | 3.862 | 0.030 | 3.893 | |
sym2CellOnto | 202.754 | 6.106 | 209.343 | |
valid_ontonames | 0 | 0 | 0 | |