Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 1481/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.3.9 (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: 2.3.9 |
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_2.3.9.tar.gz |
StartedAt: 2025-08-08 20:42:55 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 20:53:26 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 631.3 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_2.3.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ontoProc.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 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 71.944 0.574 73.023 siblings_TAG 40.249 0.549 41.482 cleanCLOnames 33.009 0.302 40.147 nomenCheckup 28.821 0.212 29.381 CLfeats 25.069 0.609 26.456 getLeavesFromTerm 19.057 0.250 19.534 fastGrep 18.576 0.253 19.066 common_classes 16.704 0.712 21.593 make_graphNEL_from_ontology_plot 16.022 0.287 20.676 liberalMap 15.198 0.152 17.592 onto_plot2 14.329 0.238 14.861 selectFromMap 14.249 0.221 14.797 mapOneNaive 14.041 0.238 14.535 getOnto 14.027 0.248 14.637 findCommonAncestors 13.999 0.266 14.549 TermSet-class 13.984 0.235 14.527 secLevGen 14.002 0.160 14.379 owl2cache 6.026 0.072 6.102 labels.owlents 5.657 0.098 5.787 ontoDiff 4.296 0.244 5.010 search_labels 0.141 0.006 6.206 bioregistry_ols_resources 0.016 0.007 5.326 * 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-arm64/Resources/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 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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 90.914 1.682 94.224
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 25.069 | 0.609 | 26.456 | |
PROSYM | 0.109 | 0.001 | 0.111 | |
TermSet-class | 13.984 | 0.235 | 14.527 | |
allGOterms | 0.041 | 0.001 | 0.042 | |
ancestors | 4.413 | 0.153 | 4.181 | |
ancestors_names | 1.047 | 0.013 | 1.060 | |
bioregistry_ols_resources | 0.016 | 0.007 | 5.326 | |
cellTypeToGO | 0.695 | 0.043 | 0.739 | |
children_names | 0.999 | 0.012 | 1.011 | |
cleanCLOnames | 33.009 | 0.302 | 40.147 | |
common_classes | 16.704 | 0.712 | 21.593 | |
ctmarks | 0 | 0 | 0 | |
cyclicSigset | 0.002 | 0.000 | 0.002 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.002 | 0.001 | 0.003 | |
fastGrep | 18.576 | 0.253 | 19.066 | |
findCommonAncestors | 13.999 | 0.266 | 14.549 | |
formalize | 0.001 | 0.000 | 0.001 | |
getLeavesFromTerm | 19.057 | 0.250 | 19.534 | |
getOnto | 14.027 | 0.248 | 14.637 | |
graph2paths | 2.649 | 0.060 | 2.712 | |
humrna | 0.003 | 0.001 | 0.003 | |
jowl2classgraph | 0.143 | 0.005 | 0.147 | |
jowl2classgraph_nio | 0.248 | 0.003 | 0.250 | |
labels.owlents | 5.657 | 0.098 | 5.787 | |
ldfToTerms | 1.032 | 0.015 | 1.048 | |
liberalMap | 15.198 | 0.152 | 17.592 | |
makeSelectInput | 0.000 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 16.022 | 0.287 | 20.676 | |
mapOneNaive | 14.041 | 0.238 | 14.535 | |
minicorpus | 0.000 | 0.000 | 0.001 | |
nomenCheckup | 28.821 | 0.212 | 29.381 | |
ontoDiff | 4.296 | 0.244 | 5.010 | |
onto_plot2 | 14.329 | 0.238 | 14.861 | |
onto_roots | 0 | 0 | 0 | |
owl2cache | 6.026 | 0.072 | 6.102 | |
packDesc2019 | 0.001 | 0.001 | 0.002 | |
packDesc2021 | 0.000 | 0.001 | 0.001 | |
packDesc2022 | 0.001 | 0.001 | 0.001 | |
packDesc2023 | 0.001 | 0.001 | 0.002 | |
parents | 1.078 | 0.011 | 1.091 | |
plot.owlents | 1.204 | 0.015 | 1.220 | |
quickOnto | 0.107 | 0.009 | 0.117 | |
recognizedPredicates | 0 | 0 | 0 | |
search_labels | 0.141 | 0.006 | 6.206 | |
secLevGen | 14.002 | 0.160 | 14.379 | |
selectFromMap | 14.249 | 0.221 | 14.797 | |
setup_entities | 0.992 | 0.011 | 1.003 | |
setup_entities2 | 0.184 | 0.004 | 0.189 | |
seur3kTab | 0.001 | 0.000 | 0.001 | |
siblings_TAG | 40.249 | 0.549 | 41.482 | |
stopWords | 0.000 | 0.000 | 0.001 | |
subclasses | 1.088 | 0.011 | 1.102 | |
sym2CellOnto | 71.944 | 0.574 | 73.023 | |
valid_ontonames | 0 | 0 | 0 | |