Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-08 12:07 -0400 (Mon, 08 Sep 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" | 4823 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 1485/2322 | 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 | ERROR | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ontoProc |
Version: 2.3.9 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ontoProc_2.3.9.tar.gz |
StartedAt: 2025-09-05 10:13:14 -0000 (Fri, 05 Sep 2025) |
EndedAt: 2025-09-05 10:53:14 -0000 (Fri, 05 Sep 2025) |
EllapsedTime: 2400.6 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: ontoProc.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ontoProc_2.3.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ontoProc.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 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 ...
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 86.947 | 3.389 | 135.258 | |
PROSYM | 0.238 | 0.008 | 0.247 | |
TermSet-class | 55.188 | 1.608 | 73.730 | |
allGOterms | 0.096 | 0.004 | 0.307 | |
ancestors | 3.238 | 0.276 | 7.757 | |
ancestors_names | 0.008 | 0.000 | 0.017 | |
bioregistry_ols_resources | 0.055 | 0.000 | 33.031 | |
cellTypeToGO | 1.814 | 0.071 | 5.351 | |
children_names | 0.011 | 0.000 | 0.035 | |
cleanCLOnames | 128.199 | 2.006 | 221.349 | |
common_classes | 62.045 | 1.943 | 92.260 | |
ctmarks | 0.000 | 0.000 | 0.001 | |
cyclicSigset | 0.058 | 0.004 | 0.062 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.005 | 0.001 | 0.009 | |
fastGrep | 75.846 | 1.681 | 106.037 | |
findCommonAncestors | 58.030 | 1.339 | 74.064 | |
formalize | 0 | 0 | 0 | |
getLeavesFromTerm | 75.033 | 1.655 | 100.282 | |
getOnto | 58.174 | 1.624 | 84.543 | |
graph2paths | 9.929 | 0.160 | 11.506 | |
humrna | 0.007 | 0.000 | 0.007 | |
jowl2classgraph | 0.445 | 0.000 | 0.462 | |
jowl2classgraph_nio | 1.018 | 0.000 | 1.099 | |
labels.owlents | 0.316 | 0.004 | 0.384 | |
ldfToTerms | 2.420 | 0.015 | 2.620 | |
liberalMap | 58.391 | 1.412 | 83.451 | |
makeSelectInput | 0.001 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 59.327 | 1.649 | 79.856 | |
mapOneNaive | 57.229 | 1.485 | 76.657 | |
minicorpus | 0.002 | 0.000 | 0.001 | |
nomenCheckup | 125.100 | 2.386 | 167.638 | |
ontoDiff | 15.309 | 1.678 | 32.261 | |
onto_plot2 | 57.836 | 1.693 | 72.781 | |
onto_roots | 0.001 | 0.000 | 0.000 | |
owl2cache | 0.028 | 0.004 | 0.032 | |
packDesc2019 | 0.004 | 0.000 | 0.004 | |
packDesc2021 | 0.003 | 0.000 | 0.003 | |
packDesc2022 | 0.003 | 0.000 | 0.003 | |
packDesc2023 | 0.003 | 0.000 | 0.004 | |
parents | 0.006 | 0.000 | 0.007 | |
plot.owlents | 0.292 | 0.008 | 0.324 | |
quickOnto | 0.464 | 0.008 | 0.498 | |
recognizedPredicates | 0 | 0 | 0 | |
search_labels | 0.485 | 0.013 | 20.965 | |
secLevGen | 54.381 | 1.818 | 69.527 | |
selectFromMap | 57.820 | 1.595 | 70.458 | |
setup_entities | 0.007 | 0.000 | 0.007 | |
setup_entities2 | 0.441 | 0.008 | 0.449 | |
seur3kTab | 0.004 | 0.000 | 0.009 | |
siblings_TAG | 162.935 | 4.425 | 232.389 | |
stopWords | 0.001 | 0.000 | 0.001 | |
subclasses | 0.007 | 0.000 | 0.011 | |