Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-11 11:48 -0400 (Mon, 11 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 1492/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.2.3 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ontoProc |
Version: 2.2.3 |
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_2.2.3.tar.gz |
StartedAt: 2025-08-08 12:20:35 -0000 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 12:35:40 -0000 (Fri, 08 Aug 2025) |
EllapsedTime: 905.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.2.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘2.2.3’ * 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 10.5Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb owl 3.3Mb * 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 54.895 2.312 63.148 CLfeats 36.213 2.101 53.541 siblings_TAG 27.085 2.026 38.031 getLeavesFromTerm 19.132 0.626 22.618 nomenCheckup 18.421 0.699 33.810 fastGrep 18.043 0.607 23.342 cleanCLOnames 16.090 0.938 20.448 common_classes 14.224 1.123 20.089 findCommonAncestors 12.325 0.754 16.057 selectFromMap 10.474 0.762 14.715 make_graphNEL_from_ontology_plot 10.073 0.642 26.093 liberalMap 9.874 0.577 20.127 ontoDiff 9.514 0.937 18.287 mapOneNaive 9.714 0.597 19.242 getOnto 9.550 0.568 13.971 onto_plot2 9.284 0.501 16.842 secLevGen 9.228 0.481 17.066 TermSet-class 8.968 0.722 12.538 ldfToTerms 2.709 0.044 5.521 search_labels 0.504 0.022 36.243 bioregistry_ols_resources 0.060 0.004 20.752 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘ontoProc’ ... ** this is package ‘ontoProc’ version ‘2.2.3’ ** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 81.316 5.161 109.088
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 36.213 | 2.101 | 53.541 | |
PROSYM | 0.239 | 0.000 | 0.239 | |
TermSet-class | 8.968 | 0.722 | 12.538 | |
allGOterms | 0.110 | 0.004 | 0.114 | |
ancestors | 4.289 | 0.453 | 4.973 | |
ancestors_names | 0.005 | 0.004 | 0.009 | |
bioregistry_ols_resources | 0.060 | 0.004 | 20.752 | |
cellTypeToGO | 2.258 | 0.104 | 2.368 | |
children_names | 0.008 | 0.000 | 0.008 | |
cleanCLOnames | 16.090 | 0.938 | 20.448 | |
common_classes | 14.224 | 1.123 | 20.089 | |
ctmarks | 0 | 0 | 0 | |
cyclicSigset | 0.009 | 0.000 | 0.009 | |
demoApp | 0.001 | 0.000 | 0.000 | |
dropStop | 0.005 | 0.000 | 0.005 | |
fastGrep | 18.043 | 0.607 | 23.342 | |
findCommonAncestors | 12.325 | 0.754 | 16.057 | |
getLeavesFromTerm | 19.132 | 0.626 | 22.618 | |
getOnto | 9.550 | 0.568 | 13.971 | |
humrna | 0.008 | 0.001 | 0.012 | |
labels.owlents | 0.387 | 0.015 | 0.816 | |
ldfToTerms | 2.709 | 0.044 | 5.521 | |
liberalMap | 9.874 | 0.577 | 20.127 | |
makeSelectInput | 0.000 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 10.073 | 0.642 | 26.093 | |
mapOneNaive | 9.714 | 0.597 | 19.242 | |
minicorpus | 0.001 | 0.000 | 0.002 | |
nomenCheckup | 18.421 | 0.699 | 33.810 | |
ontoDiff | 9.514 | 0.937 | 18.287 | |
onto_plot2 | 9.284 | 0.501 | 16.842 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 0.033 | 0.001 | 0.044 | |
packDesc2019 | 0.004 | 0.000 | 0.004 | |
packDesc2021 | 0.003 | 0.000 | 0.004 | |
packDesc2022 | 0.003 | 0.000 | 0.003 | |
packDesc2023 | 0.003 | 0.000 | 0.004 | |
parents | 0.007 | 0.000 | 0.007 | |
plot.owlents | 1.229 | 0.048 | 1.279 | |
quickOnto | 0.490 | 0.024 | 0.518 | |
recognizedPredicates | 0.000 | 0.000 | 0.001 | |
search_labels | 0.504 | 0.022 | 36.243 | |
secLevGen | 9.228 | 0.481 | 17.066 | |
selectFromMap | 10.474 | 0.762 | 14.715 | |
setup_entities | 0.007 | 0.000 | 0.008 | |
setup_entities2 | 0.479 | 0.023 | 0.504 | |
seur3kTab | 0.003 | 0.000 | 0.004 | |
siblings_TAG | 27.085 | 2.026 | 38.031 | |
stopWords | 0.001 | 0.000 | 0.002 | |
subclasses | 0.004 | 0.004 | 0.008 | |
sym2CellOnto | 54.895 | 2.312 | 63.148 | |
valid_ontonames | 0.001 | 0.000 | 0.000 | |