| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-02-19 11:32 -0500 (Thu, 19 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4868 |
| 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 1513/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ontoProc 2.5.0 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| See other builds for ontoProc in R Universe. | ||||||||||||||
|
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: 2.5.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ontoProc_2.5.0.tar.gz |
| StartedAt: 2026-02-19 02:41:11 -0500 (Thu, 19 Feb 2026) |
| EndedAt: 2026-02-19 03:21:01 -0500 (Thu, 19 Feb 2026) |
| EllapsedTime: 2390.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ontoProc.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ontoProc_2.5.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ontoProc.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘2.5.0’
* 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 1.6Mb
data 1.8Mb
ontoRda 2.7Mb
owl 3.4Mb
* 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 212.915 8.020 222.736
cleanCLOnames 148.426 6.347 204.052
siblings_TAG 116.873 4.908 122.477
fastGrep 91.580 3.609 110.745
nomenCheckup 88.589 2.363 91.212
common_classes 75.759 4.454 94.278
CLfeats 66.136 4.440 71.318
getLeavesFromTerm 64.675 2.143 67.612
getOnto 60.163 2.690 68.162
findCommonAncestors 47.682 2.416 53.923
make_graphNEL_from_ontology_plot 45.115 1.115 47.553
selectFromMap 42.822 2.002 45.101
liberalMap 42.106 1.919 44.282
secLevGen 41.537 2.235 44.994
onto_plot2 41.116 1.932 43.265
mapOneNaive 41.028 1.888 43.155
TermSet-class 38.961 1.921 41.113
ontoDiff 11.467 1.775 13.780
graph2paths 8.912 0.089 9.023
plot.owlents 4.543 0.296 78.387
search_labels 0.391 0.013 14.071
bioregistry_ols_resources 0.050 0.004 11.982
* 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-3.23-bioc/meat/ontoProc.Rcheck/00check.log’
for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ontoProc’ ... ** this is package ‘ontoProc’ version ‘2.5.0’ ** 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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
269.416 5.518 276.639
ontoProc.Rcheck/ontoProc-Ex.timings
| name | user | system | elapsed | |
| CLfeats | 66.136 | 4.440 | 71.318 | |
| PROSYM | 0.227 | 0.003 | 0.230 | |
| TermSet-class | 38.961 | 1.921 | 41.113 | |
| allGOterms | 0.091 | 0.003 | 0.095 | |
| ancestors | 2.189 | 0.455 | 2.536 | |
| ancestors_names | 0.010 | 0.005 | 0.007 | |
| bioregistry_ols_resources | 0.050 | 0.004 | 11.982 | |
| cellTypeToGO | 1.698 | 0.084 | 1.783 | |
| children_names | 0.003 | 0.003 | 0.006 | |
| cleanCLOnames | 148.426 | 6.347 | 204.052 | |
| common_classes | 75.759 | 4.454 | 94.278 | |
| ctmarks | 0 | 0 | 0 | |
| cyclicSigset | 0.007 | 0.002 | 0.010 | |
| demoApp | 0 | 0 | 0 | |
| dropStop | 0.006 | 0.001 | 0.006 | |
| fastGrep | 91.580 | 3.609 | 110.745 | |
| findCommonAncestors | 47.682 | 2.416 | 53.923 | |
| formalize | 0.000 | 0.001 | 0.001 | |
| getLeavesFromTerm | 64.675 | 2.143 | 67.612 | |
| getOnto | 60.163 | 2.690 | 68.162 | |
| graph2paths | 8.912 | 0.089 | 9.023 | |
| humrna | 0.006 | 0.001 | 0.007 | |
| jowl2classgraph | 0.319 | 0.002 | 0.322 | |
| jowl2classgraph_nio | 0.836 | 0.030 | 0.869 | |
| labels.owlents | 0.000 | 0.000 | 0.001 | |
| ldfToTerms | 2.368 | 0.023 | 2.392 | |
| liberalMap | 42.106 | 1.919 | 44.282 | |
| makeSelectInput | 0.000 | 0.000 | 0.001 | |
| make_graphNEL_from_ontology_plot | 45.115 | 1.115 | 47.553 | |
| mapOneNaive | 41.028 | 1.888 | 43.155 | |
| minicorpus | 0.000 | 0.001 | 0.002 | |
| nomenCheckup | 88.589 | 2.363 | 91.212 | |
| ontoDiff | 11.467 | 1.775 | 13.780 | |
| onto_plot2 | 41.116 | 1.932 | 43.265 | |
| onto_roots | 0.000 | 0.000 | 0.001 | |
| owl2cache | 0.025 | 0.010 | 0.076 | |
| packDesc2019 | 0.003 | 0.001 | 0.004 | |
| packDesc2021 | 0.001 | 0.001 | 0.003 | |
| packDesc2022 | 0.002 | 0.000 | 0.003 | |
| packDesc2023 | 0.003 | 0.000 | 0.003 | |
| parents | 0.005 | 0.000 | 0.007 | |
| plot.owlents | 4.543 | 0.296 | 78.387 | |
| quickOnto | 0.367 | 0.015 | 0.384 | |
| recognizedPredicates | 0 | 0 | 0 | |
| search_labels | 0.391 | 0.013 | 14.071 | |
| secLevGen | 41.537 | 2.235 | 44.994 | |
| selectFromMap | 42.822 | 2.002 | 45.101 | |
| setup_entities | 0.005 | 0.001 | 0.007 | |
| setup_entities2 | 0.362 | 0.011 | 0.373 | |
| seur3kTab | 0.002 | 0.001 | 0.005 | |
| siblings_TAG | 116.873 | 4.908 | 122.477 | |
| stopWords | 0.000 | 0.001 | 0.002 | |
| subclasses | 0.007 | 0.000 | 0.008 | |
| sym2CellOnto | 212.915 | 8.020 | 222.736 | |
| valid_ontonames | 0.000 | 0.000 | 0.001 | |