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This page was generated on 2025-08-04 12:05 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 1479/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.3.8  (landing page)
Vincent Carey
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: c5f7bf8
git_last_commit_date: 2025-08-02 05:52:05 -0400 (Sat, 02 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  YES
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for ontoProc on nebbiolo2

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.

raw results


Summary

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: 2025-08-04 01:04:29 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 01:40:26 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 2156.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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                     205.043  5.605 211.309
cleanCLOnames                    142.890  3.424 168.610
siblings_TAG                     113.792  1.317 115.969
nomenCheckup                      87.955  1.555  89.808
fastGrep                          85.856  1.250  97.383
common_classes                    74.096  1.507  95.592
CLfeats                           68.953  1.822  71.632
findCommonAncestors               66.067  1.024  77.404
getOnto                           58.519  0.686  62.555
getLeavesFromTerm                 57.679  0.636  58.583
liberalMap                        45.740  2.022  51.453
onto_plot2                        42.182  1.608  44.038
selectFromMap                     42.668  0.804  43.709
make_graphNEL_from_ontology_plot  41.661  0.991  43.029
secLevGen                         40.925  0.867  42.180
mapOneNaive                       40.747  0.463  41.446
TermSet-class                     37.625  0.512  38.385
labels.owlents                    23.795  1.524  25.905
owl2cache                         15.401  1.208  12.131
ontoDiff                          11.381  0.546  12.386
ancestors                         10.101  0.353  11.996
graph2paths                       10.207  0.132  10.747
search_labels                      0.450  0.015  14.604
bioregistry_ols_resources          0.039  0.016  12.874
* 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.


Installation output

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)

Tests output

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 
259.372   3.639 264.452 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats68.953 1.82271.632
PROSYM0.2370.0020.239
TermSet-class37.625 0.51238.385
allGOterms0.0960.0030.100
ancestors10.101 0.35311.996
ancestors_names3.8400.0973.937
bioregistry_ols_resources 0.039 0.01612.874
cellTypeToGO1.5440.1181.663
children_names3.7510.1283.879
cleanCLOnames142.890 3.424168.610
common_classes74.096 1.50795.592
ctmarks000
cyclicSigset0.0130.0000.013
demoApp000
dropStop0.0070.0020.020
fastGrep85.856 1.25097.383
findCommonAncestors66.067 1.02477.404
formalize0.0000.0000.001
getLeavesFromTerm57.679 0.63658.583
getOnto58.519 0.68662.555
graph2paths10.207 0.13210.747
humrna0.0130.0000.027
jowl2classgraph0.7270.0121.332
jowl2classgraph_nio1.5280.0092.642
labels.owlents23.795 1.52425.905
ldfToTerms3.5670.0794.365
liberalMap45.740 2.02251.453
makeSelectInput0.0010.0000.000
make_graphNEL_from_ontology_plot41.661 0.99143.029
mapOneNaive40.747 0.46341.446
minicorpus0.0010.0000.002
nomenCheckup87.955 1.55589.808
ontoDiff11.381 0.54612.386
onto_plot242.182 1.60844.038
onto_roots000
owl2cache15.401 1.20812.131
packDesc20190.0020.0020.004
packDesc20210.0020.0010.003
packDesc20220.0030.0000.002
packDesc20230.0020.0010.002
parents3.8150.2164.032
plot.owlents4.6730.1034.777
quickOnto0.3890.0120.401
recognizedPredicates000
search_labels 0.450 0.01514.604
secLevGen40.925 0.86742.180
selectFromMap42.668 0.80443.709
setup_entities3.5600.0463.605
setup_entities20.4980.0190.516
seur3kTab0.0030.0000.004
siblings_TAG113.792 1.317115.969
stopWords0.0010.0010.001
subclasses3.7840.0443.828
sym2CellOnto205.043 5.605211.309
valid_ontonames000