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This page was generated on 2025-08-12 12:10 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1481/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.3.9  (landing page)
Vincent Carey
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: 5f3aa83
git_last_commit_date: 2025-08-07 12:32:39 -0400 (Thu, 07 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for ontoProc on lconway

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: 2.3.9
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: 2025-08-11 22:58:43 -0400 (Mon, 11 Aug 2025)
EndedAt: 2025-08-11 23:32:35 -0400 (Mon, 11 Aug 2025)
EllapsedTime: 2032.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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                     220.237  2.509 224.541
siblings_TAG                     128.533  1.705 131.758
cleanCLOnames                    104.281  2.059 128.571
nomenCheckup                     100.907  0.873 103.419
CLfeats                           74.837 10.496 176.733
fastGrep                          63.106  1.273  65.230
getLeavesFromTerm                 59.775  1.109  61.834
common_classes                    49.294  2.140  53.531
TermSet-class                     46.861  4.282  89.831
make_graphNEL_from_ontology_plot  48.707  0.959  50.380
liberalMap                        48.918  0.680  50.214
mapOneNaive                       46.479  0.773  54.200
selectFromMap                     45.484  0.864  46.911
findCommonAncestors               44.687  1.035  46.548
getOnto                           44.986  0.726  46.430
onto_plot2                        42.239  0.674  43.253
secLevGen                         42.328  0.543  43.327
ontoDiff                          13.004  0.691  14.297
graph2paths                        9.273  0.053   9.369
search_labels                      0.460  0.019  18.590
bioregistry_ols_resources          0.047  0.024  28.651
* 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.


Installation output

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-x86_64/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)

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-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 
287.206   4.899 295.978 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats 74.837 10.496176.733
PROSYM0.3020.0080.314
TermSet-class46.861 4.28289.831
allGOterms0.1290.0060.253
ancestors0.4800.4751.761
ancestors_names0.0070.0210.031
bioregistry_ols_resources 0.047 0.02428.651
cellTypeToGO1.8400.1712.045
children_names0.0070.0020.009
cleanCLOnames104.281 2.059128.571
common_classes49.294 2.14053.531
ctmarks000
cyclicSigset0.0060.0000.006
demoApp000
dropStop0.0040.0030.008
fastGrep63.106 1.27365.230
findCommonAncestors44.687 1.03546.548
formalize0.0010.0000.001
getLeavesFromTerm59.775 1.10961.834
getOnto44.986 0.72646.430
graph2paths9.2730.0539.369
humrna0.0070.0020.010
jowl2classgraph0.3540.0030.359
jowl2classgraph_nio0.8340.0080.845
labels.owlents0.2670.0120.285
ldfToTerms2.7180.0372.770
liberalMap48.918 0.68050.214
makeSelectInput000
make_graphNEL_from_ontology_plot48.707 0.95950.380
mapOneNaive46.479 0.77354.200
minicorpus0.0010.0020.003
nomenCheckup100.907 0.873103.419
ontoDiff13.004 0.69114.297
onto_plot242.239 0.67443.253
onto_roots0.0010.0000.001
owl2cache0.0250.0010.025
packDesc20190.0040.0020.007
packDesc20210.0030.0010.004
packDesc20220.0030.0020.004
packDesc20230.0030.0120.015
parents0.0050.0010.006
plot.owlents0.2570.0130.273
quickOnto0.3830.0230.410
recognizedPredicates000
search_labels 0.460 0.01918.590
secLevGen42.328 0.54343.327
selectFromMap45.484 0.86446.911
setup_entities0.0060.0010.006
setup_entities20.4210.0140.438
seur3kTab0.0030.0010.005
siblings_TAG128.533 1.705131.758
stopWords0.0010.0010.003
subclasses0.0070.0010.008
sym2CellOnto220.237 2.509224.541
valid_ontonames000