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This page was generated on 2025-08-30 12:09 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1484/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.3.9  (landing page)
Vincent Carey
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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 24.04.3 LTS) / x86_64  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 13.7.7 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 taishan

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.

raw results


Summary

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: 2025-08-29 09:51:50 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 10:31:51 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 2400.6 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: ontoProc.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
sym2CellOnto                     289.893  4.249 300.708
siblings_TAG                     164.046  1.681 174.867
cleanCLOnames                    129.342  5.979 194.493
nomenCheckup                     127.429  1.231 131.938
CLfeats                           86.593  1.452 100.008
getLeavesFromTerm                 77.109  0.710  81.363
fastGrep                          75.125  0.684  78.803
common_classes                    63.140  1.177  77.916
selectFromMap                     59.280  1.537  63.818
make_graphNEL_from_ontology_plot  59.969  0.641  64.263
onto_plot2                        59.463  0.706  63.268
liberalMap                        59.560  0.476  63.244
findCommonAncestors               59.416  0.613  64.013
getOnto                           59.055  0.674  63.364
mapOneNaive                       58.152  0.436  61.595
secLevGen                         55.939  1.872  61.077
TermSet-class                     55.269  0.538  60.144
ontoDiff                          15.294  0.327  22.364
graph2paths                       10.550  0.069  10.645
search_labels                      0.546  0.088  19.055
bioregistry_ols_resources          0.044  0.003  16.127
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’

Installation output

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)

Tests output

ontoProc.Rcheck/tests/test.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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")

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats 86.593 1.452100.008
PROSYM0.2430.0000.244
TermSet-class55.269 0.53860.144
allGOterms0.0930.0040.097
ancestors3.0060.2803.601
ancestors_names0.0080.0000.008
bioregistry_ols_resources 0.044 0.00316.127
cellTypeToGO1.7140.0991.850
children_names0.0070.0000.007
cleanCLOnames129.342 5.979194.493
common_classes63.140 1.17777.916
ctmarks0.0010.0000.000
cyclicSigset0.0570.0040.061
demoApp000
dropStop0.0050.0000.008
fastGrep75.125 0.68478.803
findCommonAncestors59.416 0.61364.013
formalize0.0000.0000.001
getLeavesFromTerm77.109 0.71081.363
getOnto59.055 0.67463.364
graph2paths10.550 0.06910.645
humrna0.0070.0000.009
jowl2classgraph0.4610.0000.463
jowl2classgraph_nio1.0610.0001.065
labels.owlents0.3560.0080.397
ldfToTerms2.5040.0202.531
liberalMap59.560 0.47663.244
makeSelectInput0.0010.0000.001
make_graphNEL_from_ontology_plot59.969 0.64164.263
mapOneNaive58.152 0.43661.595
minicorpus0.0020.0000.001
nomenCheckup127.429 1.231131.938
ontoDiff15.294 0.32722.364
onto_plot259.463 0.70663.268
onto_roots0.0010.0000.000
owl2cache0.0310.0000.030
packDesc20190.0040.0000.005
packDesc20210.0020.0000.003
packDesc20220.0030.0000.004
packDesc20230.0030.0000.003
parents0.0060.0000.007
plot.owlents0.2980.0040.303
quickOnto0.4720.0120.487
recognizedPredicates0.0000.0000.001
search_labels 0.546 0.08819.055
secLevGen55.939 1.87261.077
selectFromMap59.280 1.53763.818
setup_entities0.0070.0000.007
setup_entities20.4420.0040.449
seur3kTab0.0040.0000.005
siblings_TAG164.046 1.681174.867
stopWords0.0010.0000.001
subclasses0.0070.0000.007
sym2CellOnto289.893 4.249300.708
valid_ontonames0.0000.0000.001