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This page was generated on 2025-09-08 12:07 -0400 (Mon, 08 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1485/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.3.9  (landing page)
Vincent Carey
Snapshot Date: 2025-09-07 13:45 -0400 (Sun, 07 Sep 2025)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: 869e292
git_last_commit_date: 2025-09-01 10:39:18 -0400 (Mon, 01 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
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: 2025-09-05 10:13:14 -0000 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 10:53:14 -0000 (Fri, 05 Sep 2025)
EllapsedTime: 2400.6 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: ontoProc.Rcheck
Warnings: NA

Command output

##############################################################################
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### 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 ...

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


Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats 86.947 3.389135.258
PROSYM0.2380.0080.247
TermSet-class55.188 1.60873.730
allGOterms0.0960.0040.307
ancestors3.2380.2767.757
ancestors_names0.0080.0000.017
bioregistry_ols_resources 0.055 0.00033.031
cellTypeToGO1.8140.0715.351
children_names0.0110.0000.035
cleanCLOnames128.199 2.006221.349
common_classes62.045 1.94392.260
ctmarks0.0000.0000.001
cyclicSigset0.0580.0040.062
demoApp000
dropStop0.0050.0010.009
fastGrep 75.846 1.681106.037
findCommonAncestors58.030 1.33974.064
formalize000
getLeavesFromTerm 75.033 1.655100.282
getOnto58.174 1.62484.543
graph2paths 9.929 0.16011.506
humrna0.0070.0000.007
jowl2classgraph0.4450.0000.462
jowl2classgraph_nio1.0180.0001.099
labels.owlents0.3160.0040.384
ldfToTerms2.4200.0152.620
liberalMap58.391 1.41283.451
makeSelectInput0.0010.0000.001
make_graphNEL_from_ontology_plot59.327 1.64979.856
mapOneNaive57.229 1.48576.657
minicorpus0.0020.0000.001
nomenCheckup125.100 2.386167.638
ontoDiff15.309 1.67832.261
onto_plot257.836 1.69372.781
onto_roots0.0010.0000.000
owl2cache0.0280.0040.032
packDesc20190.0040.0000.004
packDesc20210.0030.0000.003
packDesc20220.0030.0000.003
packDesc20230.0030.0000.004
parents0.0060.0000.007
plot.owlents0.2920.0080.324
quickOnto0.4640.0080.498
recognizedPredicates000
search_labels 0.485 0.01320.965
secLevGen54.381 1.81869.527
selectFromMap57.820 1.59570.458
setup_entities0.0070.0000.007
setup_entities20.4410.0080.449
seur3kTab0.0040.0000.009
siblings_TAG162.935 4.425232.389
stopWords0.0010.0000.001
subclasses0.0070.0000.011