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This page was generated on 2025-08-28 12:04 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4613
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4556
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1483/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.3.9  (landing page)
Vincent Carey
Snapshot Date: 2025-08-27 13:45 -0400 (Wed, 27 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 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: 2.3.9
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_2.3.9.tar.gz
StartedAt: 2025-08-28 01:34:33 -0400 (Thu, 28 Aug 2025)
EndedAt: 2025-08-28 02:09:24 -0400 (Thu, 28 Aug 2025)
EllapsedTime: 2090.4 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_2.3.9.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 24.04.3 LTS
* using session charset: UTF-8
* 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                     203.803  6.819 211.186
cleanCLOnames                    132.987  3.559 159.956
siblings_TAG                     114.708  4.658 120.223
nomenCheckup                      86.568  1.974  88.840
fastGrep                          84.450  3.794 100.634
common_classes                    77.340  3.641 102.091
CLfeats                           69.929  4.968  75.940
getLeavesFromTerm                 60.241  1.728  62.462
getOnto                           55.580  3.603  60.678
findCommonAncestors               53.143  1.986  63.950
liberalMap                        43.981  2.793  49.012
make_graphNEL_from_ontology_plot  42.836  1.599  44.727
selectFromMap                     42.169  1.587  44.025
onto_plot2                        41.302  1.835  43.369
mapOneNaive                       40.519  1.536  42.320
TermSet-class                     39.511  2.360  42.132
secLevGen                         38.357  2.223  40.901
ontoDiff                          12.026  2.325  14.846
graph2paths                       12.597  0.099  14.987
search_labels                      0.437  0.035  14.866
bioregistry_ols_resources          0.070  0.009  12.605
* 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 ‘2.3.9’
** 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-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 
265.593   9.534 276.817 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats69.929 4.96875.940
PROSYM0.2370.0090.246
TermSet-class39.511 2.36042.132
allGOterms0.0980.0030.101
ancestors0.6280.1360.714
ancestors_names0.0130.0010.007
bioregistry_ols_resources 0.070 0.00912.605
cellTypeToGO1.5500.0771.627
children_names0.0050.0000.005
cleanCLOnames132.987 3.559159.956
common_classes 77.340 3.641102.091
ctmarks0.0010.0000.000
cyclicSigset0.0190.0010.041
demoApp0.0010.0000.000
dropStop0.0110.0010.026
fastGrep 84.450 3.794100.634
findCommonAncestors53.143 1.98663.950
formalize0.0010.0000.001
getLeavesFromTerm60.241 1.72862.462
getOnto55.580 3.60360.678
graph2paths12.597 0.09914.987
humrna0.0060.0020.009
jowl2classgraph0.3950.0040.402
jowl2classgraph_nio0.9140.0050.957
labels.owlents0.2350.0020.237
ldfToTerms4.5850.0474.903
liberalMap43.981 2.79349.012
makeSelectInput000
make_graphNEL_from_ontology_plot42.836 1.59944.727
mapOneNaive40.519 1.53642.320
minicorpus0.0000.0010.001
nomenCheckup86.568 1.97488.840
ontoDiff12.026 2.32514.846
onto_plot241.302 1.83543.369
onto_roots000
owl2cache0.0220.0030.026
packDesc20190.0020.0010.003
packDesc20210.0020.0000.003
packDesc20220.0010.0010.002
packDesc20230.0030.0000.002
parents0.0040.0010.005
plot.owlents0.2200.0040.223
quickOnto0.3330.0070.342
recognizedPredicates000
search_labels 0.437 0.03514.866
secLevGen38.357 2.22340.901
selectFromMap42.169 1.58744.025
setup_entities0.0060.0000.006
setup_entities20.3430.0150.358
seur3kTab0.0030.0000.003
siblings_TAG114.708 4.658120.223
stopWords0.0010.0010.001
subclasses0.0060.0000.006
sym2CellOnto203.803 6.819211.186
valid_ontonames0.0000.0000.001