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This page was generated on 2025-08-11 11:48 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1492/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.2.3  (landing page)
Vincent Carey
Snapshot Date: 2025-08-07 13:40 -0400 (Thu, 07 Aug 2025)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: RELEASE_3_21
git_last_commit: 17f883d
git_last_commit_date: 2025-08-02 05:50:41 -0400 (Sat, 02 Aug 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ontoProc on kunpeng2

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: 2.2.3
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_2.2.3.tar.gz
StartedAt: 2025-08-08 12:20:35 -0000 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 12:35:40 -0000 (Fri, 08 Aug 2025)
EllapsedTime: 905.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

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_2.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘2.2.3’
* 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 10.5Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      1.8Mb
    ontoRda   2.8Mb
    owl       3.3Mb
* 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                     54.895  2.312  63.148
CLfeats                          36.213  2.101  53.541
siblings_TAG                     27.085  2.026  38.031
getLeavesFromTerm                19.132  0.626  22.618
nomenCheckup                     18.421  0.699  33.810
fastGrep                         18.043  0.607  23.342
cleanCLOnames                    16.090  0.938  20.448
common_classes                   14.224  1.123  20.089
findCommonAncestors              12.325  0.754  16.057
selectFromMap                    10.474  0.762  14.715
make_graphNEL_from_ontology_plot 10.073  0.642  26.093
liberalMap                        9.874  0.577  20.127
ontoDiff                          9.514  0.937  18.287
mapOneNaive                       9.714  0.597  19.242
getOnto                           9.550  0.568  13.971
onto_plot2                        9.284  0.501  16.842
secLevGen                         9.228  0.481  17.066
TermSet-class                     8.968  0.722  12.538
ldfToTerms                        2.709  0.044   5.521
search_labels                     0.504  0.022  36.243
bioregistry_ols_resources         0.060  0.004  20.752
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck/00check.log’
for details.


Installation output

ontoProc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ontoProc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘ontoProc’ ...
** this is package ‘ontoProc’ version ‘2.2.3’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 81.316   5.161 109.088 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats36.213 2.10153.541
PROSYM0.2390.0000.239
TermSet-class 8.968 0.72212.538
allGOterms0.1100.0040.114
ancestors4.2890.4534.973
ancestors_names0.0050.0040.009
bioregistry_ols_resources 0.060 0.00420.752
cellTypeToGO2.2580.1042.368
children_names0.0080.0000.008
cleanCLOnames16.090 0.93820.448
common_classes14.224 1.12320.089
ctmarks000
cyclicSigset0.0090.0000.009
demoApp0.0010.0000.000
dropStop0.0050.0000.005
fastGrep18.043 0.60723.342
findCommonAncestors12.325 0.75416.057
getLeavesFromTerm19.132 0.62622.618
getOnto 9.550 0.56813.971
humrna0.0080.0010.012
labels.owlents0.3870.0150.816
ldfToTerms2.7090.0445.521
liberalMap 9.874 0.57720.127
makeSelectInput0.0000.0000.001
make_graphNEL_from_ontology_plot10.073 0.64226.093
mapOneNaive 9.714 0.59719.242
minicorpus0.0010.0000.002
nomenCheckup18.421 0.69933.810
ontoDiff 9.514 0.93718.287
onto_plot2 9.284 0.50116.842
onto_roots0.0000.0000.001
owl2cache0.0330.0010.044
packDesc20190.0040.0000.004
packDesc20210.0030.0000.004
packDesc20220.0030.0000.003
packDesc20230.0030.0000.004
parents0.0070.0000.007
plot.owlents1.2290.0481.279
quickOnto0.4900.0240.518
recognizedPredicates0.0000.0000.001
search_labels 0.504 0.02236.243
secLevGen 9.228 0.48117.066
selectFromMap10.474 0.76214.715
setup_entities0.0070.0000.008
setup_entities20.4790.0230.504
seur3kTab0.0030.0000.004
siblings_TAG27.085 2.02638.031
stopWords0.0010.0000.002
subclasses0.0040.0040.008
sym2CellOnto54.895 2.31263.148
valid_ontonames0.0010.0000.000