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This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
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 1475/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.1.7  (landing page)
Vincent Carey
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: 091f8da
git_last_commit_date: 2025-03-13 13:01:15 -0400 (Thu, 13 Mar 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for ontoProc on nebbiolo1

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: 2.1.7
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ontoProc_2.1.7.tar.gz
StartedAt: 2025-03-14 00:32:59 -0400 (Fri, 14 Mar 2025)
EndedAt: 2025-03-14 00:54:42 -0400 (Fri, 14 Mar 2025)
EllapsedTime: 1303.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ontoProc_2.1.7.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: 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘2.1.7’
* 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  9.7Mb
  sub-directories of 1Mb or more:
    app       1.6Mb
    data      1.8Mb
    ontoRda   2.7Mb
    owl       3.0Mb
* 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                     51.221  2.088  57.442
siblings_TAG                     35.042  2.616  39.866
CLfeats                          28.687  1.945  31.534
labels.owlents                   26.946  1.836  35.045
owl2cache                        22.690  2.134  23.305
ontoDiff                         18.059  1.638  26.769
make_graphNEL_from_ontology_plot 17.125  1.294  23.161
getLeavesFromTerm                17.587  0.600  20.617
nomenCheckup                     16.534  0.973  19.162
onto_plot2                       15.311  1.315  24.945
getOnto                          14.927  1.164  23.034
fastGrep                         13.818  0.877  14.921
selectFromMap                    13.398  1.119  16.502
cleanCLOnames                    12.537  1.205  14.047
liberalMap                       12.196  1.428  14.174
ancestors                        11.507  0.953  13.214
common_classes                   11.085  1.172  12.491
mapOneNaive                      10.293  1.237  11.971
plot.owlents                      9.957  0.617  18.631
TermSet-class                     8.437  0.491   9.154
secLevGen                         7.783  1.043   9.306
findCommonAncestors               7.569  0.646   8.445
parents                           7.265  0.449  11.967
subclasses                        6.532  0.159   7.886
setup_entities                    5.007  0.146   5.154
ldfToTerms                        4.316  0.266   5.056
search_labels                     0.503  0.071 145.829
bioregistry_ols_resources         0.039  0.023  14.355
* 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-3.21-bioc/meat/ontoProc.Rcheck/00check.log’
for details.


Installation output

ontoProc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ontoProc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ontoProc’ ...
** this is package ‘ontoProc’ version ‘2.1.7’
** 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: 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 
136.020   8.178 145.640 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats28.687 1.94531.534
PROSYM0.2150.0020.217
TermSet-class8.4370.4919.154
allGOterms0.0910.0030.094
ancestors11.507 0.95313.214
ancestors_names3.8460.2034.049
bioregistry_ols_resources 0.039 0.02314.355
cellTypeToGO1.5750.1301.705
children_names3.9180.1064.025
cleanCLOnames12.537 1.20514.047
common_classes11.085 1.17212.491
ctmarks0.0010.0000.000
cyclicSigset0.0070.0000.007
demoApp000
dropStop0.0030.0020.005
fastGrep13.818 0.87714.921
findCommonAncestors7.5690.6468.445
getLeavesFromTerm17.587 0.60020.617
getOnto14.927 1.16423.034
humrna0.0090.0010.009
labels.owlents26.946 1.83635.045
ldfToTerms4.3160.2665.056
liberalMap12.196 1.42814.174
makeSelectInput0.0000.0000.001
make_graphNEL_from_ontology_plot17.125 1.29423.161
mapOneNaive10.293 1.23711.971
minicorpus0.0020.0000.002
nomenCheckup16.534 0.97319.162
ontoDiff18.059 1.63826.769
onto_plot215.311 1.31524.945
onto_roots0.0000.0000.001
owl2cache22.690 2.13423.305
packDesc20190.0040.0070.025
packDesc20210.0020.0040.013
packDesc20220.0040.0020.014
packDesc20230.0040.0030.011
parents 7.265 0.44911.967
plot.owlents 9.957 0.61718.631
quickOnto0.5640.1130.824
recognizedPredicates0.0000.0010.001
search_labels 0.503 0.071145.829
secLevGen7.7831.0439.306
selectFromMap13.398 1.11916.502
setup_entities5.0070.1465.154
setup_entities20.9800.0461.026
seur3kTab0.0040.0000.007
siblings_TAG35.042 2.61639.866
stopWords0.0010.0020.003
subclasses6.5320.1597.886
sym2CellOnto51.221 2.08857.442
valid_ontonames0.0000.0010.000