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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1456/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.1.3  (landing page)
Vincent Carey
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: e973100
git_last_commit_date: 2024-12-04 13:09:36 -0500 (Wed, 04 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 2.1.3
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_2.1.3.tar.gz
StartedAt: 2024-12-24 09:30:42 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:50:08 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 1166.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

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_2.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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 ‘2.1.3’
* 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                     50.745  1.184  58.266
CLfeats                          34.345  0.915  45.426
siblings_TAG                     29.390  1.574  39.784
nomenCheckup                     19.641  0.551  33.009
getLeavesFromTerm                18.837  0.638  22.591
fastGrep                         18.549  0.587  21.868
cleanCLOnames                    16.026  0.858  19.737
common_classes                   13.770  0.641  18.922
findCommonAncestors              11.378  0.362  14.672
TermSet-class                    10.500  0.195  13.452
liberalMap                       10.072  0.605  20.034
make_graphNEL_from_ontology_plot 10.033  0.563  27.718
mapOneNaive                      10.098  0.386  30.548
getOnto                           9.448  0.477  12.718
secLevGen                         9.264  0.509  13.021
ontoDiff                          9.222  0.387  16.358
selectFromMap                     9.254  0.354  13.005
onto_plot2                        9.039  0.273  11.712
ldfToTerms                        2.679  0.080   5.943
labels.owlents                    0.966  0.336  46.286
search_labels                     0.488  0.070 105.302
bioregistry_ols_resources         0.049  0.026  19.821
* 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-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘ontoProc’ ...
** 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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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 
203.612   6.798 290.633 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats34.345 0.91545.426
PROSYM0.2270.0040.231
TermSet-class10.500 0.19513.452
allGOterms0.0960.0000.097
ancestors0.5640.0610.659
ancestors_names0.0050.0040.009
bioregistry_ols_resources 0.049 0.02619.821
cellTypeToGO1.7110.1081.822
children_names0.0080.0000.008
cleanCLOnames16.026 0.85819.737
common_classes13.770 0.64118.922
ctmarks000
cyclicSigset0.0090.0000.008
demoApp0.0010.0000.000
dropStop0.0050.0000.004
fastGrep18.549 0.58721.868
findCommonAncestors11.378 0.36214.672
getLeavesFromTerm18.837 0.63822.591
getOnto 9.448 0.47712.718
humrna0.0080.0000.008
labels.owlents 0.966 0.33646.286
ldfToTerms2.6790.0805.943
liberalMap10.072 0.60520.034
makeSelectInput0.0010.0000.001
make_graphNEL_from_ontology_plot10.033 0.56327.718
mapOneNaive10.098 0.38630.548
minicorpus0.0020.0000.013
nomenCheckup19.641 0.55133.009
ontoDiff 9.222 0.38716.358
onto_plot2 9.039 0.27311.712
onto_roots000
owl2cache0.0340.0000.044
packDesc20190.0050.0000.005
packDesc20210.0030.0000.005
packDesc20220.0040.0000.006
packDesc20230.0040.0000.004
parents0.0080.0000.010
plot.owlents0.3300.0000.333
recognizedPredicates0.0000.0000.001
search_labels 0.488 0.070105.302
secLevGen 9.264 0.50913.021
selectFromMap 9.254 0.35413.005
setup_entities0.0080.0000.009
setup_entities20.4980.0120.512
seur3kTab0.0040.0000.007
siblings_TAG29.390 1.57439.784
stopWords0.0010.0000.002
subclasses0.0080.0000.008
sym2CellOnto50.745 1.18458.266
valid_ontonames000