Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 1475/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.1.7 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 28.687 | 1.945 | 31.534 | |
PROSYM | 0.215 | 0.002 | 0.217 | |
TermSet-class | 8.437 | 0.491 | 9.154 | |
allGOterms | 0.091 | 0.003 | 0.094 | |
ancestors | 11.507 | 0.953 | 13.214 | |
ancestors_names | 3.846 | 0.203 | 4.049 | |
bioregistry_ols_resources | 0.039 | 0.023 | 14.355 | |
cellTypeToGO | 1.575 | 0.130 | 1.705 | |
children_names | 3.918 | 0.106 | 4.025 | |
cleanCLOnames | 12.537 | 1.205 | 14.047 | |
common_classes | 11.085 | 1.172 | 12.491 | |
ctmarks | 0.001 | 0.000 | 0.000 | |
cyclicSigset | 0.007 | 0.000 | 0.007 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.003 | 0.002 | 0.005 | |
fastGrep | 13.818 | 0.877 | 14.921 | |
findCommonAncestors | 7.569 | 0.646 | 8.445 | |
getLeavesFromTerm | 17.587 | 0.600 | 20.617 | |
getOnto | 14.927 | 1.164 | 23.034 | |
humrna | 0.009 | 0.001 | 0.009 | |
labels.owlents | 26.946 | 1.836 | 35.045 | |
ldfToTerms | 4.316 | 0.266 | 5.056 | |
liberalMap | 12.196 | 1.428 | 14.174 | |
makeSelectInput | 0.000 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 17.125 | 1.294 | 23.161 | |
mapOneNaive | 10.293 | 1.237 | 11.971 | |
minicorpus | 0.002 | 0.000 | 0.002 | |
nomenCheckup | 16.534 | 0.973 | 19.162 | |
ontoDiff | 18.059 | 1.638 | 26.769 | |
onto_plot2 | 15.311 | 1.315 | 24.945 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 22.690 | 2.134 | 23.305 | |
packDesc2019 | 0.004 | 0.007 | 0.025 | |
packDesc2021 | 0.002 | 0.004 | 0.013 | |
packDesc2022 | 0.004 | 0.002 | 0.014 | |
packDesc2023 | 0.004 | 0.003 | 0.011 | |
parents | 7.265 | 0.449 | 11.967 | |
plot.owlents | 9.957 | 0.617 | 18.631 | |
quickOnto | 0.564 | 0.113 | 0.824 | |
recognizedPredicates | 0.000 | 0.001 | 0.001 | |
search_labels | 0.503 | 0.071 | 145.829 | |
secLevGen | 7.783 | 1.043 | 9.306 | |
selectFromMap | 13.398 | 1.119 | 16.502 | |
setup_entities | 5.007 | 0.146 | 5.154 | |
setup_entities2 | 0.980 | 0.046 | 1.026 | |
seur3kTab | 0.004 | 0.000 | 0.007 | |
siblings_TAG | 35.042 | 2.616 | 39.866 | |
stopWords | 0.001 | 0.002 | 0.003 | |
subclasses | 6.532 | 0.159 | 7.886 | |
sym2CellOnto | 51.221 | 2.088 | 57.442 | |
valid_ontonames | 0.000 | 0.001 | 0.000 | |