Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-02-04 11:43 -0500 (Tue, 04 Feb 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) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4716 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
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 1467/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.1.4 (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 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 2.1.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ontoProc_2.1.4.tar.gz |
StartedAt: 2025-02-03 22:12:49 -0500 (Mon, 03 Feb 2025) |
EndedAt: 2025-02-03 22:28:42 -0500 (Mon, 03 Feb 2025) |
EllapsedTime: 953.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ontoProc_2.1.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘2.1.4’ * 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 10.4Mb 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 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 48.693 1.247 51.036 CLfeats 33.293 8.436 84.979 siblings_TAG 26.595 1.234 28.724 fastGrep 20.154 0.749 31.330 getLeavesFromTerm 19.610 1.059 36.713 nomenCheckup 19.494 0.536 25.288 cleanCLOnames 14.664 1.212 18.258 common_classes 13.717 0.940 19.403 findCommonAncestors 12.892 0.580 22.483 TermSet-class 10.121 1.474 19.111 getOnto 10.774 0.631 18.086 mapOneNaive 10.581 0.476 15.919 make_graphNEL_from_ontology_plot 10.495 0.463 14.273 liberalMap 10.179 0.388 12.197 secLevGen 8.663 0.358 9.585 ontoDiff 8.213 0.706 9.453 onto_plot2 8.334 0.371 8.933 selectFromMap 8.209 0.334 8.788 search_labels 0.402 0.042 89.097 bioregistry_ols_resources 0.051 0.019 16.905 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ontoProc’ ... ** this is package ‘ontoProc’ version ‘2.1.4’ ** 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) (2025-01-22 r87618) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 159.582 9.111 174.100
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 33.293 | 8.436 | 84.979 | |
PROSYM | 0.251 | 0.067 | 0.761 | |
TermSet-class | 10.121 | 1.474 | 19.111 | |
allGOterms | 0.091 | 0.002 | 0.093 | |
ancestors | 0.361 | 0.304 | 0.793 | |
ancestors_names | 0.006 | 0.015 | 0.022 | |
bioregistry_ols_resources | 0.051 | 0.019 | 16.905 | |
cellTypeToGO | 2.016 | 0.264 | 2.383 | |
children_names | 0.006 | 0.001 | 0.008 | |
cleanCLOnames | 14.664 | 1.212 | 18.258 | |
common_classes | 13.717 | 0.940 | 19.403 | |
ctmarks | 0.001 | 0.000 | 0.001 | |
cyclicSigset | 0.009 | 0.000 | 0.019 | |
demoApp | 0.000 | 0.000 | 0.006 | |
dropStop | 0.005 | 0.002 | 0.009 | |
fastGrep | 20.154 | 0.749 | 31.330 | |
findCommonAncestors | 12.892 | 0.580 | 22.483 | |
getLeavesFromTerm | 19.610 | 1.059 | 36.713 | |
getOnto | 10.774 | 0.631 | 18.086 | |
humrna | 0.008 | 0.002 | 0.021 | |
labels.owlents | 0.599 | 0.479 | 1.942 | |
ldfToTerms | 3.363 | 0.083 | 3.880 | |
liberalMap | 10.179 | 0.388 | 12.197 | |
makeSelectInput | 0.001 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 10.495 | 0.463 | 14.273 | |
mapOneNaive | 10.581 | 0.476 | 15.919 | |
minicorpus | 0.001 | 0.001 | 0.002 | |
nomenCheckup | 19.494 | 0.536 | 25.288 | |
ontoDiff | 8.213 | 0.706 | 9.453 | |
onto_plot2 | 8.334 | 0.371 | 8.933 | |
onto_roots | 0.001 | 0.000 | 0.001 | |
owl2cache | 0.023 | 0.001 | 0.025 | |
packDesc2019 | 0.003 | 0.002 | 0.006 | |
packDesc2021 | 0.003 | 0.002 | 0.006 | |
packDesc2022 | 0.002 | 0.001 | 0.005 | |
packDesc2023 | 0.003 | 0.002 | 0.005 | |
parents | 0.007 | 0.001 | 0.008 | |
plot.owlents | 0.239 | 0.009 | 0.249 | |
recognizedPredicates | 0.001 | 0.000 | 0.000 | |
search_labels | 0.402 | 0.042 | 89.097 | |
secLevGen | 8.663 | 0.358 | 9.585 | |
selectFromMap | 8.209 | 0.334 | 8.788 | |
setup_entities | 0.005 | 0.001 | 0.006 | |
setup_entities2 | 0.383 | 0.012 | 0.398 | |
seur3kTab | 0.004 | 0.001 | 0.005 | |
siblings_TAG | 26.595 | 1.234 | 28.724 | |
stopWords | 0.001 | 0.001 | 0.003 | |
subclasses | 0.006 | 0.002 | 0.008 | |
sym2CellOnto | 48.693 | 1.247 | 51.036 | |
valid_ontonames | 0 | 0 | 0 | |