Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1464/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.0.0 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 2.0.0 |
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_2.0.0.tar.gz |
StartedAt: 2024-12-21 03:48:42 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 04:04:00 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 917.9 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_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘2.0.0’ * 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 ... NOTE 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 ... OK * 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 ... OK * 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 ... NOTE Note: found 162 marked UTF-8 strings * 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 53.326 0.939 56.806 CLfeats 40.032 1.301 45.586 siblings_TAG 30.058 1.057 34.679 owl2cache 19.919 0.371 23.089 fastGrep 18.048 0.469 19.619 nomenCheckup 17.136 0.455 18.599 labels.owlents 16.473 0.426 20.818 getLeavesFromTerm 15.230 0.346 16.670 cleanCLOnames 15.073 0.379 16.728 ancestors 14.389 0.491 14.411 common_classes 13.833 0.665 15.572 TermSet-class 11.259 0.415 12.736 findCommonAncestors 11.168 0.426 12.668 secLevGen 10.510 0.405 18.344 selectFromMap 10.401 0.378 17.380 mapOneNaive 10.277 0.327 11.637 getOnto 9.972 0.307 11.452 liberalMap 9.933 0.344 11.574 make_graphNEL_from_ontology_plot 9.782 0.353 11.181 onto_plot2 8.578 0.362 10.204 search_labels 0.507 0.050 86.647 bioregistry_ols_resources 0.054 0.017 16.848 * 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-3.20-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/4.4-arm64/Resources/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)
ontoProc.Rcheck/tests/test.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 137.819 6.195 154.194
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 40.032 | 1.301 | 45.586 | |
PROSYM | 0.399 | 0.005 | 0.404 | |
TermSet-class | 11.259 | 0.415 | 12.736 | |
allGOterms | 0.131 | 0.003 | 0.134 | |
ancestors | 14.389 | 0.491 | 14.411 | |
ancestors_names | 3.741 | 0.112 | 3.860 | |
bioregistry_ols_resources | 0.054 | 0.017 | 16.848 | |
cellTypeToGO | 2.218 | 0.122 | 2.362 | |
children_names | 2.619 | 0.039 | 2.700 | |
cleanCLOnames | 15.073 | 0.379 | 16.728 | |
common_classes | 13.833 | 0.665 | 15.572 | |
ctmarks | 0.001 | 0.000 | 0.000 | |
cyclicSigset | 0.006 | 0.000 | 0.006 | |
demoApp | 0.000 | 0.000 | 0.001 | |
dropStop | 0.004 | 0.002 | 0.006 | |
fastGrep | 18.048 | 0.469 | 19.619 | |
findCommonAncestors | 11.168 | 0.426 | 12.668 | |
getLeavesFromTerm | 15.230 | 0.346 | 16.670 | |
getOnto | 9.972 | 0.307 | 11.452 | |
humrna | 0.009 | 0.002 | 0.012 | |
labels.owlents | 16.473 | 0.426 | 20.818 | |
ldfToTerms | 3.681 | 0.049 | 3.740 | |
liberalMap | 9.933 | 0.344 | 11.574 | |
makeSelectInput | 0.000 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 9.782 | 0.353 | 11.181 | |
mapOneNaive | 10.277 | 0.327 | 11.637 | |
minicorpus | 0.002 | 0.002 | 0.003 | |
nomenCheckup | 17.136 | 0.455 | 18.599 | |
onto_plot2 | 8.578 | 0.362 | 10.204 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 19.919 | 0.371 | 23.089 | |
packDesc2019 | 0.003 | 0.002 | 0.005 | |
packDesc2021 | 0.002 | 0.002 | 0.004 | |
packDesc2022 | 0.002 | 0.002 | 0.004 | |
packDesc2023 | 0.002 | 0.002 | 0.004 | |
parents | 3.089 | 0.039 | 3.127 | |
plot.owlents | 4.097 | 0.058 | 4.159 | |
recognizedPredicates | 0 | 0 | 0 | |
search_labels | 0.507 | 0.050 | 86.647 | |
secLevGen | 10.510 | 0.405 | 18.344 | |
selectFromMap | 10.401 | 0.378 | 17.380 | |
setup_entities | 3.470 | 0.042 | 3.514 | |
setup_entities2 | 0.452 | 0.012 | 0.464 | |
seur3kTab | 0.004 | 0.001 | 0.006 | |
siblings_TAG | 30.058 | 1.057 | 34.679 | |
stopWords | 0.001 | 0.002 | 0.004 | |
subclasses | 3.801 | 0.056 | 3.856 | |
sym2CellOnto | 53.326 | 0.939 | 56.806 | |
valid_ontonames | 0 | 0 | 0 | |