Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-15 21:54 -0400 (Tue, 15 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
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 1475/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.26.4 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | 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: 1.26.4 |
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_1.26.4.tar.gz |
StartedAt: 2024-10-14 09:16:14 -0400 (Mon, 14 Oct 2024) |
EndedAt: 2024-10-14 09:42:50 -0400 (Mon, 14 Oct 2024) |
EllapsedTime: 1595.7 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_1.26.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘1.26.4’ * 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 ... NOTE installed size is 10.0Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb owl 2.9Mb * 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 whether startup messages can be suppressed ... 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 70.385 1.923 81.943 CLfeats 49.654 2.817 62.676 siblings_TAG 43.230 1.962 50.590 labels.owlents 43.263 1.829 91.464 owl2cache 34.420 1.174 62.204 ancestors 32.631 1.567 38.831 nomenCheckup 27.864 1.762 33.811 fastGrep 28.048 0.954 33.618 getLeavesFromTerm 26.957 0.919 56.194 cleanCLOnames 24.708 0.890 29.297 common_classes 19.854 1.636 25.458 TermSet-class 16.319 0.986 20.366 findCommonAncestors 16.188 0.815 20.341 liberalMap 14.962 1.316 20.814 getOnto 14.372 1.272 41.139 make_graphNEL_from_ontology_plot 14.512 0.721 17.931 mapOneNaive 14.304 0.728 16.638 secLevGen 13.949 0.669 16.834 selectFromMap 13.800 0.717 17.010 onto_plot2 13.652 0.690 27.738 plot.owlents 12.405 0.341 21.151 subclasses 11.411 0.285 13.273 ancestors_names 10.947 0.507 12.569 search_labels 11.089 0.324 13.748 setup_entities 10.827 0.285 12.645 parents 10.767 0.295 23.020 children_names 10.719 0.293 12.404 ldfToTerms 4.489 0.145 5.249 * 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-3.19-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-x86_64/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 13 ] > > > proc.time() user system elapsed 151.353 7.837 189.641
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 49.654 | 2.817 | 62.676 | |
PROSYM | 0.421 | 0.010 | 0.485 | |
TermSet-class | 16.319 | 0.986 | 20.366 | |
allGOterms | 0.166 | 0.005 | 0.206 | |
ancestors | 32.631 | 1.567 | 38.831 | |
ancestors_names | 10.947 | 0.507 | 12.569 | |
cellTypeToGO | 3.433 | 0.260 | 4.228 | |
children_names | 10.719 | 0.293 | 12.404 | |
cleanCLOnames | 24.708 | 0.890 | 29.297 | |
common_classes | 19.854 | 1.636 | 25.458 | |
ctmarks | 0.000 | 0.001 | 0.001 | |
cyclicSigset | 0.015 | 0.001 | 0.017 | |
demoApp | 0.000 | 0.000 | 0.001 | |
dropStop | 0.006 | 0.004 | 0.011 | |
fastGrep | 28.048 | 0.954 | 33.618 | |
findCommonAncestors | 16.188 | 0.815 | 20.341 | |
getLeavesFromTerm | 26.957 | 0.919 | 56.194 | |
getOnto | 14.372 | 1.272 | 41.139 | |
humrna | 0.011 | 0.005 | 0.066 | |
labels.owlents | 43.263 | 1.829 | 91.464 | |
ldfToTerms | 4.489 | 0.145 | 5.249 | |
liberalMap | 14.962 | 1.316 | 20.814 | |
makeSelectInput | 0.001 | 0.001 | 0.002 | |
make_graphNEL_from_ontology_plot | 14.512 | 0.721 | 17.931 | |
mapOneNaive | 14.304 | 0.728 | 16.638 | |
minicorpus | 0.002 | 0.003 | 0.008 | |
nomenCheckup | 27.864 | 1.762 | 33.811 | |
onto_plot2 | 13.652 | 0.690 | 27.738 | |
onto_roots | 0.001 | 0.001 | 0.002 | |
owl2cache | 34.420 | 1.174 | 62.204 | |
packDesc2019 | 0.007 | 0.005 | 0.043 | |
packDesc2021 | 0.005 | 0.003 | 0.035 | |
packDesc2022 | 0.006 | 0.004 | 0.015 | |
packDesc2023 | 0.006 | 0.003 | 0.036 | |
parents | 10.767 | 0.295 | 23.020 | |
plot.owlents | 12.405 | 0.341 | 21.151 | |
recognizedPredicates | 0.000 | 0.001 | 0.001 | |
search_labels | 11.089 | 0.324 | 13.748 | |
secLevGen | 13.949 | 0.669 | 16.834 | |
selectFromMap | 13.800 | 0.717 | 17.010 | |
setup_entities | 10.827 | 0.285 | 12.645 | |
seur3kTab | 0.006 | 0.003 | 0.011 | |
siblings_TAG | 43.230 | 1.962 | 50.590 | |
stopWords | 0.002 | 0.003 | 0.006 | |
subclasses | 11.411 | 0.285 | 13.273 | |
sym2CellOnto | 70.385 | 1.923 | 81.943 | |
valid_ontonames | 0.000 | 0.000 | 0.002 | |