Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-17 11:43 -0400 (Tue, 17 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
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 1446/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.27.4 (landing page) Vincent Carey
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ontoProc |
Version: 1.27.4 |
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_1.27.4.tar.gz |
StartedAt: 2024-09-17 07:38:34 -0000 (Tue, 17 Sep 2024) |
EndedAt: 2024-09-17 07:53:20 -0000 (Tue, 17 Sep 2024) |
EllapsedTime: 885.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.27.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘1.27.4’ * 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 loading without being on the library search path ... 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 50.784 0.946 57.364 CLfeats 33.621 1.104 45.027 siblings_TAG 28.828 0.643 37.668 owl2cache 24.157 1.389 20.421 labels.owlents 23.204 0.830 22.754 getLeavesFromTerm 19.183 0.312 24.363 ancestors 16.834 0.561 17.825 fastGrep 16.405 0.172 19.297 common_classes 15.590 0.531 19.019 nomenCheckup 15.745 0.352 19.466 cleanCLOnames 15.656 0.355 18.867 findCommonAncestors 10.233 0.271 13.195 getOnto 10.000 0.275 14.223 liberalMap 9.233 0.787 16.576 TermSet-class 9.720 0.295 12.720 selectFromMap 9.492 0.271 12.756 make_graphNEL_from_ontology_plot 8.967 0.425 14.231 secLevGen 9.111 0.271 12.390 onto_plot2 9.102 0.256 12.365 mapOneNaive 8.938 0.319 15.098 plot.owlents 7.668 0.028 7.711 subclasses 7.516 0.061 7.591 children_names 6.937 0.116 7.065 ancestors_names 6.571 0.184 6.768 search_labels 6.665 0.060 6.739 setup_entities 6.582 0.114 6.718 parents 6.574 0.008 6.595 * 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-3.20-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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)
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: 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 13 ] > > > proc.time() user system elapsed 97.929 7.504 125.533
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 33.621 | 1.104 | 45.027 | |
PROSYM | 0.243 | 0.000 | 0.244 | |
TermSet-class | 9.720 | 0.295 | 12.720 | |
allGOterms | 0.097 | 0.006 | 0.103 | |
ancestors | 16.834 | 0.561 | 17.825 | |
ancestors_names | 6.571 | 0.184 | 6.768 | |
cellTypeToGO | 1.658 | 0.128 | 1.788 | |
children_names | 6.937 | 0.116 | 7.065 | |
cleanCLOnames | 15.656 | 0.355 | 18.867 | |
common_classes | 15.590 | 0.531 | 19.019 | |
ctmarks | 0.001 | 0.000 | 0.000 | |
cyclicSigset | 0.009 | 0.000 | 0.009 | |
demoApp | 0.001 | 0.000 | 0.000 | |
dropStop | 0.004 | 0.000 | 0.004 | |
fastGrep | 16.405 | 0.172 | 19.297 | |
findCommonAncestors | 10.233 | 0.271 | 13.195 | |
getLeavesFromTerm | 19.183 | 0.312 | 24.363 | |
getOnto | 10.000 | 0.275 | 14.223 | |
humrna | 0.003 | 0.004 | 0.008 | |
labels.owlents | 23.204 | 0.830 | 22.754 | |
ldfToTerms | 2.904 | 0.100 | 3.011 | |
liberalMap | 9.233 | 0.787 | 16.576 | |
makeSelectInput | 0.001 | 0.000 | 0.000 | |
make_graphNEL_from_ontology_plot | 8.967 | 0.425 | 14.231 | |
mapOneNaive | 8.938 | 0.319 | 15.098 | |
minicorpus | 0.000 | 0.001 | 0.002 | |
nomenCheckup | 15.745 | 0.352 | 19.466 | |
onto_plot2 | 9.102 | 0.256 | 12.365 | |
onto_roots | 0.001 | 0.000 | 0.000 | |
owl2cache | 24.157 | 1.389 | 20.421 | |
packDesc2019 | 0.005 | 0.000 | 0.004 | |
packDesc2021 | 0.000 | 0.003 | 0.003 | |
packDesc2022 | 0.000 | 0.003 | 0.003 | |
packDesc2023 | 0.003 | 0.000 | 0.003 | |
parents | 6.574 | 0.008 | 6.595 | |
plot.owlents | 7.668 | 0.028 | 7.711 | |
recognizedPredicates | 0 | 0 | 0 | |
search_labels | 6.665 | 0.060 | 6.739 | |
secLevGen | 9.111 | 0.271 | 12.390 | |
selectFromMap | 9.492 | 0.271 | 12.756 | |
setup_entities | 6.582 | 0.114 | 6.718 | |
seur3kTab | 0.004 | 0.000 | 0.004 | |
siblings_TAG | 28.828 | 0.643 | 37.668 | |
stopWords | 0.000 | 0.001 | 0.002 | |
subclasses | 7.516 | 0.061 | 7.591 | |
sym2CellOnto | 50.784 | 0.946 | 57.364 | |
valid_ontonames | 0.001 | 0.000 | 0.000 | |