Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:42 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
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 | |||||||||
palomino7 | 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: 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: 2024-10-18 06:33:34 -0400 (Fri, 18 Oct 2024) |
EndedAt: 2024-10-18 06:47:36 -0400 (Fri, 18 Oct 2024) |
EllapsedTime: 841.2 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: 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 13.6.6 * 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 55.379 1.414 92.282 CLfeats 40.008 1.671 46.829 siblings_TAG 30.296 1.084 34.978 fastGrep 19.621 0.527 22.131 owl2cache 18.860 0.436 20.014 nomenCheckup 18.170 0.455 19.672 getLeavesFromTerm 17.465 0.472 19.204 labels.owlents 16.722 0.468 17.429 cleanCLOnames 15.508 0.474 17.406 common_classes 13.854 1.079 16.235 ancestors 12.094 0.570 12.857 TermSet-class 11.569 0.479 13.425 findCommonAncestors 11.262 0.530 12.930 liberalMap 10.650 0.413 12.118 mapOneNaive 10.022 0.382 11.440 make_graphNEL_from_ontology_plot 10.020 0.351 11.453 selectFromMap 10.008 0.355 11.567 getOnto 9.831 0.381 11.564 secLevGen 9.615 0.370 11.062 onto_plot2 8.602 0.333 10.169 * 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-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 4.4.1 (2024-06-14) -- "Race for Your Life" 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 13 ] > > > proc.time() user system elapsed 93.572 4.199 105.861
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 40.008 | 1.671 | 46.829 | |
PROSYM | 0.372 | 0.004 | 0.377 | |
TermSet-class | 11.569 | 0.479 | 13.425 | |
allGOterms | 0.138 | 0.003 | 0.144 | |
ancestors | 12.094 | 0.570 | 12.857 | |
ancestors_names | 3.589 | 0.160 | 3.768 | |
cellTypeToGO | 1.568 | 0.078 | 1.694 | |
children_names | 2.859 | 0.052 | 2.944 | |
cleanCLOnames | 15.508 | 0.474 | 17.406 | |
common_classes | 13.854 | 1.079 | 16.235 | |
ctmarks | 0.000 | 0.001 | 0.000 | |
cyclicSigset | 0.006 | 0.000 | 0.006 | |
demoApp | 0.000 | 0.000 | 0.001 | |
dropStop | 0.004 | 0.003 | 0.007 | |
fastGrep | 19.621 | 0.527 | 22.131 | |
findCommonAncestors | 11.262 | 0.530 | 12.930 | |
getLeavesFromTerm | 17.465 | 0.472 | 19.204 | |
getOnto | 9.831 | 0.381 | 11.564 | |
humrna | 0.009 | 0.002 | 0.011 | |
labels.owlents | 16.722 | 0.468 | 17.429 | |
ldfToTerms | 3.765 | 0.055 | 3.844 | |
liberalMap | 10.650 | 0.413 | 12.118 | |
makeSelectInput | 0.001 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 10.020 | 0.351 | 11.453 | |
mapOneNaive | 10.022 | 0.382 | 11.440 | |
minicorpus | 0.002 | 0.001 | 0.003 | |
nomenCheckup | 18.170 | 0.455 | 19.672 | |
onto_plot2 | 8.602 | 0.333 | 10.169 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 18.860 | 0.436 | 20.014 | |
packDesc2019 | 0.003 | 0.002 | 0.006 | |
packDesc2021 | 0.002 | 0.002 | 0.004 | |
packDesc2022 | 0.002 | 0.002 | 0.004 | |
packDesc2023 | 0.002 | 0.001 | 0.004 | |
parents | 3.241 | 0.046 | 3.297 | |
plot.owlents | 4.080 | 0.064 | 4.159 | |
recognizedPredicates | 0.000 | 0.001 | 0.000 | |
search_labels | 3.773 | 0.059 | 3.851 | |
secLevGen | 9.615 | 0.370 | 11.062 | |
selectFromMap | 10.008 | 0.355 | 11.567 | |
setup_entities | 3.588 | 0.053 | 3.666 | |
seur3kTab | 0.004 | 0.001 | 0.005 | |
siblings_TAG | 30.296 | 1.084 | 34.978 | |
stopWords | 0.002 | 0.001 | 0.003 | |
subclasses | 3.251 | 0.045 | 3.315 | |
sym2CellOnto | 55.379 | 1.414 | 92.282 | |
valid_ontonames | 0.000 | 0.000 | 0.001 | |