Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-03 10:21 -0400 (Wed, 03 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4480 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4511 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4469 |
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 1.26.0 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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: 1.26.0 |
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_1.26.0.tar.gz |
StartedAt: 2024-07-01 08:59:46 -0400 (Mon, 01 Jul 2024) |
EndedAt: 2024-07-01 09:25:31 -0400 (Mon, 01 Jul 2024) |
EllapsedTime: 1544.8 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_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘1.26.0’ * 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 10.0Mb 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 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 72.559 1.922 90.715 CLfeats 50.309 2.803 64.528 siblings_TAG 44.314 2.092 89.847 plot.owlents 42.019 1.400 47.561 owl2cache 35.174 1.222 44.819 ancestors 34.098 1.870 41.381 fastGrep 27.489 0.897 31.534 getLeavesFromTerm 27.094 0.806 32.308 cleanCLOnames 24.312 0.910 29.464 nomenCheckup 23.758 0.855 48.676 common_classes 21.738 1.475 27.272 findCommonAncestors 17.056 0.862 22.704 TermSet-class 16.444 0.962 20.645 mapOneNaive 16.067 1.149 38.155 onto_plot2 14.456 1.172 34.810 make_graphNEL_from_ontology_plot 14.766 0.665 35.382 liberalMap 14.684 0.664 26.652 getOnto 14.424 0.654 16.941 selectFromMap 14.171 0.762 33.093 secLevGen 14.223 0.700 18.024 subclasses 11.693 0.332 14.027 ancestors_names 11.099 0.543 13.415 setup_entities 10.979 0.311 15.380 children_names 10.825 0.295 12.446 parents 10.738 0.289 12.470 ldfToTerms 4.547 0.084 5.004 * 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 4.4.0 (2024-04-24) -- "Puppy Cup" 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 153.346 7.730 189.482
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 50.309 | 2.803 | 64.528 | |
PROSYM | 0.406 | 0.009 | 0.465 | |
TermSet-class | 16.444 | 0.962 | 20.645 | |
allGOterms | 0.163 | 0.006 | 0.188 | |
ancestors | 34.098 | 1.870 | 41.381 | |
ancestors_names | 11.099 | 0.543 | 13.415 | |
cellTypeToGO | 3.479 | 0.266 | 4.130 | |
children_names | 10.825 | 0.295 | 12.446 | |
cleanCLOnames | 24.312 | 0.910 | 29.464 | |
common_classes | 21.738 | 1.475 | 27.272 | |
ctmarks | 0.000 | 0.001 | 0.001 | |
cyclicSigset | 0.016 | 0.001 | 0.019 | |
demoApp | 0.000 | 0.000 | 0.001 | |
dropStop | 0.006 | 0.005 | 0.013 | |
fastGrep | 27.489 | 0.897 | 31.534 | |
findCommonAncestors | 17.056 | 0.862 | 22.704 | |
getLeavesFromTerm | 27.094 | 0.806 | 32.308 | |
getOnto | 14.424 | 0.654 | 16.941 | |
humrna | 0.013 | 0.003 | 0.016 | |
ldfToTerms | 4.547 | 0.084 | 5.004 | |
liberalMap | 14.684 | 0.664 | 26.652 | |
makeSelectInput | 0.001 | 0.000 | 0.012 | |
make_graphNEL_from_ontology_plot | 14.766 | 0.665 | 35.382 | |
mapOneNaive | 16.067 | 1.149 | 38.155 | |
minicorpus | 0.002 | 0.003 | 0.005 | |
nomenCheckup | 23.758 | 0.855 | 48.676 | |
onto_plot2 | 14.456 | 1.172 | 34.810 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 35.174 | 1.222 | 44.819 | |
packDesc2019 | 0.007 | 0.004 | 0.014 | |
packDesc2021 | 0.005 | 0.004 | 0.010 | |
packDesc2022 | 0.006 | 0.004 | 0.012 | |
packDesc2023 | 0.006 | 0.003 | 0.012 | |
parents | 10.738 | 0.289 | 12.470 | |
plot.owlents | 42.019 | 1.400 | 47.561 | |
recognizedPredicates | 0.001 | 0.001 | 0.002 | |
secLevGen | 14.223 | 0.700 | 18.024 | |
selectFromMap | 14.171 | 0.762 | 33.093 | |
setup_entities | 10.979 | 0.311 | 15.380 | |
seur3kTab | 0.007 | 0.003 | 0.010 | |
siblings_TAG | 44.314 | 2.092 | 89.847 | |
stopWords | 0.003 | 0.003 | 0.013 | |
subclasses | 11.693 | 0.332 | 14.027 | |
sym2CellOnto | 72.559 | 1.922 | 90.715 | |
valid_ontonames | 0.000 | 0.001 | 0.001 | |