Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:39:40 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 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 1.26.0 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 2024-05-03 23:45:02 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 23:59:16 -0400 (Fri, 03 May 2024) |
EllapsedTime: 853.5 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 beta (2024-04-14 r86421) * 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 12.7.1 * 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 47.066 1.218 49.100 CLfeats 34.162 3.327 51.215 siblings_TAG 27.404 1.295 29.900 getLeavesFromTerm 19.506 0.782 39.002 fastGrep 19.211 0.825 30.407 plot.owlents 18.420 0.824 19.477 ancestors 15.027 2.382 20.118 common_classes 15.902 1.139 22.297 owl2cache 15.446 0.648 16.293 TermSet-class 11.197 3.735 34.289 cleanCLOnames 14.307 0.553 21.465 findCommonAncestors 13.737 0.646 24.037 nomenCheckup 13.529 0.446 16.252 getOnto 10.944 0.824 19.190 liberalMap 10.871 0.659 15.674 mapOneNaive 10.751 0.578 13.061 make_graphNEL_from_ontology_plot 10.660 0.558 17.019 onto_plot2 9.198 0.535 10.082 selectFromMap 8.906 0.549 9.991 secLevGen 8.843 0.409 15.768 ancestors_names 4.572 0.937 7.188 subclasses 5.251 0.171 5.464 children_names 4.896 0.130 5.076 ldfToTerms 3.589 0.077 5.417 * 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 beta (2024-04-14 r86421) -- "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 89.713 4.804 103.828
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 34.162 | 3.327 | 51.215 | |
PROSYM | 0.256 | 0.059 | 0.984 | |
TermSet-class | 11.197 | 3.735 | 34.289 | |
allGOterms | 0.108 | 0.006 | 0.117 | |
ancestors | 15.027 | 2.382 | 20.118 | |
ancestors_names | 4.572 | 0.937 | 7.188 | |
cellTypeToGO | 1.900 | 0.195 | 2.300 | |
children_names | 4.896 | 0.130 | 5.076 | |
cleanCLOnames | 14.307 | 0.553 | 21.465 | |
common_classes | 15.902 | 1.139 | 22.297 | |
ctmarks | 0.000 | 0.001 | 0.000 | |
cyclicSigset | 0.009 | 0.001 | 0.018 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.004 | 0.002 | 0.007 | |
fastGrep | 19.211 | 0.825 | 30.407 | |
findCommonAncestors | 13.737 | 0.646 | 24.037 | |
getLeavesFromTerm | 19.506 | 0.782 | 39.002 | |
getOnto | 10.944 | 0.824 | 19.190 | |
humrna | 0.008 | 0.003 | 0.027 | |
ldfToTerms | 3.589 | 0.077 | 5.417 | |
liberalMap | 10.871 | 0.659 | 15.674 | |
makeSelectInput | 0.001 | 0.001 | 0.001 | |
make_graphNEL_from_ontology_plot | 10.660 | 0.558 | 17.019 | |
mapOneNaive | 10.751 | 0.578 | 13.061 | |
minicorpus | 0.001 | 0.001 | 0.002 | |
nomenCheckup | 13.529 | 0.446 | 16.252 | |
onto_plot2 | 9.198 | 0.535 | 10.082 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 15.446 | 0.648 | 16.293 | |
packDesc2019 | 0.004 | 0.001 | 0.006 | |
packDesc2021 | 0.002 | 0.001 | 0.004 | |
packDesc2022 | 0.003 | 0.002 | 0.005 | |
packDesc2023 | 0.003 | 0.002 | 0.004 | |
parents | 4.518 | 0.186 | 4.898 | |
plot.owlents | 18.420 | 0.824 | 19.477 | |
recognizedPredicates | 0.000 | 0.001 | 0.001 | |
secLevGen | 8.843 | 0.409 | 15.768 | |
selectFromMap | 8.906 | 0.549 | 9.991 | |
setup_entities | 4.498 | 0.106 | 4.645 | |
seur3kTab | 0.002 | 0.001 | 0.005 | |
siblings_TAG | 27.404 | 1.295 | 29.900 | |
stopWords | 0.002 | 0.002 | 0.003 | |
subclasses | 5.251 | 0.171 | 5.464 | |
sym2CellOnto | 47.066 | 1.218 | 49.100 | |
valid_ontonames | 0.000 | 0.000 | 0.001 | |