Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:39:43 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1456/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.25.8 (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 | ||||||||||
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: 1.25.8 |
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_1.25.8.tar.gz |
StartedAt: 2024-03-27 22:55:28 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 23:10:31 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 903.6 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_1.25.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 ‘1.25.8’ * 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 43.884 1.258 47.544 CLfeats 32.281 8.704 78.217 siblings_TAG 31.142 1.293 33.470 plot.owlents 20.946 0.879 22.167 fastGrep 20.156 1.464 48.255 getLeavesFromTerm 19.669 1.178 38.594 ancestors 16.908 2.672 27.090 owl2cache 18.515 0.830 19.592 cleanCLOnames 17.537 1.015 25.639 nomenCheckup 15.949 0.545 16.951 common_classes 14.914 1.188 34.608 TermSet-class 11.053 2.872 24.690 secLevGen 10.248 0.453 11.185 getOnto 9.446 0.855 14.733 make_graphNEL_from_ontology_plot 9.441 0.621 10.516 onto_plot2 9.380 0.445 10.150 liberalMap 9.170 0.502 10.139 findCommonAncestors 8.411 1.011 22.884 mapOneNaive 8.769 0.418 9.483 subclasses 8.544 0.288 8.913 selectFromMap 8.375 0.404 9.091 setup_entities 7.308 0.321 7.847 children_names 6.644 0.539 7.262 parents 6.563 0.235 6.877 ancestors_names 6.201 0.242 6.517 * 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 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 91.587 5.047 99.752
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 32.281 | 8.704 | 78.217 | |
PROSYM | 0.292 | 0.011 | 0.307 | |
TermSet-class | 11.053 | 2.872 | 24.690 | |
allGOterms | 0.110 | 0.005 | 0.116 | |
ancestors | 16.908 | 2.672 | 27.090 | |
ancestors_names | 6.201 | 0.242 | 6.517 | |
cellTypeToGO | 1.980 | 0.252 | 2.426 | |
children_names | 6.644 | 0.539 | 7.262 | |
cleanCLOnames | 17.537 | 1.015 | 25.639 | |
common_classes | 14.914 | 1.188 | 34.608 | |
ctmarks | 0.001 | 0.000 | 0.001 | |
cyclicSigset | 0.009 | 0.000 | 0.009 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.005 | 0.003 | 0.010 | |
fastGrep | 20.156 | 1.464 | 48.255 | |
findCommonAncestors | 8.411 | 1.011 | 22.884 | |
getLeavesFromTerm | 19.669 | 1.178 | 38.594 | |
getOnto | 9.446 | 0.855 | 14.733 | |
humrna | 0.007 | 0.002 | 0.010 | |
ldfToTerms | 2.963 | 0.103 | 3.135 | |
liberalMap | 9.170 | 0.502 | 10.139 | |
makeSelectInput | 0.001 | 0.001 | 0.002 | |
make_graphNEL_from_ontology_plot | 9.441 | 0.621 | 10.516 | |
mapOneNaive | 8.769 | 0.418 | 9.483 | |
minicorpus | 0.001 | 0.002 | 0.003 | |
nomenCheckup | 15.949 | 0.545 | 16.951 | |
onto_plot2 | 9.380 | 0.445 | 10.150 | |
onto_roots | 0 | 0 | 0 | |
owl2cache | 18.515 | 0.830 | 19.592 | |
packDesc2019 | 0.003 | 0.002 | 0.005 | |
packDesc2021 | 0.002 | 0.002 | 0.004 | |
packDesc2022 | 0.003 | 0.002 | 0.005 | |
packDesc2023 | 0.004 | 0.002 | 0.005 | |
parents | 6.563 | 0.235 | 6.877 | |
plot.owlents | 20.946 | 0.879 | 22.167 | |
recognizedPredicates | 0.000 | 0.001 | 0.001 | |
secLevGen | 10.248 | 0.453 | 11.185 | |
selectFromMap | 8.375 | 0.404 | 9.091 | |
setup_entities | 7.308 | 0.321 | 7.847 | |
seur3kTab | 0.004 | 0.002 | 0.006 | |
siblings_TAG | 31.142 | 1.293 | 33.470 | |
stopWords | 0.001 | 0.002 | 0.003 | |
subclasses | 8.544 | 0.288 | 8.913 | |
sym2CellOnto | 43.884 | 1.258 | 47.544 | |
valid_ontonames | 0 | 0 | 0 | |