Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:38 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1445/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.25.6 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | 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: 1.25.6 |
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_1.25.6.tar.gz |
StartedAt: 2024-03-02 07:57:57 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 08:24:09 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1571.6 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_1.25.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 ‘1.25.6’ * 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 R 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 71.609 2.103 88.266 CLfeats 48.245 3.029 60.811 plot.owlents 48.445 1.829 66.099 siblings_TAG 44.366 2.130 55.702 owl2cache 41.310 1.746 76.772 ancestors 38.720 2.257 48.494 common_classes 30.061 3.097 41.789 getLeavesFromTerm 30.092 1.149 61.218 fastGrep 25.855 0.962 57.690 nomenCheckup 25.631 0.889 42.342 cleanCLOnames 23.575 0.810 28.518 setup_entities 15.811 0.598 19.511 subclasses 15.622 0.563 18.110 children_names 15.511 0.563 18.611 TermSet-class 15.009 0.873 18.550 findCommonAncestors 15.110 0.763 35.836 parents 14.962 0.647 16.384 ancestors_names 15.041 0.565 18.308 secLevGen 14.524 0.810 24.191 selectFromMap 14.350 0.674 17.609 make_graphNEL_from_ontology_plot 13.974 0.669 17.318 onto_plot2 13.619 0.826 21.375 liberalMap 13.617 0.671 16.847 getOnto 13.227 0.733 19.979 mapOneNaive 13.265 0.691 16.314 ldfToTerms 4.740 0.103 5.729 * 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) (2024-01-16 r85808) -- "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 156.943 8.377 202.313
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 48.245 | 3.029 | 60.811 | |
PROSYM | 0.409 | 0.008 | 0.493 | |
TermSet-class | 15.009 | 0.873 | 18.550 | |
allGOterms | 0.161 | 0.005 | 0.191 | |
ancestors | 38.720 | 2.257 | 48.494 | |
ancestors_names | 15.041 | 0.565 | 18.308 | |
cellTypeToGO | 3.465 | 0.259 | 4.717 | |
children_names | 15.511 | 0.563 | 18.611 | |
cleanCLOnames | 23.575 | 0.810 | 28.518 | |
common_classes | 30.061 | 3.097 | 41.789 | |
ctmarks | 0.001 | 0.001 | 0.001 | |
cyclicSigset | 0.015 | 0.001 | 0.026 | |
demoApp | 0.001 | 0.000 | 0.001 | |
dropStop | 0.006 | 0.005 | 0.022 | |
fastGrep | 25.855 | 0.962 | 57.690 | |
findCommonAncestors | 15.110 | 0.763 | 35.836 | |
getLeavesFromTerm | 30.092 | 1.149 | 61.218 | |
getOnto | 13.227 | 0.733 | 19.979 | |
humrna | 0.012 | 0.004 | 0.022 | |
ldfToTerms | 4.740 | 0.103 | 5.729 | |
liberalMap | 13.617 | 0.671 | 16.847 | |
makeSelectInput | 0.001 | 0.001 | 0.002 | |
make_graphNEL_from_ontology_plot | 13.974 | 0.669 | 17.318 | |
mapOneNaive | 13.265 | 0.691 | 16.314 | |
minicorpus | 0.002 | 0.003 | 0.008 | |
nomenCheckup | 25.631 | 0.889 | 42.342 | |
onto_plot2 | 13.619 | 0.826 | 21.375 | |
onto_roots | 0.001 | 0.002 | 0.003 | |
owl2cache | 41.310 | 1.746 | 76.772 | |
packDesc2019 | 0.007 | 0.007 | 0.599 | |
packDesc2021 | 0.005 | 0.005 | 0.010 | |
packDesc2022 | 0.006 | 0.006 | 0.012 | |
packDesc2023 | 0.006 | 0.013 | 0.020 | |
parents | 14.962 | 0.647 | 16.384 | |
plot.owlents | 48.445 | 1.829 | 66.099 | |
recognizedPredicates | 0.001 | 0.001 | 0.002 | |
secLevGen | 14.524 | 0.810 | 24.191 | |
selectFromMap | 14.350 | 0.674 | 17.609 | |
setup_entities | 15.811 | 0.598 | 19.511 | |
seur3kTab | 0.006 | 0.003 | 0.016 | |
siblings_TAG | 44.366 | 2.130 | 55.702 | |
stopWords | 0.002 | 0.003 | 0.010 | |
subclasses | 15.622 | 0.563 | 18.110 | |
sym2CellOnto | 71.609 | 2.103 | 88.266 | |
valid_ontonames | 0.001 | 0.001 | 0.002 | |