Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1464/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 2.0.0 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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: 2.0.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ontoProc_2.0.0.tar.gz |
StartedAt: 2024-12-20 03:51:54 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:11:19 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1164.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ontoProc_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘2.0.0’ * 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 10.5Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb owl 3.3Mb * 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 loading without being on the library search path ... 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 58.652 3.446 64.700 CLfeats 29.936 3.001 33.906 nomenCheckup 27.833 2.365 39.452 labels.owlents 25.860 1.927 34.052 owl2cache 24.651 2.126 28.672 siblings_TAG 23.720 2.522 26.974 make_graphNEL_from_ontology_plot 16.883 1.453 23.411 secLevGen 14.999 1.113 26.167 fastGrep 13.724 1.190 15.155 getLeavesFromTerm 13.605 1.287 15.214 selectFromMap 12.325 1.301 14.372 cleanCLOnames 12.430 0.978 13.655 liberalMap 12.057 1.173 14.922 ancestors 10.590 0.538 12.669 common_classes 9.213 1.359 10.929 mapOneNaive 8.890 1.001 10.134 findCommonAncestors 8.797 1.009 10.110 TermSet-class 9.264 0.358 9.913 getOnto 7.671 0.852 8.810 onto_plot2 7.282 0.551 8.121 subclasses 6.260 0.603 6.865 parents 5.505 0.175 6.524 setup_entities 5.046 0.489 5.891 plot.owlents 5.103 0.146 5.330 search_labels 0.805 0.095 131.574 bioregistry_ols_resources 0.039 0.016 12.007 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 12 ] > > > proc.time() user system elapsed 125.285 4.022 135.276
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 29.936 | 3.001 | 33.906 | |
PROSYM | 0.213 | 0.003 | 0.216 | |
TermSet-class | 9.264 | 0.358 | 9.913 | |
allGOterms | 0.115 | 0.002 | 0.117 | |
ancestors | 10.590 | 0.538 | 12.669 | |
ancestors_names | 3.863 | 0.294 | 4.157 | |
bioregistry_ols_resources | 0.039 | 0.016 | 12.007 | |
cellTypeToGO | 2.049 | 0.126 | 2.174 | |
children_names | 3.929 | 0.222 | 4.151 | |
cleanCLOnames | 12.430 | 0.978 | 13.655 | |
common_classes | 9.213 | 1.359 | 10.929 | |
ctmarks | 0.000 | 0.000 | 0.001 | |
cyclicSigset | 0.005 | 0.001 | 0.006 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.003 | 0.000 | 0.003 | |
fastGrep | 13.724 | 1.190 | 15.155 | |
findCommonAncestors | 8.797 | 1.009 | 10.110 | |
getLeavesFromTerm | 13.605 | 1.287 | 15.214 | |
getOnto | 7.671 | 0.852 | 8.810 | |
humrna | 0.006 | 0.003 | 0.008 | |
labels.owlents | 25.860 | 1.927 | 34.052 | |
ldfToTerms | 3.873 | 0.146 | 4.019 | |
liberalMap | 12.057 | 1.173 | 14.922 | |
makeSelectInput | 0.001 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 16.883 | 1.453 | 23.411 | |
mapOneNaive | 8.890 | 1.001 | 10.134 | |
minicorpus | 0.002 | 0.000 | 0.002 | |
nomenCheckup | 27.833 | 2.365 | 39.452 | |
onto_plot2 | 7.282 | 0.551 | 8.121 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 24.651 | 2.126 | 28.672 | |
packDesc2019 | 0.008 | 0.004 | 0.012 | |
packDesc2021 | 0.004 | 0.002 | 0.006 | |
packDesc2022 | 0.005 | 0.001 | 0.006 | |
packDesc2023 | 0.007 | 0.001 | 0.008 | |
parents | 5.505 | 0.175 | 6.524 | |
plot.owlents | 5.103 | 0.146 | 5.330 | |
recognizedPredicates | 0.001 | 0.000 | 0.000 | |
search_labels | 0.805 | 0.095 | 131.574 | |
secLevGen | 14.999 | 1.113 | 26.167 | |
selectFromMap | 12.325 | 1.301 | 14.372 | |
setup_entities | 5.046 | 0.489 | 5.891 | |
setup_entities2 | 0.380 | 0.027 | 0.406 | |
seur3kTab | 0.002 | 0.001 | 0.004 | |
siblings_TAG | 23.720 | 2.522 | 26.974 | |
stopWords | 0.001 | 0.001 | 0.002 | |
subclasses | 6.260 | 0.603 | 6.865 | |
sym2CellOnto | 58.652 | 3.446 | 64.700 | |
valid_ontonames | 0 | 0 | 0 | |