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This page was generated on 2024-09-06 08:10 -0400 (Fri, 06 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
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 1446/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.27.4 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | 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: 1.27.4 |
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_1.27.4.tar.gz |
StartedAt: 2024-09-06 03:25:30 -0400 (Fri, 06 Sep 2024) |
EndedAt: 2024-09-06 03:39:47 -0400 (Fri, 06 Sep 2024) |
EllapsedTime: 857.6 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_1.27.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘1.27.4’ * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 45.623 1.151 48.754 CLfeats 27.266 1.133 29.455 siblings_TAG 24.726 0.860 26.479 owl2cache 13.988 1.040 11.135 getLeavesFromTerm 14.671 0.273 15.197 labels.owlents 13.816 0.837 12.959 fastGrep 13.648 0.312 14.244 cleanCLOnames 12.504 0.897 14.261 common_classes 12.099 0.951 13.432 nomenCheckup 11.675 0.412 12.346 ancestors 9.667 0.527 10.964 make_graphNEL_from_ontology_plot 8.141 0.660 9.057 getOnto 8.218 0.256 8.772 selectFromMap 8.028 0.384 8.773 findCommonAncestors 7.987 0.304 8.575 TermSet-class 7.706 0.288 8.341 secLevGen 7.664 0.272 8.216 liberalMap 7.467 0.424 8.215 onto_plot2 7.564 0.304 8.153 mapOneNaive 6.501 0.272 7.063 * 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 4.4.1 (2024-06-14) -- "Race for Your Life" 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 13 ] > > > proc.time() user system elapsed 87.262 3.339 100.858
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 27.266 | 1.133 | 29.455 | |
PROSYM | 0.216 | 0.004 | 0.220 | |
TermSet-class | 7.706 | 0.288 | 8.341 | |
allGOterms | 0.097 | 0.000 | 0.097 | |
ancestors | 9.667 | 0.527 | 10.964 | |
ancestors_names | 4.042 | 0.211 | 4.295 | |
cellTypeToGO | 2.109 | 0.115 | 2.307 | |
children_names | 4.030 | 0.184 | 4.219 | |
cleanCLOnames | 12.504 | 0.897 | 14.261 | |
common_classes | 12.099 | 0.951 | 13.432 | |
ctmarks | 0.001 | 0.000 | 0.000 | |
cyclicSigset | 0.005 | 0.000 | 0.005 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.004 | 0.000 | 0.003 | |
fastGrep | 13.648 | 0.312 | 14.244 | |
findCommonAncestors | 7.987 | 0.304 | 8.575 | |
getLeavesFromTerm | 14.671 | 0.273 | 15.197 | |
getOnto | 8.218 | 0.256 | 8.772 | |
humrna | 0.007 | 0.000 | 0.007 | |
labels.owlents | 13.816 | 0.837 | 12.959 | |
ldfToTerms | 2.323 | 0.100 | 2.423 | |
liberalMap | 7.467 | 0.424 | 8.215 | |
makeSelectInput | 0 | 0 | 0 | |
make_graphNEL_from_ontology_plot | 8.141 | 0.660 | 9.057 | |
mapOneNaive | 6.501 | 0.272 | 7.063 | |
minicorpus | 0.001 | 0.000 | 0.002 | |
nomenCheckup | 11.675 | 0.412 | 12.346 | |
onto_plot2 | 7.564 | 0.304 | 8.153 | |
onto_roots | 0.001 | 0.000 | 0.000 | |
owl2cache | 13.988 | 1.040 | 11.135 | |
packDesc2019 | 0.004 | 0.000 | 0.004 | |
packDesc2021 | 0.002 | 0.000 | 0.003 | |
packDesc2022 | 0.003 | 0.000 | 0.003 | |
packDesc2023 | 0.003 | 0.000 | 0.003 | |
parents | 3.364 | 0.072 | 3.436 | |
plot.owlents | 4.065 | 0.096 | 4.162 | |
recognizedPredicates | 0.000 | 0.000 | 0.001 | |
search_labels | 3.724 | 0.072 | 3.797 | |
secLevGen | 7.664 | 0.272 | 8.216 | |
selectFromMap | 8.028 | 0.384 | 8.773 | |
setup_entities | 3.417 | 0.056 | 3.473 | |
seur3kTab | 0.003 | 0.000 | 0.004 | |
siblings_TAG | 24.726 | 0.860 | 26.479 | |
stopWords | 0.002 | 0.000 | 0.002 | |
subclasses | 3.580 | 0.048 | 3.627 | |
sym2CellOnto | 45.623 | 1.151 | 48.754 | |
valid_ontonames | 0.001 | 0.000 | 0.000 | |