Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | 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 | 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: 2024-11-20 06:58:53 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 07:11:48 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 774.4 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 ‘/media/volume/teran2_disk/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 37.130 1.220 40.403 CLfeats 20.698 1.028 23.380 siblings_TAG 17.545 0.661 30.997 owl2cache 11.950 1.101 19.339 labels.owlents 11.731 0.965 11.766 getLeavesFromTerm 10.732 0.225 11.341 fastGrep 10.420 0.289 11.501 ancestors 9.164 0.725 10.902 common_classes 8.156 0.379 8.999 cleanCLOnames 7.787 0.232 8.364 nomenCheckup 7.032 0.213 8.167 selectFromMap 6.734 0.283 9.773 secLevGen 6.489 0.209 13.808 findCommonAncestors 6.073 0.261 6.689 make_graphNEL_from_ontology_plot 5.664 0.408 6.527 TermSet-class 4.953 0.227 5.584 liberalMap 4.876 0.238 5.486 plot.owlents 4.804 0.058 10.632 getOnto 4.380 0.239 5.052 onto_plot2 4.289 0.227 5.288 parents 3.250 0.115 6.028 search_labels 0.300 0.019 71.317 bioregistry_ols_resources 0.033 0.005 11.476 * 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 ‘/media/volume/teran2_disk/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 ‘/media/volume/teran2_disk/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 88.751 4.420 110.330
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 20.698 | 1.028 | 23.380 | |
PROSYM | 0.150 | 0.001 | 0.151 | |
TermSet-class | 4.953 | 0.227 | 5.584 | |
allGOterms | 0.081 | 0.003 | 0.084 | |
ancestors | 9.164 | 0.725 | 10.902 | |
ancestors_names | 2.978 | 0.004 | 3.420 | |
bioregistry_ols_resources | 0.033 | 0.005 | 11.476 | |
cellTypeToGO | 1.080 | 0.038 | 1.123 | |
children_names | 3.171 | 0.010 | 3.182 | |
cleanCLOnames | 7.787 | 0.232 | 8.364 | |
common_classes | 8.156 | 0.379 | 8.999 | |
ctmarks | 0.000 | 0.000 | 0.001 | |
cyclicSigset | 0.004 | 0.000 | 0.004 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.003 | 0.000 | 0.003 | |
fastGrep | 10.420 | 0.289 | 11.501 | |
findCommonAncestors | 6.073 | 0.261 | 6.689 | |
getLeavesFromTerm | 10.732 | 0.225 | 11.341 | |
getOnto | 4.380 | 0.239 | 5.052 | |
humrna | 0.006 | 0.000 | 0.006 | |
labels.owlents | 11.731 | 0.965 | 11.766 | |
ldfToTerms | 1.509 | 0.037 | 1.547 | |
liberalMap | 4.876 | 0.238 | 5.486 | |
makeSelectInput | 0.000 | 0.001 | 0.001 | |
make_graphNEL_from_ontology_plot | 5.664 | 0.408 | 6.527 | |
mapOneNaive | 4.094 | 0.173 | 4.622 | |
minicorpus | 0.001 | 0.000 | 0.001 | |
nomenCheckup | 7.032 | 0.213 | 8.167 | |
onto_plot2 | 4.289 | 0.227 | 5.288 | |
onto_roots | 0 | 0 | 0 | |
owl2cache | 11.950 | 1.101 | 19.339 | |
packDesc2019 | 0.003 | 0.001 | 0.007 | |
packDesc2021 | 0.002 | 0.001 | 0.006 | |
packDesc2022 | 0.002 | 0.000 | 0.002 | |
packDesc2023 | 0.002 | 0.000 | 0.005 | |
parents | 3.250 | 0.115 | 6.028 | |
plot.owlents | 4.804 | 0.058 | 10.632 | |
recognizedPredicates | 0 | 0 | 0 | |
search_labels | 0.300 | 0.019 | 71.317 | |
secLevGen | 6.489 | 0.209 | 13.808 | |
selectFromMap | 6.734 | 0.283 | 9.773 | |
setup_entities | 3.800 | 0.035 | 4.768 | |
setup_entities2 | 0.705 | 0.002 | 1.613 | |
seur3kTab | 0.003 | 0.000 | 0.009 | |
siblings_TAG | 17.545 | 0.661 | 30.997 | |
stopWords | 0.001 | 0.001 | 0.001 | |
subclasses | 3.849 | 0.001 | 3.856 | |
sym2CellOnto | 37.130 | 1.220 | 40.403 | |
valid_ontonames | 0 | 0 | 0 | |