Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:36:11 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 1460/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.24.0 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.24.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ontoProc_1.24.0.tar.gz |
StartedAt: 2024-03-28 00:56:35 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 01:17:55 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 1279.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ontoProc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ontoProc_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ontoProc.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘1.24.0’ * 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 7.1Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocFileCache’ All declared Imports should be used. * 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 ... OK * 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 84.309 4.257 100.685 siblings_TAG 51.037 5.769 78.190 CLfeats 38.645 3.306 45.521 common_classes 31.948 3.009 40.145 nomenCheckup 25.101 1.417 34.624 getLeavesFromTerm 21.287 0.939 22.841 fastGrep 21.002 1.091 22.847 secLevGen 16.701 0.728 26.676 selectFromMap 15.413 0.925 23.916 TermSet-class 15.086 1.099 16.773 cleanCLOnames 15.304 0.787 16.661 onto_plot2 15.139 0.914 20.906 liberalMap 13.370 0.771 14.559 make_graphNEL_from_ontology_plot 11.623 1.131 13.084 mapOneNaive 11.378 0.611 14.377 findCommonAncestors 10.271 0.577 11.175 getOnto 8.529 0.505 9.372 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ontoProc.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/ontoProc.Rcheck/00check.log’ for details.
ontoProc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ontoProc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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 7 ] > > > proc.time() user system elapsed 110.550 8.108 202.322
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 38.645 | 3.306 | 45.521 | |
PROSYM | 0.234 | 0.000 | 0.234 | |
TermSet-class | 15.086 | 1.099 | 16.773 | |
allGOterms | 0.155 | 0.010 | 0.165 | |
cellTypeToGO | 1.634 | 0.065 | 1.699 | |
cleanCLOnames | 15.304 | 0.787 | 16.661 | |
common_classes | 31.948 | 3.009 | 40.145 | |
ctmarks | 0 | 0 | 0 | |
cyclicSigset | 0.002 | 0.004 | 0.006 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.004 | 0.000 | 0.004 | |
fastGrep | 21.002 | 1.091 | 22.847 | |
findCommonAncestors | 10.271 | 0.577 | 11.175 | |
getLeavesFromTerm | 21.287 | 0.939 | 22.841 | |
getOnto | 8.529 | 0.505 | 9.372 | |
humrna | 0.006 | 0.002 | 0.008 | |
ldfToTerms | 2.454 | 0.048 | 2.502 | |
liberalMap | 13.370 | 0.771 | 14.559 | |
makeSelectInput | 0 | 0 | 0 | |
make_graphNEL_from_ontology_plot | 11.623 | 1.131 | 13.084 | |
mapOneNaive | 11.378 | 0.611 | 14.377 | |
minicorpus | 0.002 | 0.000 | 0.003 | |
nomenCheckup | 25.101 | 1.417 | 34.624 | |
onto_plot2 | 15.139 | 0.914 | 20.906 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
packDesc2019 | 0.005 | 0.005 | 0.020 | |
packDesc2021 | 0.005 | 0.000 | 0.005 | |
packDesc2022 | 0.007 | 0.000 | 0.022 | |
packDesc2023 | 0.006 | 0.000 | 0.006 | |
recognizedPredicates | 0.001 | 0.000 | 0.000 | |
secLevGen | 16.701 | 0.728 | 26.676 | |
selectFromMap | 15.413 | 0.925 | 23.916 | |
seur3kTab | 0.005 | 0.001 | 0.022 | |
siblings_TAG | 51.037 | 5.769 | 78.190 | |
stopWords | 0.001 | 0.000 | 0.002 | |
sym2CellOnto | 84.309 | 4.257 | 100.685 | |
valid_ontonames | 0.001 | 0.000 | 0.000 | |