Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:40 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 1475/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ontoProc 1.26.0 (landing page) Vincent Carey
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the ontoProc package: - 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: 1.26.0 |
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_1.26.0.tar.gz |
StartedAt: 2024-05-06 23:32:30 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 23:36:29 -0400 (Mon, 06 May 2024) |
EllapsedTime: 238.6 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_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/ontoProc.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘1.26.0’ * 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 10.0Mb 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 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: cumu description packDesc2021 packDesc2022 PRID PROSYM rdatadateadded stopWords SYMBOL 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 16.933 0.306 17.560 CLfeats 12.034 0.439 13.247 siblings_TAG 8.474 0.345 9.392 plot.owlents 7.511 0.171 10.164 getLeavesFromTerm 6.396 0.136 6.703 fastGrep 5.840 0.148 6.267 common_classes 5.001 0.319 5.561 selectFromMap 4.821 0.183 6.399 cleanCLOnames 4.727 0.172 5.085 secLevGen 4.487 0.174 5.755 * 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-mac-arm64/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-arm64/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 version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 28.224 1.112 30.221
ontoProc.Rcheck/ontoProc-Ex.timings
name | user | system | elapsed | |
CLfeats | 12.034 | 0.439 | 13.247 | |
PROSYM | 0.115 | 0.002 | 0.117 | |
TermSet-class | 3.388 | 0.151 | 3.702 | |
allGOterms | 0.041 | 0.001 | 0.043 | |
ancestors | 4.613 | 0.145 | 4.379 | |
ancestors_names | 1.108 | 0.013 | 1.121 | |
cellTypeToGO | 0.697 | 0.037 | 0.738 | |
children_names | 1.213 | 0.016 | 1.230 | |
cleanCLOnames | 4.727 | 0.172 | 5.085 | |
common_classes | 5.001 | 0.319 | 5.561 | |
ctmarks | 0 | 0 | 0 | |
cyclicSigset | 0.002 | 0.000 | 0.002 | |
demoApp | 0 | 0 | 0 | |
dropStop | 0.001 | 0.001 | 0.002 | |
fastGrep | 5.840 | 0.148 | 6.267 | |
findCommonAncestors | 3.378 | 0.152 | 3.687 | |
getLeavesFromTerm | 6.396 | 0.136 | 6.703 | |
getOnto | 2.576 | 0.126 | 2.881 | |
humrna | 0.003 | 0.001 | 0.003 | |
ldfToTerms | 1.242 | 0.017 | 1.259 | |
liberalMap | 2.665 | 0.137 | 2.957 | |
makeSelectInput | 0.000 | 0.000 | 0.001 | |
make_graphNEL_from_ontology_plot | 3.248 | 0.162 | 3.676 | |
mapOneNaive | 2.553 | 0.137 | 2.849 | |
minicorpus | 0.001 | 0.000 | 0.001 | |
nomenCheckup | 4.471 | 0.145 | 4.770 | |
onto_plot2 | 2.623 | 0.099 | 2.889 | |
onto_roots | 0.000 | 0.000 | 0.001 | |
owl2cache | 4.035 | 0.061 | 4.212 | |
packDesc2019 | 0.001 | 0.000 | 0.008 | |
packDesc2021 | 0.001 | 0.000 | 0.007 | |
packDesc2022 | 0.001 | 0.001 | 0.001 | |
packDesc2023 | 0.001 | 0.001 | 0.002 | |
parents | 1.344 | 0.014 | 1.905 | |
plot.owlents | 7.511 | 0.171 | 10.164 | |
recognizedPredicates | 0.000 | 0.000 | 0.001 | |
secLevGen | 4.487 | 0.174 | 5.755 | |
selectFromMap | 4.821 | 0.183 | 6.399 | |
setup_entities | 1.747 | 0.030 | 1.791 | |
seur3kTab | 0.001 | 0.000 | 0.002 | |
siblings_TAG | 8.474 | 0.345 | 9.392 | |
stopWords | 0.000 | 0.001 | 0.001 | |
subclasses | 1.132 | 0.015 | 1.147 | |
sym2CellOnto | 16.933 | 0.306 | 17.560 | |
valid_ontonames | 0 | 0 | 0 | |