############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rols_3.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rols.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rols/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rols’ version ‘3.4.0’ * 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 ‘rols’ can be installed ... OK * checking installed package size ... OK * 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 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘rols-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Ontologies > ### Title: Ontologies > ### Aliases: Ontologies Ontology olsLinks olsLinks,Ontology olsConfig > ### olsConfig,Ontology olsVersion olsVersion,character > ### olsVersion,Ontology olsVersion,Ontologies olsLoaded > ### olsLoaded,character olsLoaded,Ontology olsLoaded,Ontologies > ### olsUpdated olsUpdated,character olsUpdated,Ontology > ### olsUpdated,Ontologies olsStatus olsStatus,character > ### olsStatus,Ontology olsStatus,Ontologies olsPrefix olsPrefix,character > ### olsPrefix,Ontology olsPrefix,Ontologies olsDesc olsDesc,character > ### olsDesc,Ontology olsDesc,Ontologies olsTitle olsTitle,character > ### olsTitle,Ontology olsTitle,Ontologies olsNamespace > ### olsNamespace,character olsNamespace,Ontology olsNamespace,Ontologies > ### ontologyUrl ontologyUrl,character ontologyUrl,Ontology > ### as.data.frame.Ontologies Ontologies,missing-method > ### Ontology,character-method Ontology,Ontology-method > ### show,Ontology-method show,Ontologies-method > ### olsVersion,character-method olsVersion,Ontology-method > ### olsVersion,Ontologies-method olsLoaded,character-method > ### olsLoaded,Ontology-method olsLoaded,Ontologies-method > ### olsLinks,Ontology-method olsConfig,Ontology-method > ### olsUpdated,character-method olsUpdated,Ontology-method > ### olsUpdated,Ontologies-method olsPrefix,character-method > ### olsPrefix,Ontology-method olsPrefix,Ontologies-method > ### olsDesc,character-method olsDesc,Ontology-method > ### olsDesc,Ontologies-method olsTitle,character-method > ### olsTitle,Ontology-method olsTitle,Ontologies-method > ### olsStatus,character-method olsStatus,Ontology-method > ### olsStatus,Ontologies-method olsNamespace,character-method > ### olsNamespace,Ontology-method olsNamespace,Ontologies-method > ### ontologyUrl,character-method ontologyUrl,Ontology-method > ### lapply,Ontologies-method [,Ontologies-method [[,Ontologies-method > ### length,Ontologies-method > > ### ** Examples > > > ############################# > ## All ontologies > (onts <- Ontologies()) Error in h(simpleError(msg, call)) : error in evaluating the argument 'X' in selecting a method for function 'lapply': error in evaluating the argument 'X' in selecting a method for function 'lapply': HTTP 404 Not Found. Calls: Ontologies ... signalCondition -> -> .handleSimpleError -> h Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ ├─rlang::try_fetch(...) 18. │ │ └─base::withCallingHandlers(...) 19. │ └─httr2::req_perform(req, path = get_path(i), mock = mock) 20. │ └─httr2:::handle_resp(req, resp, error_call = error_call) 21. │ └─rlang::cnd_signal(cnd) 22. │ └─rlang:::signal_abort(cnd) 23. │ └─base::signalCondition(cnd) 24. ├─base (local) ``(``) 25. └─base::.handleSimpleError(...) 26. └─base (local) h(simpleError(msg, call)) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ] Error: Test failures Execution halted * 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: 2 ERRORs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/rols.Rcheck/00check.log’ for details.