Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:38:10 -0400 (Wed, 17 Apr 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" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1789/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rols 2.30.2 (landing page) Laurent Gatto
| 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 | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the rols package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rols.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: rols |
Version: 2.30.2 |
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_2.30.2.tar.gz |
StartedAt: 2024-04-16 08:03:53 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 08:05:28 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 95.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: rols.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_2.30.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/rols.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rols/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rols’ version ‘2.30.2’ * 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 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 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: CVParam > ### Title: Controlled Vocabulary > ### Aliases: CVParam charIsCVParam cvCharToCVPar as.character.CVParam > ### show,CVParam-method rep,CVParam-method > > ### ** Examples > > > ## User param > CVParam(name = "A user param", value = "the value") [, , A user param, the value] > ## CVParam ESI from PSI's Mass Spectrometry ontology > Term("MS", "MS:1000073") Error in (function (cond) : error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error. Calls: Term ... abort -> signal_abort -> signalCondition -> <Anonymous> 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: 5. │ └─rols:::.Ontology(...) 6. │ └─methods::new(`<chr>`, ...) 7. │ ├─methods::initialize(value, ...) 8. │ └─methods::initialize(value, ...) 9. ├─httr2::resp_body_json(req_perform(request(url))) 10. │ └─httr2:::check_response(resp) 11. │ └─httr2:::is_response(resp) 12. └─httr2::req_perform(request(url)) 13. └─httr2:::handle_resp(req, resp, error_call = error_call) 14. └─httr2:::resp_abort(resp, req, body, call = error_call) 15. └─rlang::abort(...) [ FAIL 12 | WARN 0 | SKIP 0 | PASS 12 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/rols.Rcheck/00check.log’ for details.
rols.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rols ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘rols’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘lapply’ from package ‘base’ in package ‘rols’ ** 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 (rols)
rols.Rcheck/tests/testthat.Rout.fail
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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. > # setting R_TESTS to empty string because of > # https://github.com/hadley/testthat/issues/144 > # revert this when that issue in R is fixed. > Sys.setenv("R_TESTS" = "") > library("testthat") > library("rols") This is 'rols' version 2.30.2 > > test_check("rols") [, , Hello, World] [ FAIL 12 | WARN 0 | SKIP 0 | PASS 12 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_CVParam.R:6:15'): User param creation ────────────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error. Backtrace: ▆ 1. ├─testthat::expect_warning(as("[MS, MS:1000073, ESI, ]", "CVParam")) at test_CVParam.R:6:15 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. ├─methods::as("[MS, MS:1000073, ESI, ]", "CVParam") 7. │ └─rols (local) asMethod(object) 8. │ ├─base::lapply(from, cvCharToCVPar) 9. │ └─base::lapply(from, cvCharToCVPar) 10. │ └─rols (local) FUN(X[[i]], ...) 11. │ └─rols::CVParam(label = from[1], accession = from[2]) 12. │ ├─rols::termLabel(Term(label, accession)) 13. │ ├─rols::Term(label, accession) 14. │ └─rols::Term(label, accession) 15. │ └─rols (local) .local(object, ...) 16. │ ├─rols::Term(Ontology(object), id) 17. │ ├─BiocGenerics::Ontology(object) 18. │ └─rols::Ontology(object) 19. │ └─rols:::makeOntology(url) 20. │ ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url)))) 21. │ │ └─rols:::.Ontology(...) 22. │ │ └─methods::new(`<chr>`, ...) 23. │ │ ├─methods::initialize(value, ...) 24. │ │ └─methods::initialize(value, ...) 25. │ ├─httr2::resp_body_json(req_perform(request(url))) 26. │ │ └─httr2:::check_response(resp) 27. │ │ └─httr2:::is_response(resp) 28. │ └─httr2::req_perform(request(url)) 29. │ └─httr2:::handle_resp(req, resp, error_call = error_call) 30. │ └─httr2:::resp_abort(resp, req, body, call = error_call) 31. │ └─rlang::abort(...) 32. │ └─rlang:::signal_abort(cnd, .file) 33. │ └─base::signalCondition(cnd) 34. ├─base (local) `<fn>`(`<ht2__500>`) 35. └─base::.handleSimpleError(...) 36. └─base (local) h(simpleError(msg, call)) ── Error ('test_CVParam.R:20:15'): CVParam creation and coercion ─────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error. Backtrace: ▆ 1. ├─rols::CVParam(label = "MS", accession = "MS:1000073") at test_CVParam.R:20:15 2. │ ├─rols::termLabel(Term(label, accession)) 3. │ ├─rols::Term(label, accession) 4. │ └─rols::Term(label, accession) 5. │ └─rols (local) .local(object, ...) 6. │ ├─rols::Term(Ontology(object), id) 7. │ ├─BiocGenerics::Ontology(object) 8. │ └─rols::Ontology(object) 9. │ └─rols:::makeOntology(url) 10. │ ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url)))) 11. │ │ └─rols:::.Ontology(...) 12. │ │ └─methods::new(`<chr>`, ...) 13. │ │ ├─methods::initialize(value, ...) 14. │ │ └─methods::initialize(value, ...) 15. │ ├─httr2::resp_body_json(req_perform(request(url))) 16. │ │ └─httr2:::check_response(resp) 17. │ │ └─httr2:::is_response(resp) 18. │ └─httr2::req_perform(request(url)) 19. │ └─httr2:::handle_resp(req, resp, error_call = error_call) 20. │ └─httr2:::resp_abort(resp, req, body, call = error_call) 21. │ └─rlang::abort(...) 22. │ └─rlang:::signal_abort(cnd, .file) 23. │ └─base::signalCondition(cnd) 24. ├─base (local) `<fn>`(`<ht2__500>`) 25. └─base::.handleSimpleError(...) 26. └─base (local) h(simpleError(msg, call)) ── Error ('test_CVParam.R:39:15'): Convert char to CVParam ───────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error. Backtrace: ▆ 1. ├─methods::as(x, "CVParam") at test_CVParam.R:39:15 2. │ └─rols (local) asMethod(object) 3. │ ├─base::lapply(from, cvCharToCVPar) 4. │ └─base::lapply(from, cvCharToCVPar) 5. │ └─rols (local) FUN(X[[i]], ...) 6. │ └─rols::CVParam(label = from[1], accession = from[2]) 7. │ ├─rols::termLabel(Term(label, accession)) 8. │ ├─rols::Term(label, accession) 9. │ └─rols::Term(label, accession) 10. │ └─rols (local) .local(object, ...) 11. │ ├─rols::Term(Ontology(object), id) 12. │ ├─BiocGenerics::Ontology(object) 13. │ └─rols::Ontology(object) 14. │ └─rols:::makeOntology(url) 15. │ ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url)))) 16. │ │ └─rols:::.Ontology(...) 17. │ │ └─methods::new(`<chr>`, ...) 18. │ │ ├─methods::initialize(value, ...) 19. │ │ └─methods::initialize(value, ...) 20. │ ├─httr2::resp_body_json(req_perform(request(url))) 21. │ │ └─httr2:::check_response(resp) 22. │ │ └─httr2:::is_response(resp) 23. │ └─httr2::req_perform(request(url)) 24. │ └─httr2:::handle_resp(req, resp, error_call = error_call) 25. │ └─httr2:::resp_abort(resp, req, body, call = error_call) 26. │ └─rlang::abort(...) 27. │ └─rlang:::signal_abort(cnd, .file) 28. │ └─base::signalCondition(cnd) 29. ├─base (local) `<fn>`(`<ht2__500>`) 30. └─base::.handleSimpleError(...) 31. └─base (local) h(simpleError(msg, call)) ── Error ('test_OlsSearch.R:2:5'): OlsSearch tgn ─────────────────────────────── <httr2_http_500/httr2_http/httr2_error/rlang_error/error/condition> Error in `req_perform(request(url))`: HTTP 500 Internal Server Error. Backtrace: ▆ 1. └─rols::OlsSearch("tgn", "PW") at test_OlsSearch.R:2:5 2. ├─httr2::resp_body_json(req_perform(request(url))) 3. │ └─httr2:::check_response(resp) 4. │ └─httr2:::is_response(resp) 5. └─httr2::req_perform(request(url)) 6. └─httr2:::handle_resp(req, resp, error_call = error_call) 7. └─httr2:::resp_abort(resp, req, body, call = error_call) 8. └─rlang::abort(...) ── Error ('test_OlsSearch.R:10:1'): OlsSearch show ───────────────────────────── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "HTTP 500 Internal Server Error.", trace = structure(list(call = list(expect_null(show(OlsSearch(q = "cell", ontology = "GO"))), quasi_label(enquo(object), label, arg = "object"), eval_bare(expr, quo_get_env(quo)), show(OlsSearch(q = "cell", ontology = "GO")), OlsSearch(q = "cell", ontology = "GO"), resp_body_json(req_perform(request(url))), check_response(resp), is_response(resp), req_perform(request(url)), handle_resp(req, resp, error_call = error_call), resp_abort(resp, req, body, call = error_call), abort(c(message, resp_auth_message(resp), info), status = status, resp = resp, class = c(glue("httr2_http_{status}"), "httr2_http", "httr2_error"), request = req, call = call)), parent = c(0L, 1L, 2L, 0L, 0L, 5L, 6L, 7L, 5L, 9L, 10L, 11L), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE), namespace = c("testthat", "testthat", "rlang", "methods", "rols", "httr2", "httr2", "httr2", "httr2", "httr2", "httr2", "rlang"), scope = c("::", "::", "::", "::", "::", "::", ":::", ":::", "::", ":::", ":::", "::"), error_frame = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE )), row.names = c(NA, -12L), version = 2L, class = c("rlang_trace", "rlib_trace", "tbl", "data.frame")), parent = NULL, status = 500L, resp = structure(list(method = "GET", url = "http://www.ebi.ac.uk/ols4/api/search?q=cell&ontology=go&rows=20", status_code = 500L, headers = structure(list(Vary = "Origin", Vary = "Access-Control-Request-Method", Vary = "Access-Control-Request-Headers", `Content-Type` = "application/json", Date = "Tue, 16 Apr 2024 12:05:08 GMT", `Transfer-Encoding` = "chunked", Connection = "close"), class = "httr2_headers"), body = as.raw(c(0x7b, 0x0a, 0x20, 0x20, 0x22, 0x74, 0x69, 0x6d, 0x65, 0x73, 0x74, 0x61, 0x6d, 0x70, 0x22, 0x20, 0x3a, 0x20, 0x22, 0x32, 0x30, 0x32, 0x34, 0x2d, 0x30, 0x34, 0x2d, 0x31, 0x36, 0x54, 0x31, 0x32, 0x3a, 0x30, 0x35, 0x3a, 0x30, 0x38, 0x2e, 0x35, 0x39, 0x35, 0x2b, 0x30, 0x30, 0x3a, 0x30, 0x30, 0x22, 0x2c, 0x0a, 0x20, 0x20, 0x22, 0x73, 0x74, 0x61, 0x74, 0x75, 0x73, 0x22, 0x20, 0x3a, 0x20, 0x35, 0x30, 0x30, 0x2c, 0x0a, 0x20, 0x20, 0x22, 0x65, 0x72, 0x72, 0x6f, 0x72, 0x22, 0x20, 0x3a, 0x20, 0x22, 0x49, 0x6e, 0x74, 0x65, 0x72, 0x6e, 0x61, 0x6c, 0x20, 0x53, 0x65, 0x72, 0x76, 0x65, 0x72, 0x20, 0x45, 0x72, 0x72, 0x6f, 0x72, 0x22, 0x2c, 0x0a, 0x20, 0x20, 0x22, 0x70, 0x61, 0x74, 0x68, 0x22, 0x20, 0x3a, 0x20, 0x22, 0x2f, 0x6f, 0x6c, 0x73, 0x34, 0x2f, 0x61, 0x70, 0x69, 0x2f, 0x73, 0x65, 0x61, 0x72, 0x63, 0x68, 0x22, 0x0a, 0x7d)), request = structure(list(url = "http://www.ebi.ac.uk/ols4/api/search?q=cell&ontology=go&rows=20", method = NULL, headers = list(), body = NULL, fields = list(), options = list(), policies = list()), class = "httr2_request"), cache = <environment>), class = "httr2_response"), request = structure(list( url = "http://www.ebi.ac.uk/ols4/api/search?q=cell&ontology=go&rows=20", method = NULL, headers = list(), body = NULL, fields = list(), options = list(), policies = list()), class = "httr2_request"), rlang = list(inherit = TRUE), call = req_perform(request(url))), class = c("httr2_http_500", "httr2_http", "httr2_error", "rlang_error", "error", "condition" )))`: error in evaluating the argument 'object' in selecting a method for function 'show': HTTP 500 Internal Server Error. Backtrace: ▆ 1. ├─testthat::expect_null(show(OlsSearch(q = "cell", ontology = "GO"))) 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─methods::show(OlsSearch(q = "cell", ontology = "GO")) 5. ├─rols::OlsSearch(q = "cell", ontology = "GO") 6. │ ├─httr2::resp_body_json(req_perform(request(url))) 7. │ │ └─httr2:::check_response(resp) 8. │ │ └─httr2:::is_response(resp) 9. │ └─httr2::req_perform(request(url)) 10. │ └─httr2:::handle_resp(req, resp, error_call = error_call) 11. │ └─httr2:::resp_abort(resp, req, body, call = error_call) 12. │ └─rlang::abort(...) 13. │ └─rlang:::signal_abort(cnd, .file) 14. │ └─base::signalCondition(cnd) 15. └─base (local) `<fn>`(`<ht2__500>`) ── Error ('test_OlsSearch.R:14:5'): OlsSearch rows ───────────────────────────── <httr2_http_500/httr2_http/httr2_error/rlang_error/error/condition> Error in `req_perform(request(url))`: HTTP 500 Internal Server Error. Backtrace: ▆ 1. └─rols::OlsSearch(q = "cell", ontology = "GO") at test_OlsSearch.R:14:5 2. ├─httr2::resp_body_json(req_perform(request(url))) 3. │ └─httr2:::check_response(resp) 4. │ └─httr2:::is_response(resp) 5. └─httr2::req_perform(request(url)) 6. └─httr2:::handle_resp(req, resp, error_call = error_call) 7. └─httr2:::resp_abort(resp, req, body, call = error_call) 8. └─rlang::abort(...) ── Error ('test_OlsSearch.R:35:5'): OlsSearch coercion ───────────────────────── <httr2_http_500/httr2_http/httr2_error/rlang_error/error/condition> Error in `req_perform(request(url))`: HTTP 500 Internal Server Error. Backtrace: ▆ 1. └─rols::OlsSearch(q = "plasma", ontology = "GO", rows = 32) at test_OlsSearch.R:35:5 2. ├─httr2::resp_body_json(req_perform(request(url))) 3. │ └─httr2:::check_response(resp) 4. │ └─httr2:::is_response(resp) 5. └─httr2::req_perform(request(url)) 6. └─httr2:::handle_resp(req, resp, error_call = error_call) 7. └─httr2:::resp_abort(resp, req, body, call = error_call) 8. └─rlang::abort(...) ── Error ('test_OlsSearch.R:50:5'): Empty olsSearch query ────────────────────── <httr2_http_500/httr2_http/httr2_error/rlang_error/error/condition> Error in `req_perform(request(url))`: HTTP 500 Internal Server Error. Backtrace: ▆ 1. └─rols::OlsSearch("asdasdasdasd", ontology = "CL") at test_OlsSearch.R:50:5 2. ├─httr2::resp_body_json(req_perform(request(url))) 3. │ └─httr2:::check_response(resp) 4. │ └─httr2:::is_response(resp) 5. └─httr2::req_perform(request(url)) 6. └─httr2:::handle_resp(req, resp, error_call = error_call) 7. └─httr2:::resp_abort(resp, req, body, call = error_call) 8. └─rlang::abort(...) ── Error ('test_Onologies.R:1:1'): (code run outside of `test_that()`) ───────── 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 500 Internal Server Error. Backtrace: ▆ 1. ├─rols::Ontologies() at test_Onologies.R:1:1 2. ├─rols::Ontologies() 3. │ └─rols:::makeOntologies() 4. │ ├─rols:::.Ontologies(...) 5. │ │ └─methods::new(`<chr>`, ...) 6. │ │ ├─methods::initialize(value, ...) 7. │ │ └─methods::initialize(value, ...) 8. │ ├─base::lapply(ols_requests(url, "ontologies"), ontologyFromJson) 9. │ └─rols:::ols_requests(url, "ontologies") 10. │ ├─base::unlist(...) 11. │ ├─base::lapply(...) 12. │ └─httr2::req_perform_iterative(...) 13. │ ├─base::tryCatch(...) 14. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ ├─rlang::try_fetch(req_perform(req, path = get_path(i)), httr2_error = httr2_error) 18. │ │ └─base::withCallingHandlers(...) 19. │ └─httr2::req_perform(req, path = get_path(i)) 20. │ └─httr2:::handle_resp(req, resp, error_call = error_call) 21. │ └─httr2:::resp_abort(resp, req, body, call = error_call) 22. │ └─rlang::abort(...) 23. │ └─rlang:::signal_abort(cnd, .file) 24. │ └─base::signalCondition(cnd) 25. ├─base (local) `<fn>`(`<ht2__500>`) 26. └─base::.handleSimpleError(...) 27. └─base (local) h(simpleError(msg, call)) ── Error ('test_Properties.R:2:5'): Property constructors ────────────────────── 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 500 Internal Server Error. Backtrace: ▆ 1. ├─rols::Properties("so") at test_Properties.R:2:5 2. ├─rols::Properties("so") 3. │ └─rols (local) .local(object, ...) 4. │ ├─base::lapply(ols_requests(url, what = "properties"), propertyFromJson) 5. │ └─rols:::ols_requests(url, what = "properties") 6. │ ├─base::unlist(...) 7. │ ├─base::lapply(...) 8. │ └─httr2::req_perform_iterative(...) 9. │ ├─base::tryCatch(...) 10. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 13. │ ├─rlang::try_fetch(req_perform(req, path = get_path(i)), httr2_error = httr2_error) 14. │ │ └─base::withCallingHandlers(...) 15. │ └─httr2::req_perform(req, path = get_path(i)) 16. │ └─httr2:::handle_resp(req, resp, error_call = error_call) 17. │ └─httr2:::resp_abort(resp, req, body, call = error_call) 18. │ └─rlang::abort(...) 19. │ └─rlang:::signal_abort(cnd, .file) 20. │ └─base::signalCondition(cnd) 21. ├─base (local) `<fn>`(`<ht2__500>`) 22. └─base::.handleSimpleError(...) 23. └─base (local) h(simpleError(msg, call)) ── Error ('test_Properties.R:29:5'): Property/ies show ───────────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'show': 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 500 Internal Server Error. Backtrace: ▆ 1. ├─testthat::expect_null(show(Properties("so"))) at test_Properties.R:29:5 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─methods::show(Properties("so")) 5. ├─rols::Properties("so") 6. ├─rols::Properties("so") 7. │ └─rols (local) .local(object, ...) 8. │ ├─base::lapply(ols_requests(url, what = "properties"), propertyFromJson) 9. │ └─rols:::ols_requests(url, what = "properties") 10. │ ├─base::unlist(...) 11. │ ├─base::lapply(...) 12. │ └─httr2::req_perform_iterative(...) 13. │ ├─base::tryCatch(...) 14. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ ├─rlang::try_fetch(req_perform(req, path = get_path(i)), httr2_error = httr2_error) 18. │ │ └─base::withCallingHandlers(...) 19. │ └─httr2::req_perform(req, path = get_path(i)) 20. │ └─httr2:::handle_resp(req, resp, error_call = error_call) 21. │ └─httr2:::resp_abort(resp, req, body, call = error_call) 22. │ └─rlang::abort(...) 23. │ └─rlang:::signal_abort(cnd, .file) 24. │ └─base::signalCondition(cnd) 25. ├─base (local) `<fn>`(`<ht2__500>`) 26. ├─base::.handleSimpleError(...) 27. │ └─base (local) h(simpleError(msg, call)) 28. └─base::.handleSimpleError(...) 29. └─base (local) h(simpleError(msg, call)) ── Error ('test_Terms.R:1:1'): (code run outside of `test_that()`) ───────────── <httr2_http_500/httr2_http/httr2_error/rlang_error/error/condition> Error in `req_perform(request(url))`: HTTP 500 Internal Server Error. Backtrace: ▆ 1. ├─BiocGenerics::Ontology("GO") at test_Terms.R:1:1 2. └─rols::Ontology("GO") 3. └─rols:::makeOntology(url) 4. ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url)))) 5. │ └─rols:::.Ontology(...) 6. │ └─methods::new(`<chr>`, ...) 7. │ ├─methods::initialize(value, ...) 8. │ └─methods::initialize(value, ...) 9. ├─httr2::resp_body_json(req_perform(request(url))) 10. │ └─httr2:::check_response(resp) 11. │ └─httr2:::is_response(resp) 12. └─httr2::req_perform(request(url)) 13. └─httr2:::handle_resp(req, resp, error_call = error_call) 14. └─httr2:::resp_abort(resp, req, body, call = error_call) 15. └─rlang::abort(...) [ FAIL 12 | WARN 0 | SKIP 0 | PASS 12 ] Error: Test failures Execution halted
rols.Rcheck/rols-Ex.timings
name | user | system | elapsed |