Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 1808/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rols 3.0.0 (landing page) Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
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: 3.0.0 |
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_3.0.0.tar.gz |
StartedAt: 2024-07-12 07:16:54 -0400 (Fri, 12 Jul 2024) |
EndedAt: 2024-07-12 07:18:04 -0400 (Fri, 12 Jul 2024) |
EllapsedTime: 69.9 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_3.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rols.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rols/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rols’ version ‘3.0.0’ * 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 ‘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: 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: 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)) [ FAIL 3 | WARN 0 | SKIP 0 | PASS 115 ] 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-3.19-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/4.4-arm64/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 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > # 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 3.0.0 > > test_check("rols") [, , Hello, World] Object of class 'OlsSearch': ontolgy: GO query: cell requested: 20 (out of 10498) response(s): 0 Object of class 'Ontologies' with 257 entries ADO, AfPO ... CCF, CPONT Object of class 'Ontologies' with 1 entries ADO Object of class 'Ontologies' with 2 entries ADO, AfPO Object of class 'Ontologies' with 3 entries ADO, AfPO, AGRO Object of class 'Ontologies' with 4 entries ADO, AfPO, AGRO, AISM Object of class 'Ontologies' with 5 entries ADO, AfPO ... AISM, AMPHX Ontology: Gene Ontology (go) The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. Loaded: 2024-07-11 Updated: 2024-07-11 Version: 2024-06-17 83855 terms 367 properties 18 individuals Object of class 'Properties' with 91 entries From the SO ontology definition, IAO_0000231 ... label, deprecated Object of class 'Properties' with 160 entries From the UBERON ontology hepatobiliary system, exocrine system ... liver serosa, liver subserosa A Property from the UBERON ontology: UBERON:0002423 Label: hepatobiliary system Object of class 'Terms' with 2736 entries From the SO ontology SO:0001959, SO:0001960 ... SO:0001957, SO:0001958 A Term from the GO ontology: GO:0032801 Label: receptor catabolic process The chemical reactions and pathways resulting in the breakdown of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. [ FAIL 3 | WARN 0 | SKIP 0 | PASS 115 ] ══ 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)) [ FAIL 3 | WARN 0 | SKIP 0 | PASS 115 ] Error: Test failures Execution halted
rols.Rcheck/rols-Ex.timings
name | user | system | elapsed |