| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-05 11:33 -0400 (Tue, 05 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4844 |
| 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 1760/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rega 1.1.0 (landing page) Igor Cervenka
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for Rega in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Rega package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rega.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: Rega |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:Rega.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings Rega_1.1.0.tar.gz |
| StartedAt: 2026-05-05 02:53:33 -0400 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 02:54:39 -0400 (Tue, 05 May 2026) |
| EllapsedTime: 66.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Rega.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:Rega.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings Rega_1.1.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/Rega.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-05 06:53:33 UTC
* checking for file ‘Rega/DESCRIPTION’ ... OK
* this is package ‘Rega’ version ‘1.1.0’
* 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 ‘Rega’ 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 loading without being on the library search path ... 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 ... OK
* 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:
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-samples_in_db.R:31:3'): samples_in_db default client path ────
Expected `samples_in_db(c("S3", "S4"))` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 4 | WARN 6 | SKIP 4 | PASS 1326 ]
Error:
! Test failures.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.24-bioc/meat/Rega.Rcheck/00check.log’
for details.
Rega.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL Rega ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘Rega’ ... ** this is package ‘Rega’ version ‘1.1.0’ ** using staged installation ** R ** 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 (Rega)
Rega.Rcheck/tests/testthat.Rout.fail
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(Rega)
>
> test_check("Rega")
New names:
* `` -> `...1`
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Validation passed!
Step 1/9 - Retrieving Raw Files
Step 2/9 - Creating Submission
Step 3/9 - Adding Samples
Step 4/9 - Adding Studies
Step 5/9 - Adding Experiments
Step 6/9 - Adding Runs
Step 7/9 - Retrieving Analysis Files
Step 8/9 - Adding Analyses
Step 9/9 - Adding Datasets
Step 1/9 - Retrieving Raw Files
Step 2/9 - Creating Submission
Step 3/9 - Adding Samples
Step 4/9 - Adding Studies
Step 5/9 - Adding Experiments
Step 6/9 - Adding Runs
Step 7/9 - Retrieving Analysis Files
Step 8/9 - Adding Analyses
Step 9/9 - Adding Datasets
Saving _problems/test-samples_in_db-11.R
Saving _problems/test-samples_in_db-16.R
Saving _problems/test-samples_in_db-19.R
Saving _problems/test-samples_in_db-31.R
[ FAIL 4 | WARN 6 | SKIP 4 | PASS 1326 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• Keyring support not available (4): 'test-dot-get_ega_username.R:6:3',
'test-dot-get_ega_username.R:17:3', 'test-dot-get_ega_username.R:33:3',
'test-dot-get_ega_username.R:74:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-samples_in_db.R:11:3'): samples_in_db works on happy paths ───
Expected `samples_in_db(c("S3", "S4"), client = mock_client)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-samples_in_db.R:14:3'): samples_in_db works on happy paths ───
Expected `samples_in_db(c("S1", "S3"), client = mock_client, retrieve = TRUE)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-samples_in_db.R:19:3'): samples_in_db works on happy paths ───
Expected `samples_in_db(long_vec, client = mock_client)` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-samples_in_db.R:31:3'): samples_in_db default client path ────
Expected `samples_in_db(c("S3", "S4"))` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 4 | WARN 6 | SKIP 4 | PASS 1326 ]
Error:
! Test failures.
Execution halted
Rega.Rcheck/Rega-Ex.timings
| name | user | system | elapsed | |
| DELIM_CONVERTERS | 0.012 | 0.000 | 0.012 | |
| add_required_str | 0 | 0 | 0 | |
| aliases_formatter | 0.002 | 0.000 | 0.002 | |
| api_function_factory | 0.033 | 0.000 | 0.034 | |
| api_name_to_label | 0.001 | 0.000 | 0.002 | |
| column_table_formatter | 0.002 | 0.000 | 0.003 | |
| create_client | 0.256 | 0.005 | 0.982 | |
| default_parser | 1.614 | 0.051 | 1.666 | |
| default_validator | 0.189 | 0.003 | 0.193 | |
| delete_submission | 0 | 0 | 0 | |
| delete_submission_contents | 0.001 | 0.000 | 0.001 | |
| dot-add_headers | 0.032 | 0.000 | 0.033 | |
| dot-add_json_validation | 0 | 0 | 0 | |
| dot-add_paths | 0 | 0 | 0 | |
| dot-add_queries | 0.041 | 0.000 | 0.042 | |
| dot-add_request_body | 0 | 0 | 0 | |
| dot-analyses_extra_validator | 0.026 | 0.000 | 0.026 | |
| dot-basic_validator | 0.015 | 0.000 | 0.014 | |
| dot-dataset_analyses_validator | 0.009 | 0.000 | 0.009 | |
| dot-datasets_extra_validator | 0.024 | 0.000 | 0.024 | |
| dot-get_ega_password | 0.020 | 0.001 | 0.022 | |
| dot-get_ega_username | 0.003 | 0.000 | 0.003 | |
| dot-get_operation_params | 0.030 | 0.002 | 0.032 | |
| dot-get_rega_key | 0.001 | 0.000 | 0.001 | |
| dot-has_analyses | 0 | 0 | 0 | |
| dot-is_client | 0 | 0 | 0 | |
| dot-is_scalar | 0.000 | 0.000 | 0.001 | |
| dot-operation_params_to_args | 0.039 | 0.000 | 0.039 | |
| dot-runs_extra_validator | 0.02 | 0.00 | 0.02 | |
| dot-studies_extra_validator | 0.018 | 0.000 | 0.019 | |
| dot-submission_validator | 0.006 | 0.001 | 0.006 | |
| dot-summarise_validation | 0.007 | 0.000 | 0.007 | |
| dot-validate_character_scalar | 0.001 | 0.000 | 0.001 | |
| dot-validate_logical_scalar | 0 | 0 | 0 | |
| ega_oauth | 0.007 | 0.000 | 0.006 | |
| ega_token | 0.159 | 0.005 | 1.275 | |
| extract_api | 0.052 | 0.001 | 0.053 | |
| extract_operation_definitions | 0.033 | 0.000 | 0.033 | |
| extract_resource_name | 0.002 | 0.000 | 0.002 | |
| fetch_files | 0.003 | 0.000 | 0.003 | |
| file_formatter | 0.002 | 0.000 | 0.002 | |
| filter_id_fields | 0.001 | 0.000 | 0.001 | |
| finalise_submission | 0.325 | 0.025 | 0.351 | |
| first_row_to_colnames | 0.002 | 0.000 | 0.002 | |
| fold_column | 0.002 | 0.000 | 0.001 | |
| format_chromosomes | 0.005 | 0.000 | 0.005 | |
| get_chr_group | 0.001 | 0.000 | 0.002 | |
| get_entry_by_title | 0.184 | 0.008 | 0.193 | |
| get_enum | 0.070 | 0.015 | 0.085 | |
| get_formatter | 0.003 | 0.001 | 0.004 | |
| get_formatter_params | 0.003 | 0.001 | 0.004 | |
| get_operation_schema | 0.030 | 0.004 | 0.034 | |
| get_or_post | 0.056 | 0.003 | 0.059 | |
| get_properties | 0.029 | 0.000 | 0.029 | |
| get_schemas | 0.022 | 0.000 | 0.022 | |
| get_sentence_number | 0.000 | 0.000 | 0.001 | |
| get_submission | 0.001 | 0.000 | 0.001 | |
| get_word_number | 0.000 | 0.000 | 0.001 | |
| has_linked_sheets | 0 | 0 | 0 | |
| is_accession | 0.001 | 0.000 | 0.000 | |
| is_provisional | 0 | 0 | 0 | |
| is_valid_http_method | 0 | 0 | 0 | |
| label_to_api_name | 0 | 0 | 0 | |
| link_sheet | 0.004 | 0.000 | 0.003 | |
| lut_add | 0.001 | 0.000 | 0.001 | |
| merge_linked_sheet | 0.002 | 0.000 | 0.002 | |
| multi_lut_add | 0.002 | 0.000 | 0.002 | |
| na_to_empty_list | 0.001 | 0.000 | 0.000 | |
| new_submission | 0.083 | 0.000 | 0.083 | |
| parse_ega_body | 0.049 | 0.002 | 0.051 | |
| parse_enum | 0.002 | 0.000 | 0.001 | |
| parse_json_body | 0.001 | 0.000 | 0.001 | |
| parse_text_body | 0.000 | 0.000 | 0.001 | |
| process_chromosomes | 0.002 | 0.001 | 0.002 | |
| process_delimited_column | 0.002 | 0.000 | 0.001 | |
| rollback_submission | 0 | 0 | 0 | |
| row_table_formatter | 0.016 | 0.000 | 0.016 | |
| samples_in_db | 0 | 0 | 0 | |
| save_log | 0 | 0 | 0 | |
| step_msg | 0.001 | 0.000 | 0.001 | |
| submit_table | 0.004 | 0.000 | 0.004 | |
| try_step | 0.001 | 0.000 | 0.001 | |
| unbox_list | 0.003 | 0.000 | 0.002 | |
| unbox_row | 0.001 | 0.001 | 0.002 | |
| use_submission | 0.001 | 0.000 | 0.001 | |
| validate_schema | 0.045 | 0.003 | 0.046 | |
| validation_to_msg | 0.002 | 0.000 | 0.002 | |
| workflow_error_handler | 0.000 | 0.000 | 0.001 | |