Last updated on 2026-08-18 20:51:32 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 43.06 | 385.39 | 428.45 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 30.37 | 279.92 | 310.29 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 34.00 | 280.19 | 314.19 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 33.00 | 274.71 | 307.71 | OK | |
| r-devel-windows-x86_64 | 1.0.1 | 48.00 | 351.00 | 399.00 | OK | |
| r-patched-linux-x86_64 | 1.0.1 | 38.97 | 370.14 | 409.11 | ERROR | |
| r-release-linux-x86_64 | 1.0.1 | 44.54 | 391.25 | 435.79 | OK | |
| r-release-macos-arm64 | 1.0.1 | 9.00 | 76.00 | 85.00 | ERROR | |
| r-release-macos-x86_64 | 1.0.1 | 29.00 | 282.00 | 311.00 | ERROR | |
| r-release-windows-x86_64 | 1.0.1 | 46.00 | 0.00 | 46.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.1 | 10.00 | 85.00 | 95.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.1 | 28.00 | 268.00 | 296.00 | ERROR | |
| r-oldrel-windows-x86_64 | 1.0.1 | 65.00 | 467.00 | 532.00 | OK |
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘BOLDconnectR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bold.fields.info
> ### Title: Retrieve metadata of the BOLD data fields
> ### Aliases: bold.fields.info
>
> ### ** Examples
>
>
> bold.field.data <- bold.fields.info()
Warning in download.file(file, tmpFile, method = method, mode = "wb", quiet = !showProgress) :
cannot open URL 'https://github.com/DNAdiversity/BCDM/raw/main/field_definitions.tsv': HTTP status was '404 Not Found'
Error in download.file(file, tmpFile, method = method, mode = "wb", quiet = !showProgress) :
cannot open URL 'https://github.com/DNAdiversity/BCDM/raw/main/field_definitions.tsv'
Calls: bold.fields.info ... withCallingHandlers -> <Anonymous> -> download.file
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘boldconnectr_workflow.Rmd’ using rmarkdown
Quitting from boldconnectr_workflow.Rmd:100-107 [summarize-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://github.com/DNAdiversity/BCDM/raw/main/field_definitions.tsv'
---
Backtrace:
▆
1. ├─BOLDconnectR::bold.data.summarize(...)
2. │ └─BOLDconnectR:::check_and_return_preset_df(...)
3. │ └─BOLDconnectR:::presets(col_groups = preset)
4. │ └─BOLDconnectR::bold.fields.info()
5. │ ├─... %>% ...
6. │ ├─base::suppressMessages(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ └─data.table::fread(...)
9. │ └─utils::download.file(...)
10. ├─dplyr::mutate(...)
11. ├─dplyr::select(., -dplyr::matches("data_type", ignore.case = TRUE))
12. ├─dplyr::mutate(...)
13. └─dplyr::select(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'boldconnectr_workflow.Rmd' failed with diagnostics:
cannot open URL 'https://github.com/DNAdiversity/BCDM/raw/main/field_definitions.tsv'
--- failed re-building ‘boldconnectr_workflow.Rmd’
SUMMARY: processing the following file failed:
‘boldconnectr_workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘boldconnectr_workflow.Rmd’ using rmarkdown
Quitting from boldconnectr_workflow.Rmd:82-94 [fetch-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://portal.boldsystems.org/api/documents/eAErSaywSk_NKy22Ci4pSi0oyU9OLchIzCkttk4rzckBALodDBg%3D/download?format=tsv&fields=processid,marker_code'
---
Backtrace:
▆
1. └─BOLDconnectR::bold.public.search(taxonomy = list("Streptocephalus"))
2. └─BOLDconnectR:::obtain_data(step4)
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─utils::download.file(download_url, destfile = temp_file, quiet = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'boldconnectr_workflow.Rmd' failed with diagnostics:
cannot open URL 'https://portal.boldsystems.org/api/documents/eAErSaywSk_NKy22Ci4pSi0oyU9OLchIzCkttk4rzckBALodDBg%3D/download?format=tsv&fields=processid,marker_code'
--- failed re-building ‘boldconnectr_workflow.Rmd’
SUMMARY: processing the following file failed:
‘boldconnectr_workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘boldconnectr_workflow.Rmd’ using rmarkdown
Quitting from boldconnectr_workflow.Rmd:121-132 [align-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'muscle'
---
Backtrace:
▆
1. ├─BOLDconnectR::bold.analyze.align(...)
2. │ └─BOLDconnectR:::gen.msa.res(...)
3. └─base::loadNamespace(x)
4. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. └─base (local) withOneRestart(expr, restarts[[1L]])
6. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'boldconnectr_workflow.Rmd' failed with diagnostics:
there is no package called 'muscle'
--- failed re-building ‘boldconnectr_workflow.Rmd’
SUMMARY: processing the following file failed:
‘boldconnectr_workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘boldconnectr_workflow.Rmd’ using rmarkdown
2026-08-19 04:55:12.863 R[91696:475476] XType: Using static font registry.
Quitting from boldconnectr_workflow.Rmd:121-132 [align-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'muscle'
---
Backtrace:
▆
1. ├─BOLDconnectR::bold.analyze.align(...)
2. │ └─BOLDconnectR:::gen.msa.res(...)
3. └─base::loadNamespace(x)
4. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. └─base (local) withOneRestart(expr, restarts[[1L]])
6. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'boldconnectr_workflow.Rmd' failed with diagnostics:
there is no package called 'muscle'
--- failed re-building ‘boldconnectr_workflow.Rmd’
SUMMARY: processing the following file failed:
‘boldconnectr_workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64