| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-08 11:35 -0500 (Mon, 08 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 952/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hca 1.19.0 (landing page) Martin Morgan
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the hca package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hca.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: hca |
| Version: 1.19.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data hca |
| StartedAt: 2025-12-07 18:01:56 -0500 (Sun, 07 Dec 2025) |
| EndedAt: 2025-12-07 18:02:15 -0500 (Sun, 07 Dec 2025) |
| EllapsedTime: 19.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data hca
###
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* checking for file ‘hca/DESCRIPTION’ ... OK
* preparing ‘hca’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘hca_manifest_vignette.Rmd’ using rmarkdown
Quitting from hca_manifest_vignette.Rmd:109-117 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.tbl_hca_column_check()`:
! At minimum, these columns must be included in your tibble:
fileId = "hits[*].files[*].uuid",
name = "hits[*].files[*].name",
fileFormat = "hits[*].files[*].format",
version = "hits[*].files[*].version",
projectTitle = "hits[*].projects[*].projectTitle[*]",
projectId = "hits[*].projects[*].projectId[*]",
url = "hits[*].files[*].url"
---
Backtrace:
▆
1. └─hca::files(filters = file_filter)
2. └─hca:::.as_tbl_hca(response$content, columns, "files_tbl_hca")
3. └─hca:::.tbl_hca_column_check(tbl_hca, required_columns, type)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'hca_manifest_vignette.Rmd' failed with diagnostics:
At minimum, these columns must be included in your tibble:
fileId = "hits[*].files[*].uuid",
name = "hits[*].files[*].name",
fileFormat = "hits[*].files[*].format",
version = "hits[*].files[*].version",
projectTitle = "hits[*].projects[*].projectTitle[*]",
projectId = "hits[*].projects[*].projectId[*]",
url = "hits[*].files[*].url"
--- failed re-building ‘hca_manifest_vignette.Rmd’
--- re-building ‘hca_vignette.Rmd’ using rmarkdown
Quitting from hca_vignette.Rmd:67-69 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.hca_GET()`:
! Bad Request (HTTP 400).
---
Backtrace:
▆
1. └─hca::projects(size = 200)
2. └─hca:::.index_GET(...)
3. └─hca:::.hca_GET(index_path)
4. └─httr::stop_for_status(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'hca_vignette.Rmd' failed with diagnostics:
Bad Request (HTTP 400).
--- failed re-building ‘hca_vignette.Rmd’
SUMMARY: processing the following files failed:
‘hca_manifest_vignette.Rmd’ ‘hca_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted