| Back to Build/check report for BioC 3.24: simplified long |
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This page was generated on 2026-05-09 15:11 -0400 (Sat, 09 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" | 4890 |
| 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 1017/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BIOCCHECK | BUILD BIN | ||||||||
| HuBMAPR 1.7.0 (landing page) Christine Hou
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for HuBMAPR in R Universe. | |||||||||||||||
|
To the developers/maintainers of the HuBMAPR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HuBMAPR.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: HuBMAPR |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 HuBMAPR |
| StartedAt: 2026-05-08 18:13:20 -0400 (Fri, 08 May 2026) |
| EndedAt: 2026-05-08 18:13:37 -0400 (Fri, 08 May 2026) |
| EllapsedTime: 17.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 HuBMAPR
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* checking for file ‘HuBMAPR/DESCRIPTION’ ... OK
* preparing ‘HuBMAPR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘hubmapr_vignettes.Rmd’ using rmarkdown
Quitting from hubmapr_vignettes.Rmd:163-169 [datasets]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_http_500>
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
---
Backtrace:
▆
1. ├─base::system.time(...)
2. └─HuBMAPR::datasets()
3. └─HuBMAPR:::.query_entity("Dataset")
4. └─httr2::req_perform_iterative(req, .rnext_req_fun, progress = FALSE)
5. ├─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. ├─rlang::try_fetch(...)
10. │ └─base::withCallingHandlers(...)
11. └─httr2::req_perform(req, path = get_path(i), mock = mock)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'hubmapr_vignettes.Rmd' failed with diagnostics:
HTTP 500 Internal Server Error.
--- failed re-building ‘hubmapr_vignettes.Rmd’
SUMMARY: processing the following file failed:
‘hubmapr_vignettes.Rmd’
Error: Vignette re-building failed.
Execution halted