| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:33 -0400 (Sat, 01 Nov 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" | 4774 |
| 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 1829/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RTCGAToolbox 2.41.0 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the RTCGAToolbox package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTCGAToolbox.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: RTCGAToolbox |
| Version: 2.41.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RTCGAToolbox |
| StartedAt: 2025-10-31 19:53:27 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 19:54:09 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 42.0 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 RTCGAToolbox
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* checking for file ‘RTCGAToolbox/DESCRIPTION’ ... OK
* preparing ‘RTCGAToolbox’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘RTCGAToolbox-vignette.Rmd’ using rmarkdown
Quitting from RTCGAToolbox-vignette.Rmd:130-134 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
▆
1. └─RTCGAToolbox::getFirehoseData(...)
2. └─RTCGAToolbox:::.files_from_html_table(fh_url)
3. ├─rvest::html_table(rvest::read_html(url))
4. ├─rvest::read_html(url)
5. └─xml2:::read_html.default(url)
6. ├─base::suppressWarnings(...)
7. │ └─base::withCallingHandlers(...)
8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
9. └─xml2:::read_xml.character(...)
10. └─xml2:::read_xml.connection(...)
11. ├─base::open(x, "rb")
12. └─base::open.connection(x, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RTCGAToolbox-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘RTCGAToolbox-vignette.Rmd’
SUMMARY: processing the following file failed:
‘RTCGAToolbox-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted