| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-07 11:32 -0500 (Fri, 07 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" | 4818 |
| 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 1972/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIAMCAT 2.15.0 (landing page) Jakob Wirbel
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the SIAMCAT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIAMCAT.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: SIAMCAT |
| Version: 2.15.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SIAMCAT |
| StartedAt: 2025-11-06 19:57:06 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 20:00:34 -0500 (Thu, 06 Nov 2025) |
| EllapsedTime: 208.2 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 SIAMCAT
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* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* preparing ‘SIAMCAT’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘SIAMCAT_confounder.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_confounder.Rmd’
--- re-building ‘SIAMCAT_holdout.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_holdout.Rmd’
--- re-building ‘SIAMCAT_meta.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_meta.Rmd’
--- re-building ‘SIAMCAT_ml_pitfalls.Rmd’ using rmarkdown
Quitting from SIAMCAT_ml_pitfalls.Rmd:340-350 [load_data_ibd]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
▆
1. ├─readr::read_tsv(paste0(data.loc, "meta_all_cd.tsv"))
2. │ └─vroom::vroom(...)
3. │ └─vroom:::vroom_(...)
4. ├─base (local) `<fn>`(`<curl>`, "rb")
5. └─base::open.connection(`<curl>`, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SIAMCAT_ml_pitfalls.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘SIAMCAT_ml_pitfalls.Rmd’
--- re-building ‘SIAMCAT_read-in.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_read-in.Rmd’
--- re-building ‘SIAMCAT_vignette.Rmd’ using rmarkdown
--- finished re-building ‘SIAMCAT_vignette.Rmd’
SUMMARY: processing the following file failed:
‘SIAMCAT_ml_pitfalls.Rmd’
Error: Vignette re-building failed.
Execution halted