| Back to Build/check report for BioC 3.24: simplified long |
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This page was generated on 2026-05-13 11:33 -0400 (Wed, 13 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" | 4893 |
| 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 2015/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIAMCAT 2.17.0 (landing page) Jakob Wirbel
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for SIAMCAT in R Universe. | ||||||||||||||
|
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: 2.17.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SIAMCAT |
| StartedAt: 2026-05-12 20:19:26 -0400 (Tue, 12 May 2026) |
| EndedAt: 2026-05-12 20:25:02 -0400 (Tue, 12 May 2026) |
| EllapsedTime: 336.4 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 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
Quitting from SIAMCAT_meta.Rmd:48-62 [load_data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! cannot open the connection
---
Backtrace:
▆
1. ├─readr::read_tsv(paste0(data.loc, "meta_all_cd.tsv"))
2. │ └─vroom::vroom(...)
3. │ └─vroom:::vroom_(...)
4. └─vroom (local) `<fn>`(`<curl>`, "rb")
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SIAMCAT_meta.Rmd' failed with diagnostics:
cannot open the connection
--- failed 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:
! cannot open the connection
---
Backtrace:
▆
1. ├─readr::read_tsv(paste0(data.loc, "meta_all_cd.tsv"))
2. │ └─vroom::vroom(...)
3. │ └─vroom:::vroom_(...)
4. └─vroom (local) `<fn>`(`<curl>`, "rb")
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 files failed:
‘SIAMCAT_meta.Rmd’ ‘SIAMCAT_ml_pitfalls.Rmd’
Error: Vignette re-building failed.
Execution halted