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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 2006/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 2.13.0  (landing page)
Jakob Wirbel
Snapshot Date: 2025-10-26 13:45 -0400 (Sun, 26 Oct 2025)
git_url: https://git.bioconductor.org/packages/SIAMCAT
git_branch: devel
git_last_commit: 6e53a76
git_last_commit_date: 2025-04-15 11:33:48 -0400 (Tue, 15 Apr 2025)
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for SIAMCAT on kjohnson3

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.

raw results


Summary

Package: SIAMCAT
Version: 2.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SIAMCAT
StartedAt: 2025-10-26 18:00:12 -0400 (Sun, 26 Oct 2025)
EndedAt: 2025-10-26 18:01:11 -0400 (Sun, 26 Oct 2025)
EllapsedTime: 58.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SIAMCAT
###
##############################################################################
##############################################################################


* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* preparing ‘SIAMCAT’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SIAMCAT_confounder.Rmd’ using rmarkdown

Quitting from SIAMCAT_confounder.Rmd:159-179 [load_motus]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. ├─readr::read_tsv(paste0(data.loc, "meta_Nielsen.tsv"))
 2. │ └─vroom::vroom(...)
 3. │   └─vroom:::vroom_(...)
 4. ├─base (local) `<fn>`(`<curl>`, "rb")
 5. └─base::open.connection(`<curl>`, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SIAMCAT_confounder.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘SIAMCAT_confounder.Rmd’

--- re-building ‘SIAMCAT_holdout.Rmd’ using rmarkdown

Quitting from SIAMCAT_holdout.Rmd:54-69 [siamcat_fr]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://zenodo.org/api/files/d81e429c-870f-44e0-a44a-2a4aa541b6c1/specI_Zeller.tsv'
---
Backtrace:
    ▆
 1. └─utils::read.table(...)
 2.   └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SIAMCAT_holdout.Rmd' failed with diagnostics:
cannot open the connection to 'https://zenodo.org/api/files/d81e429c-870f-44e0-a44a-2a4aa541b6c1/specI_Zeller.tsv'
--- failed 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 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_meta.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘SIAMCAT_meta.Rmd’

--- re-building ‘SIAMCAT_ml_pitfalls.Rmd’ using rmarkdown
2025-10-26 18:01:01.273 R[6308:551279756] XType: Using static font registry.

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 files failed:
  ‘SIAMCAT_confounder.Rmd’ ‘SIAMCAT_holdout.Rmd’ ‘SIAMCAT_meta.Rmd’
  ‘SIAMCAT_ml_pitfalls.Rmd’

Error: Vignette re-building failed.
Execution halted