Multiple platform build/check report for BioC 3.21 - BUILD results for TRONCO on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4459
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*

BUILD results for TRONCO on palomino7

To the developers/maintainers of the TRONCO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TRONCO.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: TRONCO

Version: 2.39.0

Command: chmod a+r TRONCO -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TRONCO

StartedAt: 2025-03-16 22:08:57 -0400 (Sun, 16 Mar 2025)

EndedAt: 2025-03-16 22:10:31 -0400 (Sun, 16 Mar 2025)

EllapsedTime: 93.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r TRONCO -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data TRONCO
###
##############################################################################
##############################################################################


* checking for file 'TRONCO/DESCRIPTION' ... OK
* preparing 'TRONCO':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'f1_introduction.rmd' using rmarkdown
--- finished re-building 'f1_introduction.rmd'

--- re-building 'f2_loading_data.Rmd' using rmarkdown
--- finished re-building 'f2_loading_data.Rmd'

--- re-building 'f3_data_visualization.Rmd' using rmarkdown
--- finished re-building 'f3_data_visualization.Rmd'

--- re-building 'f4_data_manipulation.Rmd' using rmarkdown
--- finished re-building 'f4_data_manipulation.Rmd'

--- re-building 'f5_model_inference.Rmd' using rmarkdown
--- finished re-building 'f5_model_inference.Rmd'

--- re-building 'f6_post_reconstruction.Rmd' using rmarkdown

Quitting from f6_post_reconstruction.Rmd:79-88 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `buildEdgeList()`:
! no slot of name "name" for this object of class "pEdge"
---
Backtrace:
    ▆
 1. └─TRONCO::tronco.plot(...)
 2.   ├─base::plot(...)
 3.   └─Rgraphviz::plot(...)
 4.     └─Rgraphviz (local) .local(x, y, ...)
 5.       └─Rgraphviz::agopen(...)
 6.         └─Rgraphviz::buildEdgeList(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'f6_post_reconstruction.Rmd' failed with diagnostics:
no slot of name "name" for this object of class "pEdge"
--- failed re-building 'f6_post_reconstruction.Rmd'

--- re-building 'f7_import_export.Rmd' using rmarkdown
--- finished re-building 'f7_import_export.Rmd'

SUMMARY: processing the following file failed:
  'f6_post_reconstruction.Rmd'

Error: Vignette re-building failed.
Execution halted