[Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz

[Ramon Diaz-Uriarte]

Dear All,

A package I maintain, OncoSimulR, is failing in all platforms with

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

(https://bioconductor.org/checkResults/3.21/bioc-LATEST/OncoSimulR/kunpeng2-buildsrc.html)

However, using the latest Rgraphviz source package, 2.51.1,  and R-devel from 2025-02-20 (r87772) on Linux, with all dependencies up to date, I am unable to reproduce the error, either running R CMD build or just executing the supposedly problematic code.


Interestingly, at least four other packages that depend on Rgraphviz seem to be failing with the same error:

- CellNOptR: https://bioconductor.org/checkResults/3.21/bioc-LATEST/CellNOptR/nebbiolo1-buildsrc.html

- CytoML: https://bioconductor.org/checkResults/3.21/bioc-LATEST/CytoML/nebbiolo1-buildsrc.html

- fowWorkspace:  https://bioconductor.org/checkResults/3.21/bioc-LATEST/flowWorkspace/nebbiolo1-buildsrc.html

- TRONCO:  https://bioconductor.org/checkResults/3.21/bioc-LATEST/TRONCO/nebbiolo1-buildsrc.html

How can I try to solve this issue?

Best,

--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-31
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 using gmail.com
       r.diaz using uam.es
       ramon.diaz using iib.uam.es

https://ligarto.org/rdiaz