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

[Robert Castelo]

Hi,

I'm experiencing a similar issue with qpgraph, which is failing on 
'nebbiolo1' (ubuntu 24.02) only:

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

giving the following error when building one of the vignettes:

--- re-building ‘qpgraphSimulate.Rnw’ using Sweave
*** buffer overflow detected ***: terminated
Aborted (core dumped)

just as Ramon below, I cannot reproduce the error either in my linux box 
with R-devel (2025-03-07 r87894) , nor with the R-devel from the 
Bioconductor docker image (2025-02-24 r87814). qpgraph is using 
Rgraphviz too, which is also failing in the same way when building the 
Rgraphviz.Rnw vignette:

--- re-building ‘Rgraphviz.Rnw’ using Sweave
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
     setequal, union


Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

     IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
     unsplit, which.max, which.min

Loading required package: grid
*** buffer overflow detected ***: terminated
Aborted (core dumped)

and I cannot reproduce this error on my machine either, Rgraphviz builds 
just fine.

does anyone here has an idea what we could do to chase this error that 
seems to be triggered by some C code in the Rgraphviz package?

something that could help diagnosing the problem is if the build 
machines could call the Sweave engine with --options="debug=TRUE", e.g.,

R CMD Sweave --options="debug=TRUE" xx.Rnw

not sure how one could do that when building a package. This would show 
in the build output the line in the vignette that is actually triggering 
the core dump.

Thanks!

robert.

On 3/7/25 03:42, Ramon Diaz-Uriarte wrote:
> 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
>
> _______________________________________________
> Bioc-devel using r-project.org  mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Medicine and Life Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514

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