Thanks Kasper, let me know if there is anything I could help with.

cheers,

robert.

On 13/3/25 22:54, Kasper Daniel Hansen wrote:
> I am actively working on Rgraphviz right now following some reports by 
> CRAN about
>   - issues with the package failing on the C23 standard
>   - issues with the package failing on Windows using the new R toolset 
> for the next R release
>   - a switch from sprintf to snprintf
> Tomas and Brian have been super helpful, and I have several times 
> though I had nailed down the issue. Currently, Rgraphviz 2.51.4 is 
> failing; it seems that I didn't manage to submit 2.51.5 in time.
>
> So I am working on it, albeit (clearly) not very successfully right 
> now. Some of the stuff I see on the build servers do not follow what I 
> see on my local machines but the changes are all related so I hope to 
> get it fixed "soon".
>
> Best,
> Kasper
>
> On Thu, Mar 13, 2025 at 1:52 PM Robert Castelo via Bioc-devel 
> <bioc-devel@r-project.org> wrote:
>
>     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
>     <http://pmax.int>, pmin, pmin.int <http://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:rdia...@gmail.com <mailto:email%3ardia...@gmail.com>
>     > r.d...@uam.es
>     > ramon.d...@iib.uam.es
>     >
>     > https://ligarto.org/rdiaz
>     >
>     > _______________________________________________
>     > Bioc-devel@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
>
>             [[alternative HTML version deleted]]
>
>     _______________________________________________
>     Bioc-devel@r-project.org mailing list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> -- 
> Best,
> Kasper


-- 
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

        [[alternative HTML version deleted]]

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