[Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz
Robert Castelo
robert@c@@te|o @end|ng |rom up|@edu
Fri Mar 14 09:22:06 CET 2025
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 using 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:rdiaz02 using gmail.com <mailto:Email%3Ardiaz02 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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>
> _______________________________________________
> Bioc-devel using 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
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