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

Mon Mar 17 15:20:02 CET 2025

We're now to version 2.51.5 and that works on everything but nebbiolo1. On
this platform it compiles but fails to build the vignettes with a buffer
overflow. This may be related to moving to snprintf from sprintf because,
well, the difference between those two functions has to do with preventing
buffer overflows (this may be completely wrong though).

I am unable to reproduce this error on
  - my mac
  - the HPC linux system I have access to
  - the bioconductor docker devel container (emulating amd64 on my M2 mac).
This test is kind of incomplete because latex is not in the docker
container, but R CMD check seems to run the vignette and only fail when it
is time to produce a PDF output

So this is looking to be harder to diagnose. I am not sure I am done with
trying with docker, but so far it didn't work (despite having the same gcc
version ad nebbiolo1).

Best,
Kasper

On Fri, Mar 14, 2025 at 9:22 AM Robert Castelo <robert.castelo using upf.edu>
wrote:

> 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, 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
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> 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
>
>

-- 
Best,
Kasper

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