[Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz
Luca Lepore
|uc@1@|epore @end|ng |rom m@||@po||m|@|t
Wed Mar 19 09:03:06 CET 2025
Dear all,
Sorry to bother you. I would like to know how to be removed from these mailing lists. I made the subscription just for a university project and now I would like to unsubscribe.
I sent an email to bioc-devel-owner using r-project.org two months ago, but I'm still receiving email.
I'm writing this email because I do not know what to do.
Thank you all for your attention
Best regards,
Luca
Inviato da Outlook per Android<https://aka.ms/AAb9ysg>
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Robert Castelo via Bioc-devel <bioc-devel using r-project.org>
Sent: Tuesday, March 18, 2025 11:53:40 AM
To: Kasper Daniel Hansen <kasperdanielhansen using gmail.com>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz
Hi Kasper,
thanks for your efforts, it seems that you wrote this email just a few
hours too early because the build reports for Monday 17th do not display
the buffer overflow error anymore for Rgraphviz:
https://bioconductor.org/checkResults/3.21/bioc-LATEST/Rgraphviz
and neither for qpgraph (hooray!):
https://bioconductor.org/checkResults/3.21/bioc-LATEST/qpgraph
although the problems described by the OP of this thread persist in the
following packages that depend on Rgraphviz:
* OncoSimulR:
https://bioconductor.org/checkResults/3.21/bioc-LATEST/OncoSimulR/kunpeng2-buildsrc.html
* 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
with the error "no slot of name "name" for this object of class "pEdge",
which seems related to Rgraphviz, which defines a class 'pEdge' as follows:
##end type can be arrow or -| or none
##which can be from, to or both
setClass("pEdge", representation(from="character",
to="character",
attrs="list",
subG="integer"),
prototype=list(subG=as.integer(0))
)
and the backtrace shown in some of the reports points out to
'Rgraphviz::buildEdgeList()'. so, maybe this problem was unrelated with
the buffer overflow after all.
I've looked at the code or 'Rgraphviz::buildEdgeList()' but I can't see
anything suspicious there.
robert.
On 3/17/25 15:20, Kasper Daniel Hansen wrote:
> 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
>> <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
>>
>> [[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
--
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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