Dear Kasper and Robert,
Regarding the "no slot of name "name" for this object of class "pEdge"" error,
the interesting thing is that:
a) this is happening for the mentioned packages
- 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
- flowWorkspace:
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
in all systems. Thus, this is happening with versions 2.51.1 in nebbiolo1
(Linux, x86_64) and 2.51.5 (remaining systems) with the exact same error. This
seems to suggest the pEdge error is possibly not related to whatever was
leading to the failure and got solved in 2.51.5 in the non-Linux-x86_64.
b) as I said in my original report, with Rgraphviz 2.51.1, I cannot reproduce
the pEdge error of OncoSimulR in Linux, x86_64
c) I found some old reports of this error here
https://stackoverflow.com/questions/29282522/setting-edge-width-in-rgraphviz
though it did not help me (I fail to see how it is related to my usage in
OncoSimulR and, as I say, I cannot reproduce the error)
Best,
R.
On Tue, 18-March-2025, at 20:01:00, Kasper Daniel Hansen
<kasperdanielhan...@gmail.com> wrote:
> Thanks,
>
> I still see the buffer overflow, but only on nebbiolo1 :
> https://bioconductor.org/checkResults/3.21/bioc-LATEST/Rgraphviz/nebbiolo1-buildsrc.html
> (and during build)
>
> The buildEdgeList is new to me, so thanks for drawing my attention.
> However, nothing has changed in that code (to my knowledge). I'll take a
> look.
>
> Best,
> Kasper
>
>
>
> On Tue, Mar 18, 2025 at 11:53 AM Robert Castelo <robert.cast...@upf.edu>
> wrote:
>
>> 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.cast...@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@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:rdia...@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
>>>
>>>
>>
>> --
>> 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
>>
>>
--
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
r.d...@uam.es
ramon.d...@iib.uam.es
https://ligarto.org/rdiaz
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