[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
Wed Mar 19 09:36:58 CET 2025
Hi Kasper,
this is really confusing, yesterday I saw a build with timestamp of
Monday 17th, where the buffer overflow error was gone, so sadly, we're
back to square one with this problem. I'll try to dig a bit more, good
luck with buildEdgeList().
robert.
On 3/18/25 20:01, Kasper Daniel Hansen 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.castelo using 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.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
>
>
>
> --
> 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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