Hi, I solved it. I had already tried following that link in the past, but it did not work at that moment. I tried again some days ago and now it's all right.
Sorry for the inconvenience Best regards, Luca Inviato da Outlook per Android<https://aka.ms/AAb9ysg> ________________________________ From: James W. MacDonald <jmac...@uw.edu> Sent: Tuesday, March 25, 2025 8:59:45 PM To: Hervé Pagès <hpages.on.git...@gmail.com>; Luca Lepore <luca1.lep...@mail.polimi.it> Cc: bioc-devel@r-project.org <bioc-devel@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 I don't think anybody needs to help Luca. It's simple enough to unsubscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel -----Original Message----- From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of Hervé Pagès Sent: Tuesday, March 25, 2025 2:18 PM To: Luca Lepore <luca1.lep...@mail.polimi.it> Cc: bioc-devel@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 !-------------------------------------------------------------------| This Message Is From an Untrusted Sender You have not previously corresponded with this sender. See https://itconnect.uw.edu/email-tags for additional information. Please contact the UW-IT Service Center, h...@uw.edu 206.221.5000, for assistance. |-------------------------------------------------------------------! Hi Luca, Were you helped with this? Your request got buried deep in a thread that has nothing to do with it so I would not be surprised if the people who can actually help you missed it. I suggest that you post again but this time do not answer an existing thread and use a clear subject line. Best of luck, H. On 19/03/2025 01:03, Luca Lepore via Bioc-devel wrote: > 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-ow...@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://urldefense.com/v3/__https://aka.ms/AAb9ysg__;!!K-Hz7m0 > Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOk > lGQTqhX1Ruh8cnB1UbSAcWbKw$ > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > Robert Castelo via Bioc-devel <bioc-devel@r-project.org> > Sent: Tuesday, March 18, 2025 11:53:40 AM > To: Kasper Daniel Hansen <kasperdanielhan...@gmail.com> > Cc: bioc-devel@r-project.org <bioc-devel@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://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21 > /bioc-LATEST/Rgraphviz__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHS > PXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UahNnNplQ$ > > and neither for qpgraph (hooray!): > > https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21 > /bioc-LATEST/qpgraph__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPX > rWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1Ub_DvXKUw$ > > although the problems described by the OP of this thread persist in > the following packages that depend on Rgraphviz: > > * OncoSimulR: > > https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/OncoSimulR/kunpeng2-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UZzVcPGqw$ > * CellNOptR: > > https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/CellNOptR/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UZFnR0GyA$ > * CytoML: > > https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/CytoML/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UamdBC8nw$ > * fowWorkspace: > > https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/flowWorkspace/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UaUwy1XHg$ > * TRONCO: > > https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21 > /bioc-LATEST/TRONCO/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoy > xWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB > 1Ubbsb2ebg$ > > 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://urldefense.com/v3/__https://bioconductor.org/checkResults/3. >>> 21/bioc-LATEST/qpgraph/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5 >>> kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1 >>> Ruh8cnB1UZvPqDHVw$ >>> >>> 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 >>> >>> <https://urldefense.com/v3/__http://pmax.int__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UbW_y-gUQ$ >>> >, pmin, pmin.int >>> <https://urldefense.com/v3/__http://pmin.int__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UbeHMM5hA$ >>> >, >>> 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://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/OncoSimulR/kunpeng2-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UZzVcPGqw$ >>> ) >>> > >>> > 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://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/CellNOptR/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UZFnR0GyA$ >>> > >>> > - >>> >>> CytoML:https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/CytoML/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UamdBC8nw$ >>> > >>> > - >>> >>> fowWorkspace:https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/flowWorkspace/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UaUwy1XHg$ >>> > >>> > - >>> >>> TRONCO:https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.21/bioc-LATEST/TRONCO/nebbiolo1-buildsrc.html__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1Ubbsb2ebg$ >>> > >>> > 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 <mailto:email%3ardia...@gmail.com> >>> > r.d...@uam.es >>> > ramon.d...@iib.uam.es >>> > >>> > >>> https://urldefense.com/v3/__https://ligarto.org/rdiaz__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1UYKy7CyXA$ >>> > >>> > _______________________________________________ >>> > Bioc-devel@r-project.org mailing list >>> > >>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bi >>> oc-devel__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ >>> 7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1Ua0lBTWKg$ >>> >>> -- >>> 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://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bi >>> oc-devel__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ >>> 7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1Ua0lBTWKg$ >>> >>> >>> >>> -- >>> 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc > -devel__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_J > Oa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1Ua0lBTWKg$ > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc > -devel__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_J > Oa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1Ua0lBTWKg$ -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com _______________________________________________ Bioc-devel@r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!muoR5kVzoyxWjk00bwdOpEtjbFEIeHSPXrWFXTufPuZ7B_JOa6oo6Asjr36sd0GOklGQTqhX1Ruh8cnB1Ua0lBTWKg$ [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
