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 > > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
