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 >> <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:rdia...@gmail.com <mailto:email%3ardia...@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
