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.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 >>> <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 > > > > -- > 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
