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