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
