Thanks, super useful. So you're saying it was working with 2.51.1? Or is it working with the release version?
Best, Kasper On Mon, Mar 24, 2025 at 12:28 PM Andrew McDavid <andrew.n.mcda...@gmail.com> wrote: > Dear Kasper and Robert, >> >> b) as I said in my original report, with Rgraphviz 2.51.1, I cannot >> reproduce the pEdge error of OncoSimulR in Linux, x86_64 > > Regarding the "no slot of name "name" for this object of class "pEdge"" > error, the interesting thing is that: > > Dear all, > > I have been trying to troubleshoot this failure in openCyto and > flowWorkspace. I have managed to reproduce it, but there are several things > I don't understand. > > 1) The source version of the package landing page > https://bioconductor.org/packages/3.21/bioc/html/Rgraphviz.html (and version > that you get with `BiocManager::install`) for Rgraphviz is 2.51.1, but the > version being used for the Bioc daily builds is 2.51.5. The binaries for > windows and mac have version number 2.51.5. This is deeply mysterious to me. > > 2) If I manually install the latest version from Kasper's github > https://github.com/kasperdanielhansen/Rgraphviz, which is the problematic > 2.51.5 version, then I can reproduce the 'no slot of name "name"' error. The > error is ultimately in Rgraphviz_buildEdgeList in src/buildEdgeList.c. Below > is the most minimal example triggering the error that I've managed to > generate so far. It hasn't been very amenable for a unit test, because the > source data are from complicated S4 classes. I certainly don't see anything > suspicious in the changeset since 2.51.1 that explains the error, but by > bisection I guess it did somehow break something in the API that > flowWorkspace is using. > > > library(Rgraphviz) > aa = list(N_0 = list(edges = 2L), N_2 = list(edges = 3L), N_3 = list( > edges = 4L), N_4 = list(edges = c(5L, 6L, 13L)), N_8 = list( > edges = integer(0)), N_9 = list(edges = integer(0)), N_13 = list( > edges = integer(0)), N_14 = list(edges = integer(0)), N_15 = list( > edges = integer(0)), N_16 = list(edges = integer(0)), N_17 = list( > edges = integer(0)), N_21 = list(edges = integer(0)), N_22 = list( > edges = integer(0))) > > edgemode_graph = "directed" > > edgeNames = c("N_0~N_2", "N_2~N_3", "N_3~N_4", "N_4~N_8", "N_4~N_9", > "N_4~N_22" > ) > > edgeAttrs = list(lty = c(`N_0~N_2` = "dotted", `N_2~N_3` = "solid", `N_3~N_4` > = "solid", > `N_4~N_8` = "solid", `N_4~N_9` = "solid", `N_4~N_22` > = "solid" > )) > > defAttrs = list(color = "black", dir = "none", weight = "1.0", label = "", > fontcolor = "black", arrowhead = "none", arrowtail = "none", > fontsize = "14", labelfontsize = "11", arrowsize = "1", > headport = "center", > layer = "", style = "solid", minlen = "1") > > > .Call("Rgraphviz_buildEdgeList", aa, edgemode_graph, list(), > edgeNames, integer(), edgeAttrs, defAttrs, PACKAGE = "Rgraphviz") # > i.e. line 45 in R/graphLayout.R > > > > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
