It works with 2.51.1 and fails with 2.51.5. I haven't tried bisecting intermediate commits yet.
On Mon, Mar 24, 2025 at 12:02 PM Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > 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
