Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz

2025-03-25 Thread Andrew McDavid
Mon, Mar 24, 2025 at 12:04 PM Andrew McDavid wrote: > 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

Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz

2025-03-25 Thread Andrew McDavid
rking 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 >

Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz

2025-03-24 Thread Andrew McDavid
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 t

Re: [Bioc-devel] Reading and storing single cell ATAC data

2016-09-23 Thread Andrew McDavid
Hi Caleb, Hopefully Herve will chime in regarding SummarizedExperiment, but yes, I think you can and should inherit from that. The `assays` slot must be an object of type `Assays`, but that does appear to include a sparse Matrix. See the comments at the top of Assays-class.R in the tarball for Summ