[Bioc-devel] autonomics devel : how to reproduce bioc build errors best ?

Dear bioc-devel, autonomics underwent continued development since its submission two years ago. The new functionality was recently pushed to autonomics devel to make it accessible to users. Not suprisingly, the green traffic lights turned red. The puzzling thing, though, is that, on my machin

Re: [Bioc-devel] autonomics devel : how to reproduce bioc build errors best ?

I just tried locally with R-devel and making sure all the package dependencies were updated and can reproduce this. I suggest making sure you have an updated installation or maybe try using the BIoconductor docker if you don't have access to R-devel. lorikern@jbcj433:~/BioconductorPackages/Sof

Re: [Bioc-devel] [question about class extension]

There aren't strict standards imposed on many of the packages in Bioconductor introducing classes, but many other packages extend and impose standards and constraints for given areas/fields/subjects. If you are considering this route, something like the following could work to determine if introd

Re: [Bioc-devel] [question about class extension]

Hi Delphine, I had a similar dilemma while developing midasHLA package. There, we wanted to have unique features names across all experiments and colData as well as mandatory metadata. To this end I wrote a new class specific to my package that extends MAE.

Re: [Bioc-devel] [question about class extension]

Pleased to try also: ``` sapply(c("SummarizedExperiment", "MultiAssayExperiment"), library, character.only = T) new <- SummarizedExperiment() metadata(new) <- list(MultiAssayExperiment()) new ``` Again, it is a preference. kind regards, Sean On Wed, Jan 24, 2024 at 6:06 AM migdal migdal wrote

[Bioc-devel] build reports for apple silicon

We're clearly producing binary builds for Apple Silicon. Why do we not have a build report for this platform? Best, Kasper [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc

Re: [Bioc-devel] build reports for apple silicon

Hi, https://bioconductor.org/checkResults/3.19/bioc-mac-arm64-LATEST/ Regards, Martin On Wed, Jan 24, 2024 at 5:55 PM Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > We're clearly producing binary builds for Apple Silicon. Why do we not have > a build report for this platform? > >

Re: [Bioc-devel] build reports for apple silicon

They are linked off the check result main page: https://bioconductor.org/checkResults/ Because we can not run them daily they are not in the main report. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & C

Re: [Bioc-devel] build reports for apple silicon

Oh. That's confusing, but now I at least know what is going on. On Wed, Jan 24, 2024 at 10:58 AM Kern, Lori wrote: > They are linked off the check result main page: > https://bioconductor.org/checkResults/ > > Because we can not run them daily they are not in the main report. > > > Lori Shepherd