Re: [Bioc-devel] Important Bioconductor Release Deadlines

2024-04-04 Thread Anatoly Sorokin
Dear Levi, minor correction: not requiring but working with. Testing against r-devel and requiring it for development are two different things. If the development and maintenance of the Bioconductor package would be my only responsibility, I wouldn't argue. But because this is a voluntary activity

Re: [Bioc-devel] Important Bioconductor Release Deadlines

2024-04-04 Thread Levi Waldron
Anatoly, delaying dependency on R 4.4 until October would mean 6 months of Bioconductor release requiring an old release of R for users. Bioconductor developers developing against r-devel means that users get a new Bioconductor release that works immediately on the new R. And I think a main purp

Re: [Bioc-devel] Important Bioconductor Release Deadlines

2024-04-04 Thread Anatoly Sorokin
Hi Henrik, thank you for the prompt reply. I'm on Mac OS 12.5. And regarding the linking version of Bioconductor and R my major complaint is the timing, if R 4.4 hasn't been released yet, why not postpone this dependency to the October release of Bioconductor? And it is also true that we have a

Re: [Bioc-devel] Important Bioconductor Release Deadlines

2024-04-04 Thread Henrik Bengtsson
Hello, these days, it's quite straight forward to have multiple versions of R installed in parallel without them conflicting with each other. I know it works out of the box on MS Windows (just install all versions you'd like), and I know there are various tools to achieve the same on macOS. I'm o

Re: [Bioc-devel] Important Bioconductor Release Deadlines

2024-04-04 Thread Anatoly Sorokin
Hi all, I'm sorry for the complaint, but do you really think it is wise to make the new release dependent on the R version which has not released yet? I have a lot of R-related projects going on apart from maintaining the Bioconductor package and I'm not comfortable installing the unreleased vers

[Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

2024-04-04 Thread Robert Castelo
hi, I'm getting duplicated entries when loading **offline** previously cached ExperimentHub resources. This code reproduces the problem: 1. If in a fresh empty cache of ExperimentHub I download 9 resources through the gDNAinRNAseqData package: library(gDNAinRNAseqData) bamfiles <- LiYu22su