[Bioc-devel] Adding additional validity checks when calling setter methods of inherited S4Vectors::DataFrame class

2025-01-02 Thread Nanda, Pariksheet via Bioc-devel
Hello S4-class boffins, How bad of an idea it is to inherit from a S4Vectors::DataFrame / DFrame S4 class to impose additional constraints on it? I'm writing a light-weight wrapper around the ToppGene web API (github com/ImmuSystems-Lab/toppgene/blob/main/R/categories.R) [1] and while it's fun

Re: [Bioc-devel] Okay to push a hotfix for an existing release?

2024-12-04 Thread Nanda, Pariksheet via Bioc-devel
Thank you, Lori and Marcel! Pariksheet ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] groHMM package error

2024-12-03 Thread Nanda, Pariksheet via Bioc-devel
Hi Tulip, I'm glad you are maintaining groHMM; I previously had not got much response from contributing bug fixes, so you may be interested in looking at and maybe integrating my fork: https://github.com/coregenomics/groHMM where the NEWS file summarizes the changes. There is also a test suite

[Bioc-devel] Okay to push a hotfix for an existing release?

2024-12-02 Thread Nanda, Pariksheet via Bioc-devel
Hello, I was wondering whether someone from the Bioconductor core team might reply to this e-mail and/or to this GitHub issue [1] to confirm Bioconductor's hotfix policy. Specifically, the web server that JASPAR2024 relies on has changed and the old server SSL certificate expired on 2024-08-31