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mikemc / speedyseq

Speedy versions of phyloseq functions
https://mikemc.github.io/speedyseq/
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Enable choosing to install stable or development version #26

Open mikemc opened 4 years ago

mikemc commented 4 years ago

Options: Put development on a dev branch (easiest); put stable version on CRAN (harder) or Bioconductor (hardest)

colinbrislawn commented 3 years ago

Any updates on this? I would be up for making a conda package our of this, but I think it's best to get it on CRAN of Bioconductor before I work with a third-party package manager.

Thanks for working to improve Phyloseq

mikemc commented 3 years ago

Hi @colinbrislawn, thanks for your interest and bringing this up again. I want to get the next major release out in the next few weeks and then will consider a CRAN submission if it seems like not too much effort. I am still somewhat hesitant for a few reasons: I consider Speedyseq to be a kludge/hack; I don't think it's great practice to be overriding functions of another package as I am here but there isn't much alternative given the stalled development of the Phyloseq project. There are further limitations to Phyloseq that I find hampering me in my own work that really warrant changes to Phyloseq itself, which seems unlikely to ever happen, and if I were trying to address I'd do so with a new (S3) data structure. For this and other reasons I do not plan to personally work to support Phyloseq usage or continue Speedyseq development beyond the end of my postdoc in ~6 months.

colinbrislawn commented 3 years ago

there isn't much alternative given the stalled development of the Phyloseq project

Yeah, I think you are right. Unless...

if I were trying to address I'd do so with a new (S3) data structure

I would love to see it! 😜

Thank you for your work on this project. It's really central to microbiome work in R