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How long does it take for the latest Bioconductor to end up on Conda? I think I saw a blog post about the challenges with this process, but I cannot find it. For example, Bioconductor 3.13 was released a week ago, but is still not available. For comparison, many CRAN packages tend to show up within a day.

Additionally, is there a way to keep track of that progress?

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I started the roll-out on the 30th in the evening. There's not much of a delay for the October Bioconductor release, but for the summer release we first have to build the newest R version and then rebuild all conda CRAN packages. It's probably not widely known, but Bioconductor packages are only compatible with a single R version. For example, the ones being released now are not compatible with R 4.0 and will not be compatible with R 4.2, but will instead only ever work with R 4.1. This is regardless of what the metadata provided by Bioconductor package authors might say, the Bioconductor core team has requested this (there's actually not even a guarantee that packages built under R 4.1.0 will work with 4.1.1, but such issues are exceedingly rare). This is why there is a multi-week delay every summer.

On the plus side, at least we're not waiting for the first bug-fix release of R to start the migration anymore.

For Bioconda we've never gotten around to making a migration tracker. If you have a local clone of Bioconda, you can run ./scripts/bioconductor/rootNodes.py --sinceNDays 2 --rootNodes to get a count of the packages completed in the past 2 days and a list of the root nodes on the dependency DAG that still need to be handled. That's how I estimate the fraction finished (currently about 600 packages).

For tracking the status on conda-forge you can see their status page: https://conda-forge.org/status/#r410

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Devon will probably add a more precise answer, until then I just link his Tweet from last week:

https://twitter.com/dpryan79/status/1394714988720308226

Edit: 31.5.21

Rollout started yesterday, should take a week to complete:
https://twitter.com/dpryan79/status/1399273322601459712

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  • $\begingroup$ That's promising. Would be great if there is was a way to track progress without waiting for the next tweet. $\endgroup$
    – burger
    May 26 at 15:39

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