[Bioc-devel] Best practices for joint release/update of BioC packages

Nitesh Turaga ntur@g@@b|oc @end|ng |rom gm@||@com
Wed Aug 25 17:48:24 CEST 2021

Hi Russell,

The deprecation usually occurs around the time of release (October 2021, but I don't have an exact date yet). 

If your collaborator has submitted the package to Bioconductor or CRAN, and it gets accepted, and you can make everything build and check cleanly before the release time, I think you should be ok. It might mean that he submits the package 'sparrow' soon for review.

The best way to do this (IMHO) is, wait for your collaborator's code to get into Bioconductor/CRAN and plan the major release around that. If it happens after this release, then do a major version update for the next release cycle (April 2022 - approx). This will add all the significant updates in your package only in the major version update to 2.0.0. In the meantime, you may consider fixing/hiding parts of the code why are failing for October 2021 release.

Another "non-traditional" way is to add your collaborator as an Author on your package and ingest parts that improve your package significantly as code within your package. So this will attribute the authorship of the code to your collaborator appropriately. Of course, this will not allow for modular and independent development of two separate packages adding a lot of complexity. (We should not consider this method for the sake of good software engineering practices)

I’m hoping other members on the team / community can provide better suggestions.  


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Aug 24, 2021, at 7:07 PM, Russell Bainer <russ.bainer using gmail.com> wrote:
> Hello All,
> I am planning a major update to my BioC package in the next release (
> https://www.bioconductor.org/packages/release/bioc/html/gCrisprTools.html),
> and some of the new functionality depends on another package that is being
> submitted for acceptance by a collaborator.
> All of the code in my package passes R/BioC check using the package in my
> collaborator's github repo, but as his code has not yet been incorporated
> into BioC my current build is failing.
> What is the recommended way to deal with a situation like this? Obviously I
> want to avoid deprecation of my own package, and obviously I could just
> hide all of the parts of the update that depend on external code. But I
> also think that my collaborator's work adds significantly to the utility of
> my package, and I want to ensure that their contributions are properly
> highlighted/celebrated in my 2.0 release.
> Thanks in advance for the input.
> -R
> 	[[alternative HTML version deleted]]
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