[Bioc-devel] Important Bioconductor Release Deadlines

[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 purpose of a 6 month devel and release cycle is to provide a comfortable period for everyone to work out new features and bugs and to resolve downstream consequences that may arise.  Delaying the Bioconductor release by a week or something might actually encourage a habit of last-week bug fixes that should be discouraged 😉. I really can’t see any way around requiring developers to test against r-devel without sacrificing timeliness and reliability for users. There are also Docker and GitHub Actions options that don’t require installing r-devel to test against it.

I think many HPC clusters now support Singularity, which is a more reliable and easier way to run packages with a compatible version of R. Installing from GitHub on an old version of R has no guarantees of being tested or working correctly even if it installs without error, and I see as a sacrifice of software reliability for convenience that can be avoided with Singularity or regular R updates.

Henrik, if Bioconductor releases weren’t tied to R releases, how could Bioconductor test them? I guess like CRAN where as long as a package says it depends on R >= 2.0 then you’re free to try installing on 2.0 even though the combination has never been tested? Maybe I worry too much about such testing since CRAN seems OK anyways, as far as we know?
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Anatoly Sorokin <lptolik using gmail.com>
Sent: Thursday, April 4, 2024 10:28:47 PM
To: Kern, Lori <Lori.Shepherd using roswellpark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Important Bioconductor Release Deadlines

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
version of R on my machine and spending time debugging it in the case of
possible problems.

At the same time, I have an error, possibly caused by a new version of
GO.db package, which BioNAR is dependent upon and I can not fix it
until the R 4.4 release on the 24th of April when I would have less than a
day to fix the possible problem and fit into R CMD build and R CMD check by
the Friday April 26th. Don't you think this is a rather tight time frame?


Sorry once again, for the complaint.

Cheers,
Anatoly

On Tue, Mar 26, 2024 at 11:06 PM Kern, Lori via Bioc-devel <
bioc-devel using r-project.org> wrote:

> Import update:  The Bioconductor Release will be May 1 following the
> release of R 4.4 on April 24.
>
> The Bioconductor 3.18 branch will be frozen Monday April 15th. After that
> date, no changes will be permitted ever on that branch.
>
> The deadline for devel Bioconductor 3.19 for packages to pass R CMD build
> and R CMD check is Friday April 26th. While you will still be able to make
> commits past this date, This ensures any changes pushed to
> git.bioconductor.org are reflected in at least one build report before
> the devel branch will be copied to a release 3.19 branch.
>
> Cheers,
>
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
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