[Bioc-devel] Important Bioconductor Release Deadlines

[Anatoly Sorokin]

Hi Henrik,

thank you for the prompt reply. I'm on Mac OS 12.5.

And regarding the linking version of Bioconductor and R my major complaint
is the timing, if R 4.4 hasn't been released yet, why not postpone this
dependency to the October release of Bioconductor?

And it is also true that we have a lot of complaints from people working on
centrally maintained machines or HPC clusters, that they have no access to
the latest R versions. So sometimes even for demonstration purposes, we had
to install the package from the GitHub source, rather than from BiocManager.

Cheers,
Anatoly

On Fri, Apr 5, 2024 at 11:57 AM Henrik Bengtsson <henrik.bengtsson using gmail.com>
wrote:

> Hello,
>
> these days, it's quite straight forward to have multiple versions of R
> installed in parallel without them conflicting with each other. I know
> it works out of the box on MS Windows (just install all versions you'd
> like), and I know there are various tools to achieve the same on
> macOS.  I'm on Linux, and I build R from source, so that solves it for
> me.  What's platform are you working on?  If you share that, I think
> you'll get 1-2-3 instructions for how to install R 4.4 pre-release
> from users on that operating system.
>
> Regarding Bioc versions being tied to specific R versions: That is a
> design decision that goes back to day one of the Bioconductor project.
> It's a rather big thing to change.  That said, I've always been in the
> camp that thinks we should move away from that model for many reasons;
> one is the friction added to developers, another is the friction added
> to end-users, and some people may be stuck with older versions of R
> and in no control of updating.
>
> Hope this helps,
>
> Henrik
>
> On Thu, Apr 4, 2024 at 7:29 PM Anatoly Sorokin <lptolik using gmail.com> wrote:
> >
> > 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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