Re: [Bioc-devel] R version dependency

[Anatoly Sorokin]

Hi,
You can even set 3.5 if your code working with that version of R, but
BiocManager won't load the latest Bioconductor version (3.19) unless you
have R 4.4.

Cheers,
Anatoly

On Tue, Apr 23, 2024 at 2:57 AM Richard Heery 
wrote:

> Hi all,
>
> I'm wondering what we should now list as the R version in the Depends
> section of the description file: the current version 4.3.3 or the
> development version 4.4?
>
> Cheers,
>
> Richard
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Important Bioconductor Release Deadlines

[Kasper Daniel Hansen]

It's a bit late, but I'll point out that the use of R-devel dates back 20y
to the inception of the Bioconductor project. So this is the way it has
always been. Of course, this is an argument of conservatism which is always
dangerous, But at least it illustrates that this is not a small change to
make.

Rig looks pretty sweet. I have been using
  https://rud.is/rswitch/
together with manual installs of snapshots from
  https://mac.r-project.org

Best,
Kasper


On Thu, Apr 18, 2024 at 12:55 AM Anatoly Sorokin  wrote:

> Dear Henrik,
>
> thank you very much for pointing me to the rig project. It works fine and I
> have two independent R versions on my machine at the moment.
>
> Thank you,
> Anatoly
>
> On Tue, Apr 9, 2024 at 4:19 AM Henrik Bengtsson <
> henrik.bengts...@gmail.com>
> wrote:
>
> > > ... I'm on Mac OS 12.5.
> >
> > I've heard good things about 'rig' (The R Installation Manager;
> > https://github.com/r-lib/rig). It can install multiple R versions in
> > parallel on macOS, Windows, and Linux, without the different versions
> > conflicting with each other.  I recommend trying it out, because being
> > able to run different versions of R is always useful, even if you're
> > not a package maintainer.
> >
> > /Henrik
> >
> > On Thu, Apr 4, 2024 at 8:08 PM Anatoly Sorokin 
> wrote:
> > >
> > > 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.bengts...@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 
> > 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@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 

Re: [Bioc-devel] R version dependency

[Hervé Pagès]

If you're submitting a new package, you might be asked to set this to R 
(>= 4.4). At least it used to be that way but I'm not sure this is still 
enforced.

Otherwise you don't need to do anything.

Best,

H.

On 4/22/24 10:56, Richard Heery wrote:
> Hi all,
>
> I'm wondering what we should now list as the R version in the Depends
> section of the description file: the current version 4.3.3 or the
> development version 4.4?
>
> Cheers,
>
> Richard
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org  mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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[Bioc-devel] R version dependency

[Richard Heery]

Hi all,

I'm wondering what we should now list as the R version in the Depends
section of the description file: the current version 4.3.3 or the
development version 4.4?

Cheers,

Richard

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Re: [Bioc-devel] singleCellTK

[Kern, Lori via Bioc-devel]

Please try to push the change to fix the gvsa issue.  We generally will only 
un-deprecate when we see a clean build/check report for at least the linux 
platform especially since the package has been failing for an extended period 
of time (since early December).




From: Bioc-devel  on behalf of Joshua 
Campbell via Bioc-devel 
Sent: Monday, April 22, 2024 8:34 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] singleCellTK

Hello,
The package singleCellTK

 is
currently slated for depreciation in Bioc devel (3.19). We have been
actively fixing the dependency issues, mainly the underlying changes in
Seurat update. We are fixing one last issue to be compatible with an update
in the GSVA package which should allow the linux and macos builds to pass
(should be done in the next day). The remaining windows build failing is
due to other BioC packages not currently passing, but this is outside of
our control.

We have also changed the maintainer as the previous maintainer left the lab.

We were hoping that the depreciation tag could be removed. We will
continue to address any other issues that pop up going forward
in release/devel.

Thanks,
Josh

--
Joshua D. Campbell, Ph.D.
Section of Computational Biomedicine
BU Chobanian & Avedisian School of Medicine
72 East Concord Street, E604B | Boston, MA 02118
Phone: (617) 358-7260 | Email: c...@bu.edu

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[Bioc-devel] singleCellTK

[Joshua Campbell via Bioc-devel]

Hello,
The package singleCellTK
 is
currently slated for depreciation in Bioc devel (3.19). We have been
actively fixing the dependency issues, mainly the underlying changes in
Seurat update. We are fixing one last issue to be compatible with an update
in the GSVA package which should allow the linux and macos builds to pass
(should be done in the next day). The remaining windows build failing is
due to other BioC packages not currently passing, but this is outside of
our control.

We have also changed the maintainer as the previous maintainer left the lab.

We were hoping that the depreciation tag could be removed. We will
continue to address any other issues that pop up going forward
in release/devel.

Thanks,
Josh

-- 
Joshua D. Campbell, Ph.D.
Section of Computational Biomedicine
BU Chobanian & Avedisian School of Medicine
72 East Concord Street, E604B | Boston, MA 02118
Phone: (617) 358-7260 | Email: c...@bu.edu

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