Re: branch master updated: gnu: Add r-loomr.

Re: branch master updated: gnu: Add r-loomr.

[Ricardo Wurmus]

Hi Roel,

> This is an automated email from the git hooks/post-receive script.
>
> roelj pushed a commit to branch master
> in repository guix.
>
> The following commit(s) were added to refs/heads/master by this push:
>      new 1f56ec0  gnu: Add r-loomr.
> 1f56ec0 is described below
>
> commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea
> Author: Roel Janssen <roel@gnu.org>
> AuthorDate: Wed Sep 9 16:56:02 2020 +0200
>
>     gnu: Add r-loomr.
>     
>     * gnu/packages/bioinformatics.scm (r-loomr): New variable.

This is not free software.  See

   https://github.com/mojaveazure/loomR/pull/24

Aside from this, I would like to say two things:

>  gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++

Let’s please not add R packages to (gnu packages bioinformatics) when it
can be avoided.  (In this case there’s no CRAN package, so it’s fine.)

> +(define-public r-loomr
> +  (package
> +   (name "r-loomr")
> +   (version "0.2.0-beta")
> +   (source (origin
> +            (method url-fetch)
> +            (uri (string-append
> +                  "https://github.com/mojaveazure/loomR/archive/"
> +                  version ".tar.gz"))

This is not okay as these generated tarballs are not stable.  I haven’t
seen these patches on guix-patches before — maybe I missed them.  But we
have been avoiding these kind of URLs since a long time and had I seen
the patches on guix-patches I and other would probably have pointed this
out.

Can you please revert this ASAP?

-- 
Ricardo

Re: branch master updated: gnu: Add r-loomr.

[Roel Janssen]

Hi Ricardo,


On Wed, 2020-09-09 at 18:02 +0200, Ricardo Wurmus wrote:
> Hi Roel,
> 
> > This is an automated email from the git hooks/post-receive script.
> > 
> > roelj pushed a commit to branch master
> > in repository guix.
> > 
> > The following commit(s) were added to refs/heads/master by this
> > push:
> >      new 1f56ec0  gnu: Add r-loomr.
> > 1f56ec0 is described below
> > 
> > commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea
> > Author: Roel Janssen <roel@gnu.org>
> > AuthorDate: Wed Sep 9 16:56:02 2020 +0200
> > 
> >     gnu: Add r-loomr.
> >     
> >     * gnu/packages/bioinformatics.scm (r-loomr): New variable.
> 
> This is not free software.  See
> 
>    https://github.com/mojaveazure/loomR/pull/24


Oh shoot. I'm sorry I didn't see this discussion!


> Aside from this, I would like to say two things:
> 
> >  gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
> 
> Let’s please not add R packages to (gnu packages bioinformatics) when
> it
> can be avoided.  (In this case there’s no CRAN package, so it’s
> fine.)

Where would I add a non-CRAN and non-Bioconductor package to?  Perhaps
this situation won't occur again, and should raise a flag, because I
think I've never had this case before.

> > +(define-public r-loomr
> > +  (package
> > +   (name "r-loomr")
> > +   (version "0.2.0-beta")
> > +   (source (origin
> > +            (method url-fetch)
> > +            (uri (string-append
> > +                  "https://github.com/mojaveazure/loomR/archive/"
> > +                  version ".tar.gz"))
> 
> This is not okay as these generated tarballs are not stable.  I
> haven’t
> seen these patches on guix-patches before — maybe I missed them.  But
> we
> have been avoiding these kind of URLs since a long time and had I
> seen
> the patches on guix-patches I and other would probably have pointed
> this
> out.
> 
> Can you please revert this ASAP?

I see you've reverted it already. Thanks for that!

I will default to submitting patches to guix-patches again.  I thought
it was trivial enough to just push.  My mistake.

Kind regards,
Roel Janssen

Re: branch master updated: gnu: Add r-loomr.

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:

>> > commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea
>> > Author: Roel Janssen <roel@gnu.org>
>> > AuthorDate: Wed Sep 9 16:56:02 2020 +0200
>> > 
>> >     gnu: Add r-loomr.
>> >     
>> >     * gnu/packages/bioinformatics.scm (r-loomr): New variable.
>> 
>> This is not free software.  See
>> 
>>    https://github.com/mojaveazure/loomR/pull/24
>
>
> Oh shoot. I'm sorry I didn't see this discussion!

It’s really not obvious.  I know because it happened to me too.  In 2018
I added r-loomr with commit fab43c6b84635200070c708d4220132be18dd239.
Then in 2019 I removed it with commit
bc70516bbae8a6388f3ed19008d3e10efd1577a7 after noticing that the author
only used GPL in the DESCRIPTION file to stop the CRAN tools from
complaining.

It’s definitely unusual and very easy to miss.

>> Aside from this, I would like to say two things:
>> 
>> >  gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
>> 
>> Let’s please not add R packages to (gnu packages bioinformatics) when
>> it
>> can be avoided.  (In this case there’s no CRAN package, so it’s
>> fine.)
>
> Where would I add a non-CRAN and non-Bioconductor package to?  Perhaps
> this situation won't occur again, and should raise a flag, because I
> think I've never had this case before.

We don’t have any good place for those packages.  It would be good to
have a dumping ground for packages like that, and for those that are on
CRAN but unusually depend on Bioconductor packages.

> I will default to submitting patches to guix-patches again.  I thought
> it was trivial enough to just push.  My mistake.

I’d say if it’s on CRAN you can go ahead and push directly (after
running “guix lint” to catch some obvious mistakes).  Bioconductor
packages need a little extra care because they are sometimes playing
loose with licenses and included third-party code; but if you feel
you’ve checked things carefully then you can also push those directly.

For third-party R packages we don’t benefit from even the little bit of
quality control that CRAN and Bioconductor impose, so we need to be
extra careful.  There it helps to send patches to guix-patches and push
them after some time.

-- 
Ricardo

Re: branch master updated: gnu: Add r-loomr.

[zimoun]

On Thu, 10 Sep 2020 at 12:40, Ricardo Wurmus <rekado@elephly.net> wrote:

> > Where would I add a non-CRAN and non-Bioconductor package to?  Perhaps
> > this situation won't occur again, and should raise a flag, because I
> > think I've never had this case before.
>
> We don’t have any good place for those packages.  It would be good to
> have a dumping ground for packages like that, and for those that are on
> CRAN but unusually depend on Bioconductor packages.

IMHO, for non-CRAN and non-Bioconductor R packages, they should go to
thematic files: bioinformatics.scm or machine-learning.scm or
name-it.scm.

However, some dependency issues could happen, and e.g., CRAN package
could be in bioconductor.scm as r-deconstructsigs -- with a comment.

Last, should CRAN packages in statistics.scm go in cran..scm or not?


All the best,
simon

Re: branch master updated: gnu: Add r-loomr.

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:

> Last, should CRAN packages in statistics.scm go in cran..scm or not?

Yes, I want statistics.scm to no longer have CRAN packages.

-- 
Ricardo