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

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

[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 0574446  gnu: Add r-bisquerna.
> 0574446 is described below
>
> commit 0574446be82ef54b925441e4283bf754a86918a9
> Author: Roel Janssen <roel@gnu.org>
> AuthorDate: Wed Sep 9 17:02:55 2020 +0200
>
>     gnu: Add r-bisquerna.
>     
>     * gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
>  1 file changed, 25 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index f8792ef..9f2fd86 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -7923,6 +7923,31 @@ manipulating genomic intervals and variables defined along a genome.")
>  on Bioconductor or which replace R functions.")
>      (license license:artistic2.0)))
>  
> +(define-public r-bisquerna
> +  (package
> +   (name "r-bisquerna")
> +   (version "1.0.4")
> +   (source (origin
> +            (method url-fetch)
> +            (uri (cran-uri "BisqueRNA" version))
> +            (sha256
> +             (base32
> +              "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))

Why is this in (gnu packages bioinformatics) and not in (gnu packages
cran)?

> +   (synopsis "Decomposition of Bulk Expression with Single-Cell
> Sequencing")

Please use lowercase where it would be normally used.

-- 
Ricardo

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

[Roel Janssen]

Hi Ricardo,

On Wed, 2020-09-09 at 18:04 +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 0574446  gnu: Add r-bisquerna.
> > 0574446 is described below
> > 
> > commit 0574446be82ef54b925441e4283bf754a86918a9
> > Author: Roel Janssen <roel@gnu.org>
> > AuthorDate: Wed Sep 9 17:02:55 2020 +0200
> > 
> >     gnu: Add r-bisquerna.
> >     
> >     * gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
> > ---
> >  gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
> >  1 file changed, 25 insertions(+)
> > 
> > diff --git a/gnu/packages/bioinformatics.scm
> > b/gnu/packages/bioinformatics.scm
> > index f8792ef..9f2fd86 100644
> > --- a/gnu/packages/bioinformatics.scm
> > +++ b/gnu/packages/bioinformatics.scm
> > @@ -7923,6 +7923,31 @@ manipulating genomic intervals and variables
> > defined along a genome.")
> >  on Bioconductor or which replace R functions.")
> >      (license license:artistic2.0)))
> >  
> > +(define-public r-bisquerna
> > +  (package
> > +   (name "r-bisquerna")
> > +   (version "1.0.4")
> > +   (source (origin
> > +            (method url-fetch)
> > +            (uri (cran-uri "BisqueRNA" version))
> > +            (sha256
> > +             (base32
> > +              "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw
> > 2"))))
> 
> Why is this in (gnu packages bioinformatics) and not in (gnu packages
> cran)?

It seemed so "bioinformatics"-specific.  But you're right, it's a CRAN
package, so that may be a better fit.  Shall I move it to CRAN?

> > +   (synopsis "Decomposition of Bulk Expression with Single-Cell
> > Sequencing")
> 
> Please use lowercase where it would be normally used.

My mistake. I will take better care of this in the future.

Kind regards,
Roel Janssen

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

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:

>> > +(define-public r-bisquerna
>> > +  (package
>> > +   (name "r-bisquerna")
>> > +   (version "1.0.4")
>> > +   (source (origin
>> > +            (method url-fetch)
>> > +            (uri (cran-uri "BisqueRNA" version))
>> > +            (sha256
>> > +             (base32
>> > +              "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw
>> > 2"))))
>> 
>> Why is this in (gnu packages bioinformatics) and not in (gnu packages
>> cran)?
>
> It seemed so "bioinformatics"-specific.  But you're right, it's a CRAN
> package, so that may be a better fit.  Shall I move it to CRAN?

If you have time to do that, yes please.  Some time ago I started a
half-hearted migration of R packages from (gnu packages bioinformatics)
to (gnu packages cran) and (gnu packages bioconductor).  It’s not
supremely important, but I think in the long term we’d like to have CRAN
things in (gnu packages cran) and Bioconductor things in (gnu packages
bioconductor), because it’s deliciously unsurprising. :)

>> > +   (synopsis "Decomposition of Bulk Expression with Single-Cell
>> > Sequencing")
>> 
>> Please use lowercase where it would be normally used.
>
> My mistake. I will take better care of this in the future.

Thank you!

Perhaps we could sprinkle some smarts over the CRAN importer to do this
automatically, but with R packages we often have names of methods that
should be upper case (like “Bayes*” or “SNPs”), so I have shied away
from developing heuristics for that.

Thanks for adding more R packages!

-- 
Ricardo

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

[zimoun]

On Thu, 10 Sep 2020 at 13:30, Ricardo Wurmus <rekado@elephly.net> wrote:

> > It seemed so "bioinformatics"-specific.  But you're right, it's a CRAN
> > package, so that may be a better fit.  Shall I move it to CRAN?
>
> If you have time to do that, yes please.  Some time ago I started a
> half-hearted migration of R packages from (gnu packages bioinformatics)
> to (gnu packages cran) and (gnu packages bioconductor).  It’s not
> supremely important, but I think in the long term we’d like to have CRAN
> things in (gnu packages cran) and Bioconductor things in (gnu packages
> bioconductor), because it’s deliciously unsurprising. :)

I agree.  And it is also on my TODO but the Copyright lines lead to a
boring task. :-)

Does it make sense to add a subsection to:
https://guix.gnu.org/manual/devel/en/guix.html#Packaging-Guidelines
about R packages?

Cheers,
simon

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

[Ricardo Wurmus]

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

> On Thu, 10 Sep 2020 at 13:30, Ricardo Wurmus <rekado@elephly.net> wrote:
>
>> > It seemed so "bioinformatics"-specific.  But you're right, it's a CRAN
>> > package, so that may be a better fit.  Shall I move it to CRAN?
>>
>> If you have time to do that, yes please.  Some time ago I started a
>> half-hearted migration of R packages from (gnu packages bioinformatics)
>> to (gnu packages cran) and (gnu packages bioconductor).  It’s not
>> supremely important, but I think in the long term we’d like to have CRAN
>> things in (gnu packages cran) and Bioconductor things in (gnu packages
>> bioconductor), because it’s deliciously unsurprising. :)
>
> I agree.  And it is also on my TODO but the Copyright lines lead to a
> boring task. :-)

It becomes a little easier with “git log --grep=package-name”.

> Does it make sense to add a subsection to:
> https://guix.gnu.org/manual/devel/en/guix.html#Packaging-Guidelines
> about R packages?

Perhaps not.  I think it may not be necessary because we don’t have that
many people contributing R packages to us and the manual already has a
lot of information that might be overwhelming.

So far we’ve been doing fine without it.  It’s a really minor point, in
my opinion.

-- 
Ricardo

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

[Roel Janssen]

On Thu, 2020-09-10 at 13:31 +0200, Ricardo Wurmus wrote:
> Roel Janssen <roel@gnu.org> writes:
> 
> > > > +(define-public r-bisquerna
> > > > +  (package
> > > > +   (name "r-bisquerna")
> > > > +   (version "1.0.4")
> > > > +   (source (origin
> > > > +            (method url-fetch)
> > > > +            (uri (cran-uri "BisqueRNA" version))
> > > > +            (sha256
> > > > +             (base32
> > > > +              "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijl
> > > > m3jw
> > > > 2"))))
> > > 
> > > Why is this in (gnu packages bioinformatics) and not in (gnu
> > > packages
> > > cran)?
> > 
> > It seemed so "bioinformatics"-specific.  But you're right, it's a
> > CRAN
> > package, so that may be a better fit.  Shall I move it to CRAN?
> 
> If you have time to do that, yes please.  Some time ago I started a
> half-hearted migration of R packages from (gnu packages
> bioinformatics)
> to (gnu packages cran) and (gnu packages bioconductor).  It’s not
> supremely important, but I think in the long term we’d like to have
> CRAN
> things in (gnu packages cran) and Bioconductor things in (gnu
> packages
> bioconductor), because it’s deliciously unsurprising. :)

I fully agree that it would be nice to have all packages originating
from CRAN in (gnu packages cram) and all things Bioconductor in (gnu
packages bioconductor).

I moved r-bisquerna and lowercased its synopsis in
66be746dc0c0f4ba3d748ed8d0983b2f9afdace8.

Kind regards,
Roel Janssen

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

[zimoun]

Dear,

On Thu, 10 Sep 2020 at 16:44, Roel Janssen <roel@gnu.org> wrote:

> > If you have time to do that, yes please.  Some time ago I started a
> > half-hearted migration of R packages from (gnu packages
> > bioinformatics)
> > to (gnu packages cran) and (gnu packages bioconductor).  It’s not
> > supremely important, but I think in the long term we’d like to have
> > CRAN
> > things in (gnu packages cran) and Bioconductor things in (gnu
> > packages
> > bioconductor), because it’s deliciously unsurprising. :)
>
> I fully agree that it would be nice to have all packages originating
> from CRAN in (gnu packages cram) and all things Bioconductor in (gnu
> packages bioconductor).

I have tried to move almost all the CRAN remaining from (gnu packages
bioinformatics) graphs and machine-learning in 43345
<http://issues.guix.gnu.org/issue/43345>.  Now, still missing the
Bioconductor ones.  And the *big* statistics...

Cheers,
simon