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Re: [outreach] Help trying to create R package
From: |
Björn Höfling |
Subject: |
Re: [outreach] Help trying to create R package |
Date: |
Wed, 17 Oct 2018 09:17:50 +0200 |
Hi Laura,
On Tue, 16 Oct 2018 22:01:58 -0300
Laura Lazzati <address@hidden> wrote:
> On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
> <address@hidden> wrote:
> >
> > Hi Laura,
> Hi! I had not answered yet because I thought I would be too verbose.
> If so, please do a Laura -v instead of Laura -vvvvvvv.
> Thanks for writing :) it encourages me a lot.
You're welcome. It's nice to hear from your progress. Verbosity-level
is fine :-)
[..]
> > Here is another one:
> >
> > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt
>
> Something I faced after writing, was that in the link one of you
> provided: [1]https://guix.mdc-berlin.de/
> I have all the packages that are already available in guix. I like
> using the guix package command to practice that too, but i found it
> practical to see packages easier. I found out that package aspi
> (https://CRAN.R-project.org/package=aspi) is not available, and I
> would like to ask you if you believe it is a good candidate.
> One available package, according to [1] is r-abe
> (https://cran.r-project.org/web/packages/abe/index.html)
Sorry I have no clue of R at all. Could someone else please answer that
question, is r-aspi a good candidate?
https://cran.r-project.org/web/packages/aspi/index.html
> I wanted to see the template, so I ran:
> $ guix import cran abe
> And got the template, that matches even the version, and everything
> stated in the site.
> But then I tried:
> $ guix package -i r-abe and got no results.
> In fact, after running the command you have just provided, r-abe is
> not appearing in the r.txt file.
> I can't understand why that is happening. Am I missing something, or
> is there maybe an inconsistency between [1] and the guix installed in
> my foreign distro?
Concerning r-abe: I don't know how the list at guix-hpc is created
, how often it is updated or if there are extra packages in there. In
your case, I suppose you lack behind:
There is a commit for r-abe from 2019-09-13, so it is only a month old.
I think you are lacking behind. Have you done a `guix pull`? That's the
command used to update the package definitions.
In case you already did a guix pull recently, and you still don't see
it, there could be a problem with your $PATH, that the wrong guix is
coming first. Do a `which guix`.
Guix should be the one in ~/.config/guix/current/bin/guix
> Just wanted to install it to run guix edit to check if the suggested
> packages were already available or if I needed to package them too,
> but I have installed r-ade4, which has both imports and suggests, and
> I have just run:
> $guix import cran ade4
> And noticed that it only states in the template the Import package
> (MASS)
If I see that right, for R we only add the "Imports" packages, as they
are absolutely needed for compiling/running. All "Suggests" can be
installed/used just at runtime. Please correct me anyone if I'm wrong,
I'm not into R.
> Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> guix download from its site, and also guix hash to convert it to
> base32:
>
> (define-public r-aspi
> (package
> (name "r-aspi")
> (version "0.2.0")
> (source
> (origin
> (method url-fetch)
> (uri (cran-uri "aspi" version))
> (sha256
> (base32
> "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
> (build-system r-build-system)
> (home-page
> "https://cran.r-project.org/web/packages/aspi/")
> (synopsis
> "Analysis of Symmetry of Parasitic Infections")
> (description
> "Tools for the analysis and visualization of bilateral asymmetry
> in parasitic infections.")
> (license gpl3+)))
> And that's were I ended up today (it is still Tuesday, almost 10pm)
I haven't done a full review, but that looks good. Next you need to get
the guix sources and prepare a patch.
That's described here:
https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
Björn
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- Re: [outreach] Help trying to create R package, (continued)
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/13
- Re: [outreach] Help trying to create R package, Catonano, 2018/10/13
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/13
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/15
- Re: [outreach] Help trying to create R package, Björn Höfling, 2018/10/16
- Re: [outreach] Help trying to create R package, Björn Höfling, 2018/10/16
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/16
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/16
- Re: [outreach] Help trying to create R package, Björn Höfling, 2018/10/16
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/16
- Re: [outreach] Help trying to create R package,
Björn Höfling <=
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/17
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/17
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/17
- Re: [outreach] Help trying to create R package, Clément Lassieur, 2018/10/17
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/17
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/17
- Re: [outreach] Help trying to create R package, Björn Höfling, 2018/10/18
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/18
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/18
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/18