Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Wed, Oct 17, 2018 at 11:27 AM Laura Lazzati
<address@hidden> wrote:
>
> On Wed, Oct 17, 2018 at 5:21 AM Gábor Boskovits <address@hidden> wrote:
> >
> > ÜHi Laura,
> >
> >
> >
> > Björn Höfling <address@hidden> ezt írta (időpont: 2018. okt. 17., Sze 9:17):
> >>
> >> 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 :-)
> Thanks :) Hope you enjoy my nerd jokes
>
> >> [..]
> >>
> >> > > 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.
> >
> > This happens, as the installed guix doesn't know where to find the package 
> > definition. There are several ways around that, for example see the -f flag 
> > of guix package, in the invoking guix package section of the manual.
> >>
> >> > 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
> >
> >
> > Yes, please run guix pull, and check which guix output.
> I have to take a look at my .bash_history, but I guess somewhere I ran
> guix pull because I recall seing something about the $PATH stuff. I
> did not run guix output. It doesn'matter, I save my machine state and
> run all that now.
You were right. I took a look at my .bashrc file, and I had an:
export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
I ran $guix pull, did the PATH export in my CLI, then checked the output of
$which guix, that was the same that was mentioned by you,
commented that previous line in .bashrc,
added  export PATH="/home/laura/.config/guix/current/bin${PATH:+:}$PATH"
and ran again the command to check the available R packages, made a
diff with the previous one, and now at least r-bae appears.
> >
> >>
> >>
> >> > 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.
> Thanks, I took a look at most of the R packages in cran site, and
> chose it because of two reasons: it has to do with bioinformatics due
> to its description, and as it does not mention imports so I found it
> easy for a first R package contribution. If it works fine, then I can
> go on packaging more complicated R packages.
>
> >> That's described here:
> >>
> >> https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> >>
> >>
> >> Björn
> >
> >
> > Best regards,
> > g_bor
>
> Thanks both!
> Regards,
> Laura
Thanks again, time to read how to go on with my contribution :)
Laura