Re: [outreach] Help trying to create R package

[Laura Lazzati <laura.lazzati.15@gmail.com>]

On Wed, Oct 17, 2018 at 5:21 AM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> ÜHi Laura,
>
>
>
> Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont: 2018. okt. 17., Sze 9:17):
>>
>> Hi Laura,
>>
>> On Tue, 16 Oct 2018 22:01:58 -0300
>> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>>
>> > On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
>> > <bjoern.hoefling@bjoernhoefling.de> 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.
>
>>
>>
>> > 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