Re: [outreach] Help trying to create R package

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

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.
>
> On Tue, 16 Oct 2018 10:13:23 -0300
> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>
> [importing problems ...]
>
> Could you solve your certificate-problem? Have you been successfully in
> importing a package?
Yes! I love reading ALL the documentation, but I focused mainly in
chapters 3 to 5, and the part about the certificate stuff is 6. That
is why I did not know about it.
>
> Unfortunately the package of your choice is already part of guix:
>
>
> $ guix package -s "rtracklayer$"
> name: r-rtracklayer
> version: 1.40.6
> outputs: out
> systems: x86_64-linux i686-linux armhf-linux aarch64-linux mips64el-linux
> dependencies: pkg-config@0.29.2 r-biocgenerics@0.26.0 r-biostrings@2.48.0
> + r-genomeinfodb@1.16.0 r-genomicalignments@1.16.0 r-genomicranges@1.32.6
> + r-iranges@2.14.11 r-rcurl@1.95-0.1.2 r-rsamtools@1.32.3 r-s4vectors@0.18.3
> + r-xml@3.98-1.16 r-xvector@0.20.0 zlib@1.2.11
> location: gnu/packages/bioinformatics.scm:7696:2
> homepage: https://bioconductor.org/packages/rtracklayer
> license: Artistic License 2.0
> synopsis: R interface to genome browsers and their annotation tracks
> description: rtracklayer is an extensible framework for interacting with
> + multiple genome browsers (currently UCSC built-in) and manipulating annotation
> + tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig
> + and 2bit built-in).  The user may export/import tracks to/from the supported
> + browsers, as well as query and modify the browser state, such as the current
> + viewport.
> relevance: 4
>
> Can you find another one?
Yes! I knew that the package was already available for guix, but I
just wanted to see the template, with guix import, to use it for
others.
>
>
> > I am trying to do my best. I am reading the documentation carefully, I
> > recall mentioning that I am that kind of person,  but I also know that
> > time counts for the contributions.
>
> Yes, you mentioned that :-) The documentation is huge, with lots of
> special concepts. I would recommend reading it only partially, whenever
> you need more information.
I have already answered this :( I know I don't have time to do things
this way, at least for the contribution(s)
>
>
> > And if I figure out how to package
> > R packages, then I can also package more packages and, whatever the
> > result of outreachy might be, well, there are more useful packages in
> > guix.
> > For instance, I tried, before of asking for help with  the example
> > shown with cairo and it worked fine, so I was  not understanding very
> > well what was happening,
> > In addition, I have just run
> > $ guix package -s "\<R\>" | recsel -p name,synopsis >>
> > outputRwithNameAndSynopsis.txt
> > and found even more R packages already installed.
>
> 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)
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?
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)

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)
>
> the carret-symbol "^" matches the beginning of the line.
> There are some empty lines, which get sorted out with the grep.
Thanks :) I knew about the regex, but everything  is always welcome :)
sometimes it is true that after reading too much info you end up
messed up if you do not have enough time to practice and try
everything.

>
>
> > Well, time to work!
>
> Good luck!
Thanks!
>
> Björn
Regards,

Laura