Re: [outreach] Help trying to create R package

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

Hi!
I don't know why when I reppied to all in my last mail some of you
were not included

On Sat, Oct 13, 2018 at 9:40 PM Laura Lazzati
<laura.lazzati.15@gmail.com> wrote:
>
> On Sat, Oct 13, 2018 at 3:25 PM Catonano <catonano@gmail.com> wrote:
> >
> > Hi Laura !
> >
> > Il giorno sab 13 ott 2018 alle ore 15:37 Laura Lazzati <laura.lazzati.15@gmail.com> ha scritto:
> > >
> > >  Hi!
> > > I'm creating a new thread so that it does not end up messy.
> > > I am reading about defining new packages, and since I have always
> > > installed R with apt, I am trying to do so with ./configure make make
> > > install to have it running on my VM, and then try to create the
> > > package and check if both works
> >
> > you don't need to package R yourself, R is already packaged and available in Guix, i believe.
> >
> > If you want to package a R based package for Guix you can use the so called Cran importer
> >
> > Try this line at the prompt
> >
> > guix import cran your-R-package
> >
> > This line invokes a so called importer and the importer should return you the recipe of your R package written in scheme
> >
> > You could append such definition to an existing Guix file (probably with some minor tweaks) and that should allow you to build the package and all the dependencies will be taken care of automatically
> >
> > I did this myself some time ago

I've reading the documentation as well as trying some commands,and
there are some problems I am facing. I don't know what I am doing
wrong.

First, I ran:
$ guix package -s r-* | recsel -p name >> resultOfSearchingRpackages.txt
And reading the output file, I found that the packages belonging to R
that are available are:
name: r-rtracklayer
name: r-rcas
name: r-qtl
name: r-ggridges
name: r-feather
I also took a look at each of them with
$guix package --show=PACKAGENAME
Then, I tried:
$ guix import cran --archive=bioconductor tracklayer

But got this output:
acktrace:
          17 (apply-smob/1 #<catch-closure 223b160>)
In ice-9/boot-9.scm:
    705:2 16 (call-with-prompt _ _ #<procedure default-prompt-handle…>)
In ice-9/eval.scm:
    619:8 15 (_ #(#(#<directory (guile-user) 22f6140>)))
In guix/ui.scm:
  1578:12 14 (run-guix-command _ . _)
In guix/scripts/import.scm:
   114:11 13 (guix-import . _)
In guix/scripts/import/cran.scm:
   107:23 12 (guix-import-cran . _)
In guix/memoization.scm:
     98:0 11 (_ #<hash-table 28ce000 0/31> ("tracklayer" #) _)
In unknown file:
          10 (_ #<procedure 28d8d60 at guix/memoization.scm:179:32 …> …)
In guix/import/cran.scm:
   349:12  9 (_ _ _)
   183:21  8 (fetch-description _ "tracklayer")
   160:15  7 (latest-bioconductor-package-version _)
In ice-9/boot-9.scm:
    829:9  6 (catch _ _ #<procedure 7fa48a6a8218 at guix/import/cra…> …)
In guix/import/cran.scm:
   153:36  5 (_)
In ice-9/boot-9.scm:
    829:9  4 (catch _ _ #<procedure 28e0b40 at guix/http-client.scm…> …)
In guix/http-client.scm:
   182:20  3 (_)
    88:25  2 (http-fetch _ #:port _ #:text? _ #:buffered? _ # _ # _ # …)
In guix/build/download.scm:
    398:4  1 (open-connection-for-uri _ #:timeout _ # _)
    296:6  0 (tls-wrap #<closed: file 27f1690> _ # _)

guix/build/download.scm:296:6: In procedure tls-wrap:
X.509 certificate of 'bioconductor.org' could not be verified:
  signer-not-found
  invalid

I don't know what's wrong, could you give me a hand?


> > In order to append the definition of your package to an existing Guix file you will probably need some more guidance, but for now you could just run the importer and let us now what you obtained
> >
> > Probably you'll need to build the package, then modify the recipe a bit, build it again... for a few times; that's ok
> >
> > You can read about the importers here
> >
> > https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-import.html#Invoking-guix-import
> >
> Thanks both of you for helping with this, since I was reading all the
> reference guide  to see how to create a package for whole R while
> thinking that there is no time for that.
> >
> > > substitute: guile: warning: failed to install locale
> > > substitute: hint: Consider installing the `glibc-utf8-locales' or
> > > `glibc-locales' package and
> > > substitute: defining `GUIX_LOCPATH', along these lines:
> > > substitute:
> > > substitute:      guix package -i glibc-utf8-locales
> > > substitute:      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
> > > substitute:
> > > substitute: See the "Application Setup" section in the manual, for more info.
> > >
> > > When I run guix package -I I get:
> > > hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> > > recutils    1.7    out
> > > /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> > > glibc-locales    2.27    out
> > > /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> > > glibc-utf8-locales    2.27    out
> > > /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> > > gfortran    7.3.0    out
> > > /gnu/store/mw65pcca7x7mmq8v2r427f3plrahhyxl-gfortran-7.3.0
> > > zlib    1.2.11    out    /gnu/store/fxiwj2wpp11sif613axdax7gmwzsg6kp-zlib-1.2.11
> > > bzip2    1.0.6    out    /gnu/store/rw1ilvs76rf2p4p0bi1fx3bffprwwb7g-bzip2-1.0.6
> > >
> > > And even at the bottom of my .bashrc I have:
> > >
> > >   export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
> > >     export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> > >     export CPATH="/home/laura/.guix-profile/include${CPATH:+:}$CPATH"
> > >     export LIBRARY_PATH="/home/laura/.guix-profile/lib${LIBRARY_PATH:+:}$LIBRARY_PATH"
> >
> > when running Guix on top of a foreign distribution, this problem is very common.
> > I lived with this for several months myself
> >
> > Reaching a solution to this can be tedious and often the solutions are short lived
> >
> > Because this has to do with how the basic C libraries provided by Guix and those provided by the foreign distro relate with each other (usually not so well)
> >
> > But this is not critical, you can successfully package some R based packages for Guix anyway
> Thank you for this too , I have been stuck with it without knowing
> "why is this happening if I have already exported, sourced just in
> case" and so on. It is a warning and things end up installed but you
> never know if it can affect something else.
> >
> > Hope this helps !

Regards!

Laura