Re: [outreach] Help trying to create R package

[Laura Lazzati]

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
<address@hidden> wrote:
>
> On Sat, Oct 13, 2018 at 3:25 PM Catonano <address@hidden> wrote:
> >
> > Hi Laura !
> >
> > Il giorno sab 13 ott 2018 alle ore 15:37 Laura Lazzati <address@hidden> 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