Re: [outreach] Help trying to create R package

["Björn Höfling" <bjoern.hoefling@bjoernhoefling.de>]

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Hi Laura,

On Mon, 15 Oct 2018 19:47:38 -0300
Laura Lazzati <laura.lazzati.15@gmail.com> wrote:

> 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?

See the last message: "certificate could not be verified".

You need to install certificates first and setup some environment
variables.

That is described here:

https://www.gnu.org/software/guix/manual/en/guix.html#X_002e509-Certificates

Can you get over that problem then?

Unfortunately, I'm getting then to another error:

guix import cran --archive=bioconductor tracklayer
Backtrace:
           9 (primitive-load "/home/bjoern/.config/guix/current/bin/…")
In guix/ui.scm:
  1583:12  8 (run-guix-command _ . _)
In guix/scripts/import.scm:
   115:11  7 (guix-import . _)
In guix/scripts/import/cran.scm:
   107:23  6 (guix-import-cran . _)
In guix/memoization.scm:
     98:0  5 (_ #<hash-table 262ebc0 0/31> ("tracklayer" #) _)
In unknown file:
           4 (_ #<procedure 26e9760 at guix/memoization.scm:179:32 …> …)
In guix/import/cran.scm:
   349:12  3 (_ _ _)
   184:26  2 (fetch-description _ _)
In guix/build-system/r.scm:
     53:8  1 (bioconductor-uri "tracklayer" #f)
In unknown file:
           0 (string-append "https://bioconductor.org/packages/rele…" …)

ERROR: In procedure string-append:
In procedure string-append: Wrong type (expecting string): #f


Currently, I don't have time to track that down further.

Either you don't have that second problem, someone else has a solution,
or I will come back to this back later.

Björn

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