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From: "Björn Höfling" <bjoern.hoefling@bjoernhoefling.de>
To: Laura Lazzati <laura.lazzati.15@gmail.com>
Cc: Guix-devel <guix-devel@gnu.org>,
	Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: Re: [outreach] Help trying to create R package
Date: Tue, 16 Oct 2018 07:44:12 +0200	[thread overview]
Message-ID: <20181016074412.54757b18@alma-ubu> (raw)
In-Reply-To: <CAPNLzUOTAZkajuKDMN50G+ToW7v2sJjZqMYCNBDyngxCgxXP_A@mail.gmail.com>

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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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  reply	other threads:[~2018-10-16  5:44 UTC|newest]

Thread overview: 46+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2018-10-13 13:36 [outreach] Help trying to create R package Laura Lazzati
2018-10-13 17:58 ` Gábor Boskovits
2018-10-13 18:25 ` Catonano
2018-10-14  0:40   ` Laura Lazzati
2018-10-15 22:47     ` Laura Lazzati
2018-10-16  5:44       ` Björn Höfling [this message]
2018-10-16  6:23         ` Björn Höfling
2018-10-16  8:28           ` Gábor Boskovits
2018-10-16 13:13             ` Laura Lazzati
2018-10-16 22:18               ` Björn Höfling
2018-10-17  1:01                 ` Laura Lazzati
2018-10-17  7:17                   ` Björn Höfling
2018-10-17  8:21                     ` Gábor Boskovits
2018-10-17 14:27                       ` Laura Lazzati
2018-10-17 16:38                         ` Laura Lazzati
2018-10-17 17:13                           ` Clément Lassieur
2018-10-17 17:50                             ` Laura Lazzati
2018-10-18  1:36                     ` Laura Lazzati
2018-10-18  6:54                       ` Björn Höfling
2018-10-18  7:50                         ` Gábor Boskovits
2018-10-18 14:49                           ` Laura Lazzati
2018-10-18 15:15                             ` Gábor Boskovits
2018-10-18 15:25                               ` Laura Lazzati
2018-10-18 15:40                                 ` Gábor Boskovits
2018-10-18 16:18                                   ` Laura Lazzati
2018-10-18 17:26                                     ` Laura Lazzati
2018-10-18 17:41                                       ` Björn Höfling
2018-10-18 18:14                             ` Ricardo Wurmus
2018-10-18 18:17                               ` Laura Lazzati
2018-10-19  1:05                                 ` Laura Lazzati
2018-10-19  3:47                                   ` Laura Lazzati
2018-10-19  6:21                                     ` Gábor Boskovits
2018-10-19  7:09                                   ` Ricardo Wurmus
2018-10-19  7:29                                     ` Gábor Boskovits
2018-10-19 18:37                                       ` Laura Lazzati
2018-10-19 18:45                                         ` Gábor Boskovits
2018-10-19 20:35                                           ` Laura Lazzati
2018-10-19 21:25                                             ` Gábor Boskovits
2018-10-19 23:10                                               ` Laura Lazzati
2018-10-20  6:08                                                 ` Björn Höfling
2018-10-20  6:34                                                   ` Gábor Boskovits
2018-10-20 13:47                                                     ` Laura Lazzati
2018-10-20 14:01                                                   ` Ludovic Courtès
2018-11-02 19:44           ` Laura Lazzati
2018-11-02 20:12             ` Gábor Boskovits
2018-11-02 20:17               ` Laura Lazzati

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