Re: [outreach] Help trying to create R package

[Björn Höfling]

On Tue, 16 Oct 2018 07:44:12 +0200
Björn Höfling <address@hidden> wrote:

> Hi Laura,
> 
> On Mon, 15 Oct 2018 19:47:38 -0300
> Laura Lazzati <address@hidden> 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.


I tracked it down:

The cause is that:

guix/import/cran.scm:

(define (latest-bioconductor-package-version name)
  "Return the version string corresponding to the latest release of the
bioconductor package NAME, or #F if the package is unknown."

actually returns #f. It's a bit said that this #f is not checked
further down. The problem is the package name. If you add an "r" before
the package name, it should work (suppose you fixed the first problem):

guix import cran --archive=bioconductor rtracklayer 

Björn

PS: I personally think the Scheme backtraces are a bit hard to read
(I'm more used to Java), especially with the "In unknown file" parts,
but anyway you can get your information out of it. Try to look at them,
read the error message carefully. Find the lines in source code. Get
your way up, where is that abnormal #f coming from?

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