Re: [outreach] Help trying to create R package

["Gábor Boskovits" <boskovits@gmail.com>]

Hello Björn,

Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
2018. okt. 16., K, 8:24):
>
> On Tue, 16 Oct 2018 07:44:12 +0200
> Björn Höfling <bjoern.hoefling@bjoernhoefling.de> wrote:
>
> > 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.
>
>
> 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
>

Thanks for having a look at this.

> 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?
>