Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Tue, Oct 16, 2018 at 5:29 AM Gábor Boskovits <address@hidden> wrote:
>
> Hello Björn,
>
> Björn Höfling <address@hidden> ezt írta (időpont:
> 2018. okt. 16., K, 8:24):
> >
> > 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
> >
>
> Thanks for having a look at this.

Thank you again!
I am trying to do my best. I am reading the documentation carefully, I
recall mentioning that I am that kind of person,  but I also know that
time counts for the contributions. And if I figure out how to package
R packages, then I can also package more packages and, whatever the
result of outreachy might be, well, there are more useful packages in
guix.
For instance, I tried, before of asking for help with  the example
shown with cairo and it worked fine, so I was  not understanding very
well what was happening,
In addition, I have just run
$ guix package -s "\<R\>" | recsel -p name,synopsis >>
outputRwithNameAndSynopsis.txt
and found even more R packages already installed.
Well, time to work!
> > 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?
> >
Regards!
Laura