Re: [outreach] Help trying to create R package

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

Hello Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
nov. 2., P, 20:45):
>>
>>
>> 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
>
> Sorry for writing again on this topic.
> Today I wanted to practice packaging an r package belonging to bioconductor, to then go on and read and work with texinfo.
> After writing on IRC channel, I realized I already had this exact problem, but thought it was a problem of other packages.
> I ran again this same command, and I am getting:
>
> $guix import cran -a bioconductor rtracklayer
> guile: warning: failed to install locale
> hint: Consider installing the `glibc-utf8-locales' or `glibc-locales' package and defining `GUIX_LOCPATH', along these lines:
>
>      guix package -i glibc-utf8-locales
>      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
>
> See the "Application Setup" section in the manual, for more info.
>
>
>
> Starting download of /tmp/guix-file.kBVFop
> From https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz...
> download failed "https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz" 404 "Not Found"
> failed to download "/tmp/guix-file.kBVFop" from "https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz"
> Backtrace
> (and the backtrace is the same).
>
> I am also new to schemas, but opened guix/import/cran.scm and saw what Bjorn was saying. I don't know why if it is not the latest package there should be a false condition, but I don't know either why I am not getting the latest version from bioconductor if it is real that, for tracklayer the latest is 42 and that file does not exist.
> Any ideas? Should I spend more time trying to figure this out or should I move on to another task, like knowing guix more deeply or learning texinfo?
>

This is not your fault, you were simply at the wrong place at the wrong time :)
Bioconductor 3.8 was released on October 31., so the importer, and
most probably all packages not having the substitues from
bioconductor are off. (It seems the release tarballs from 3.7 were
removed.) There is a comment in the importer that all bioconductor
packages should be updated together. We should ask Ricardo later how
to proceed regarding this.

>
> Regards!
> Laura

Best regards,
g_bor