Import of bioconductor data packages.

Import of bioconductor data packages.

[Philippe Veber]

Hi all,

I am trying to import a bioconductor package that depends on a bioconductor
data package. While the command for the software package works fine :

guix import cran --archive=bioconductor ChIPQC

the one for the data package doesn't :

$ guix import cran --archive=bioconductor TxDb.Celegans.UCSC.ce6.ensGene
error: failed to retrieve package information from "
https://cran.r-project.org/web/packages/TxDb.Celegans.UCSC.ce6.ensGene/DESCRIPTION":
404 ("Not Found")

I tried reading the code in guix for CRAN import, and it seems that the
case for data package has been taken care of (and as a matter of fact there
are already several data packages in the distribution), but I can't find
the way to invoke it.

Thanks for any help!
Philippe.

Re: Import of bioconductor data packages.

[Ricardo Wurmus]

Hi Philippe,

> I am trying to import a bioconductor package that depends on a bioconductor
> data package. While the command for the software package works fine :
>
> guix import cran --archive=bioconductor ChIPQC
>
> the one for the data package doesn't :
>
> $ guix import cran --archive=bioconductor TxDb.Celegans.UCSC.ce6.ensGene
> error: failed to retrieve package information from "
> https://cran.r-project.org/web/packages/TxDb.Celegans.UCSC.ce6.ensGene/DESCRIPTION":
> 404 ("Not Found")

I think we may be able to work around this.  In the past we fetched the
DESCRIPTION file directly via HTTP.  This wasn’t possible for data
packages as they were not stored in the shared SVN repository, and the
DESCRIPTION files thus were not available via HTTP.

When Bioconductor retired their SVN repository we switched to
downloading the target tarball and extracting the DESCRIPTION file from
there.  We aren’t doing this for experiment or data packages yet, but I
think we can easily fix this now.

I’ll give this a shot soon.

--
Ricardo

Re: Import of bioconductor data packages.

[Ricardo Wurmus]

Ricardo Wurmus <rekado@elephly.net> writes:

> When Bioconductor retired their SVN repository we switched to
> downloading the target tarball and extracting the DESCRIPTION file from
> there.  We aren’t doing this for experiment or data packages yet, but I
> think we can easily fix this now.
>
> I’ll give this a shot soon.

Commit 5063deab08 adds this feature to the importer.  You can now import
annotation and experiment packages from Bioconductor.

-- 
Ricardo

Re: Import of bioconductor data packages.

[Philippe Veber]

It works just fine, thanks a lot Ricardo! Now I'm going to prepare a patch
for the new packages I've inserted in bioconductor.

Le ven. 16 août 2019 à 15:10, Ricardo Wurmus <rekado@elephly.net> a écrit :

>
> Ricardo Wurmus <rekado@elephly.net> writes:
>
> > When Bioconductor retired their SVN repository we switched to
> > downloading the target tarball and extracting the DESCRIPTION file from
> > there.  We aren’t doing this for experiment or data packages yet, but I
> > think we can easily fix this now.
> >
> > I’ll give this a shot soon.
>
> Commit 5063deab08 adds this feature to the importer.  You can now import
> annotation and experiment packages from Bioconductor.
>
> --
> Ricardo
>
>