[Bioc-devel] How to update the data in a data package?

[Nicolas Delhomme]

Hej Laurent!

Thanks, that's perfect. I was exactly missing the "data_store"; https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/pRnaSeqTutorial/data that is.

Hope all is well in the UK!

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On 5 Sep 2013, at 22:02, Laurent Gatto wrote:

> Dear Nico,
> 
> On 5 September 2013 20:39, Nicolas Delhomme <delhomme at embl.de> wrote:
> > Hej Bioc!
> >
> > I'd like to update the data in that data package:
> >
> > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RnaSeqTutorial/
> >
> > but as the data is not stored in SVN, I'm not sure how I'm supposed to do it.
> 
> The Experiment Data Packages section in http://master.bioconductor.org/developers/source-control/ describes how to obtain the package.
> 
> Different parts of the package reside on different urls. For example, for my pRolocdata data package
> 
> $  svn info
> Path: .
> Working Copy Root Path: /home/lgatto/dev/01_svn/datapkgs/pRolocdata
> URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/pRolocdata
> [...]
> $  svn info data
> Path: data
> Working Copy Root Path: /home/lgatto/dev/01_svn/datapkgs/pRolocdata/data
> URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/pRolocdata/data
> [...]
> $  svn info inst/extdata 
> Path: inst/extdata
> Working Copy Root Path: /home/lgatto/dev/01_svn/datapkgs/pRolocdata/inst/extdata
> URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/pRolocdata/inst/extdata
> [...]
> 
> In you case
> - https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/pRnaSeqTutorial
> - https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/pRnaSeqTutorial/data
> 
> When you commit, make sure to commit form the respective directories; do not add data and inst/extdata to https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/pRnaSeqTutorial, as svn status could indicate:
> 
> $svn status
> ?       data
> ?       inst/extdata
> 
> Hope this helps.
> 
> Laurent
> 
> > Thanks,
> >
> > Nico
> >
> > ---------------------------------------------------------------
> > Nicolas Delhomme
> >
> > Genome Biology Computational Support
> >
> > European Molecular Biology Laboratory
> >
> > Tel: +49 6221 387 8310
> > Email: nicolas.delhomme at embl.de
> > Meyerhofstrasse 1 - Postfach 10.2209
> > 69102 Heidelberg, Germany
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel