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

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