Question

How to update the data in an experimental data package

1

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paul.theodor.pyl ▴ 10

@paultheodorpyl-6798

Last seen 10.1 years ago

Germany

Hi there,

I am the maintainer of an experimentdata package (h5vcData) and I want to update the contents to the new genome release version. I realised that there is some separation between the package itself and the data it contains, so a simple

svn co https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/h5vcData

doesn't give me access to the actual data that I need to modify.

Thanks for suggestions on how to handle this.

- Paul

experimentdata update • 1.7k views

ADD COMMENT • link updated 10.1 years ago by Laurent Gatto 1.6k • written 10.1 years ago by paul.theodor.pyl ▴ 10

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Hi Paul,

Please remember that any question about the development of your package is better asked on the bioc-devel mailing list. So we can keep this support site clean and focused on helping the end users. Thanks!

H.

ADD REPLY • link 10.1 years ago Hervé Pagès 16k

score 0 · Answer 1 · 2014-09-30

0

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 4 months ago

United States

The data is in:

https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/h5vcData/

Dan

ADD COMMENT • link 10.1 years ago Dan Tenenbaum ★ 8.2k

score 0 · Answer 2 · 2014-09-30

Note also that the data and ./inst/extdata live in a different repository than the rest of the package, and must be commited independently. See the 'Experiment Data Packages' in http://master.bioconductor.org/developers/how-to/source-control/ and the REAMDE file [1] for details.

Hope this helps.

Laurent

[1] https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/README.txt