[Bioc-devel] experimental data packages and git-lfs

[Turaga, Nitesh]

Hi Levi,

The external_data_store.txt file is not needed anymore.

The current git.bioconductor.org server does not store files in the LFS mode, so you can just add a file, commit and push. But for Github, you might have to use LFS for such large files. I’ll look into this more and get back to you with a detailed reply.

Best,

Nitesh

> On Sep 5, 2017, at 4:49 PM, Levi Waldron <lwaldron.research at gmail.com> wrote:
> 
> Also, can I now remove external_data_store.txt?
> 
> $ cat external_data_store.txt
> data
> inst/extdata
> 
> 
> On Tue, Sep 5, 2017 at 4:38 PM, Levi Waldron <lwaldron.research at gmail.com>
> wrote:
> 
>> Are a couple extra commands needed at https://www.bioconductor.
>> org/developers/how-to/git/maintain-github-bioc/ for experimental data
>> packages? I followed the instructions here for curatedOvarianData, but got
>> GitHub warnings on push:
>> 
>> remote: warning: GH001: Large files detected. You may want to try Git
>> Large File Storage - https://git-lfs.github.com.
>> remote: warning: See http://git.io/iEPt8g for more information.
>> remote: warning: File data/TCGA_eset.rda is 53.10 MB; this is larger than
>> GitHub's recommended maximum file size of 50.00 MB
>> 
>> So I followed the instructions at https://git-lfs.github.com/:
>> 
>> git lfs track "*.rda"
>> git add .gitattributes
>> git commit -a
>> 
>> Does this seem correct, and is there anything else to know for
>> experimental data packages with large files?
>> 
>> --
>> Levi Waldron
>> http://www.waldronlab.org
>> Assistant Professor of Biostatistics     CUNY School of Public Health
>> US: +1 646-364-9616 <+1%20646-364-9616>
>>         Skype: levi.waldron
>> 
> 
> 
> 
> -- 
> Levi Waldron
> http://www.waldronlab.org
> Assistant Professor of Biostatistics     CUNY School of Public Health
> US: +1 646-364-9616                                           Skype:
> levi.waldron
> 
> 	[[alternative HTML version deleted]]
> 
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