Hi Anatoly,
Let's keep this conversation on the bioc-devel mailing list where it
started.
On 26/08/2021 02:46, Anatoly Sorokin wrote:
Hi Hervé,
thank you for your answer. Does this mean that the SQLite file will be
downloaded separately and kept in some cache?
Yes.
And another question: does this mean that there should be two packages,
one for code and another one for the database?
Yes. One is what we call the software package and the other one the
accompanying data package.
Cheers,
H.
On Wed, Aug 25, 2021 at 6:58 AM Hervé Pagès <hpages.on.git...@gmail.com
<mailto:hpages.on.git...@gmail.com>> wrote:
Hi Anatoly,
What kind of data is in your SQLite database? The Bioconductor approach
for this is to provide the data as a separate data annotation or data
experiment package. More precisely, the data itself should go on
AnnotationHub or ExperimentHub. It should be associated with a "Hub
package", that is, a data package that documents it and explains how to
retrieve it from AnnotationHub or ExperimentHub. See vignettes in the
HubPub package for more information:
http://bioconductor.org/packages/HubPub
<http://bioconductor.org/packages/HubPub>
Best,
H.
On 24/08/2021 17:53, Nitesh Turaga wrote:
> Hi,
>
> We don’t have LFS support on the Bioconductor git server.
>
> I would suggest finding an alternative.
>
> Best,
>
>
>
>
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
>
>> On Aug 24, 2021, at 6:18 PM, Anatoly Sorokin <lpto...@gmail.com
<mailto:lpto...@gmail.com>> wrote:
>>
>> Hi all,
>>
>> we have developed a package that provides access to the data in
the locally
>> stored SQLite database. The GitHub Action successfully built the
package,
>> but in Bioconductor, it got an error. The only reason for the
error is that
>> the database itself is stored on GitHub via git-lfs, and the R
code got an
>> lfs placeholder instead of the actual database.
>>
>> Is it possible to activate lfs within Bioconductor automatic
building
>> server? The database is tiny (80 Mb), but I don't want to have
it as a
>> regular git object.
>>
>> Thank you,
>> Anatoly
>>
>> [[alternative HTML version deleted]]
>>
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>
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>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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