[Bioc-devel] Git lfs support

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Wed Aug 25 07:58:57 CEST 2021

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:




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 <lptolik using 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]]
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

More information about the Bioc-devel mailing list