New York 14263
From: Bioc-devel on behalf of Anatoly
Sorokin
Sent: Monday, September 13, 2021 10:08 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Git lfs support
Hi, sorry to bother you again, but I'm completely lost: how could I test
that m
artment of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel on behalf of
> Anatoly Sorokin
> *Sent:* Friday, September 10, 2021 5:56 AM
> *To:* bioc-devel@r-proje
6 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Git lfs support
Hi Herv�,
I've made a new package with metadata.csv, as described in
CreateAnAnnotationPackage
vignette.
The data is located on the public service as a zipped SQLite database. So
I've set both SourceType an
Hi Hervé,
I've made a new package with metadata.csv, as described in
CreateAnAnnotationPackage
vignette.
The data is located on the public service as a zipped SQLite database. So
I've set both SourceType and DispatchClass as 'Zip'.
>From AnnotationHub::DispatchClassList() I expect that I should h
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
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
packag
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 wrote:
>
> Hi all,
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 c
