[Bioc-devel] Including large files for the package

[Vincent Carey]

On Thu, Aug 31, 2023 at 7:28 AM Martin Grigorov <martin.grigorov using gmail.com>
wrote:

> Hello,
>
> Perhaps you could use https://bioconductor.r-universe.dev/BiocFileCache to
> download the big file on demand.
> The benefit is that the file would be stored in ~/.cache/R/yourPackage/
> (for Linux; something similar for Windows/Mac) and reused between sessions.
>

Thanks Martin.  I think that is a possible approach, but the proposals at
http://contributions.bioconductor.org/non-software.html?q=AnnotationHub#annotationexperiment-hub-packages
should also be considered.

Ali, if the documentation regarding *Hub contributions is unclear, please
file an
issue or write back here with the difficulties so that we can improve the
material and
the methods!

Thanks!



>
> Regards,
> Martin
>
> On Tue, Aug 29, 2023 at 5:15 AM Ali Sajid Imami <ali.sajid.imami using gmail.com
> >
> wrote:
>
> > Hi BioConductor Team,
> >
> > I am a PhD Candidate in the Cognitive Disorders Research lab at the
> > university of Toledo. I am responsible for a number of R packages and our
> > intention is to submit them to bioconductor over the next several
> months. I
> > had just submitted a package drugfindR (
> > https://github.com/CogDisResLab/drugfindR). This was immediately closed
> as
> > my repo had a single file over the 5MB limit.
> >
> > I wanted to ask both if you would reconsider/make an exception or guide
> me
> > in the right direction.
> >
> > This package serves as a way to quickly learch through the LINCS data
> > stored at the ilincs.org portal. The file in question is one of three
> > metadata files that allows the package to function efficiently and
> without
> > having to go through the expensive network requests. It would really be
> > helpful if we could include the file as is. I do not expect more files
> like
> > that to be added to the package at all.
> >
> > Barring that, I have seen the suggestion of using AnnotationHub or
> > ExperimentHub. While I have gone through the documentation, I'm not
> > entirely sure how those services work. Are those services where we can
> > store the data itself or we are expected to host the data elsewhere and
> > create lightweight "pointer" packages. Similarly, I'm not entirely sure
> > which Hub this would go to.
> >
> > Any advice or guidance will be appreciated.
> >
> >
> > Regards,
> > Dr. Ali Sajid Imami
> > LinkedIn <https://pk.linkedin.com/pub/ali-sajid-imami/50/956/2a6>
> >
> >         [[alternative HTML version deleted]]
> >
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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>
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