[Bioc-devel] Flexibility for submitting a new ExperimentData-package

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Mon Nov 28 16:44:50 CET 2022

Thank you for this note.  We cannot modify the system to accept this
package.  If we can help with aspects
of compatibility problems related to ExperimentHub let us know.

On Thu, Nov 24, 2022 at 1:58 AM Daniel Laajala <teelaa using utu.fi> wrote:

> Dear Bioconductor devs,
> thanks for all the hard work. Regarding if there's any leeway in how
> ExperimentData-packages are structured:
> We started working a few years back on a "curatedPCaData" R-package for
> curating prostate cancer multi-'omics datasets. We followed the structure
> of a family of similar packages, e.g. readily on bioc:
> https://bioconductor.org/packages/release/data/experiment/html/curatedBreastData.html
> https://bioconductor.org/packages/release/data/experiment/html/curatedOvarianData.html
> With the data in a satisfactory form, we were now hoping to submit the
> package to Bioconductor. However, due to the size of
> MultiAssayExperiment-objects, the package is auto-rejected:
> https://github.com/Bioconductor/Contributions/issues/2804
> The data-raw/-files we can discard, as we provided these just for extra
> user convenience.
> However, the mae_*.rda files are essential MultiAssayExperiment objects
> (as a standard format for multi-'omics in Bioc), but these are right now
> too large for the bot.
> Reading the package structure instructions, we were under the impression
> that this old structure for ExperimentData would still be ok for
> Bioconductor; the package passed checks (R CMD check and BiocCheck) with
> minor NOTEs. Our current GitHub is at:
> https://github.com/Syksy/curatedPCaData
> Our package already has citations (with code provided there-in for
> extracting and processing relevant data from the package), has been forked,
> has collaborators using it as-is, etc, so revamping it to e.g.
> ExperimentHub-structure would most likely cause quite major compatibility
> issues.
> Would there be any chance of approaching Bioconductor with the package
> roughly in its current format inspired by these older curated-packages,
> even if it is not in the updated ideal ExperimentData-format?
> Kind regards,
> Teemu Daniel Laajala
>         [[alternative HTML version deleted]]
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