[Bioc-devel] Acceptable dataset origins besides ExperimentHub

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Fri Nov 13 19:17:45 CET 2020

Hi Hector --

caching means that the file is downloaded once per computer, so when, for instance, you edit your vignette and need to rebuild it, you don't have to re-download the data.

I don't think your static vignette is suitable for Bioconductor -- it sounds like you are trying to provide a full 'reproducible' analysis, maybe in support of a publication or other product of your research. But the computational demands of the full analysis is beyond the scope of what can be supported by our build system. I think you would be better off finding another solution, for instance exploring GitHub 'actions' and docker containers to build the vignette, and github.io to make the built vignette available to interested users. I don't know whether the computational demands of your vignette can be satisfied by GitHub actions, or whether you would run into limitations of time and space there, too -- it would be worth figuring out before embarking on that solution.

Because the Bioconductor build system would not build the vignette, the advice remains that the static vignette should NOT be included in your Bioconductor package.

Martin Morgan

On 11/13/20, 7:13 AM, "Bioc-devel on behalf of Hector Gracia" <bioc-devel-bounces using r-project.org on behalf of hgracia using ibecbarcelona.eu> wrote:

    Thanks Lori for your answer.

    I am not sure about the benefits of use BiocFileCache in this case, because data is only needed to run a more extensive tutorial based on large dataset. This dataset is not needed for the functionality of the package and is just a one time download.

    Besides that, i have annother question related.
    In the review of the package you(Lori) told me that a static vigente don�t was recommended because static vignettes have a tendency to get stale and i am agree with that.
    I have the R markdown of this extended tutorial and the point is that if i execute it can take more that one hour to download the data and process it. So, besides a static vigente, is there other way of doing it and don�t overpass the package build limit of bioconductor?


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