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waldronlab / bugsigdbr

R-side access to published microbial signatures from BugSigDB
https://bioconductor.org/packages/bugsigdbr
GNU General Public License v3.0
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Pulling from github causes BiocCheck error #19

Closed lgeistlinger closed 3 years ago

lgeistlinger commented 3 years ago

@jwokaty @lwaldron just a heads up that our rework of bugsigdbr pulling from github/BugSigDBExports (https://github.com/waldronlab/BugSigDB/issues/94#issuecomment-903121949) is causing us a BiocCheck error:

ERROR: Avoid references to external hosting platforms
      Found in files:
        bugsigdb.R (line 13, column 22)

I had experienced this before when I tried pulling from dropbox for another package, but here it seems to imply that Bioc doesn't like us to pull files from github. I am not sure how to best address this and whether this would also apply to pulling files from zenodo. We might need some input from the core team. Maybe @LiNk-NY has the corresponding best practices for us?

lgeistlinger commented 3 years ago

Not a clean solution (rather a hack), but masking the github url with a tinyurl works if we just wanted the error to go away. Would still be good to understand what's the recommended Bioc solution for such situations.

LiNk-NY commented 3 years ago

Hi Ludwig, @lgeistlinger

Yes, there is some discussion here https://github.com/Bioconductor/BiocCheck/issues/75 as to the reasons.

The best bet is to either put the data in the package (if it is small enough) or on Experiment/Annotation-Hub.

lgeistlinger commented 3 years ago

Thank you @LiNk-NY for pointing us to the corresponding BiocCheck issue. @jwokaty: just as an FYI, I just discussed with @lwaldron and following his remarks on the BiocCheck issue and the suitability of the current solution for our purposes we decided to go ahead as-is.