stanstrup/PeakABro

Where to distribute the package?

Opened this issue · 4 comments

jorainer commented

@stanstrup, I was wondering where you plan to distribute/add the package? Do you want to add it to CRAN or Bioconductor (I would not host exclusively on github)?.
I personally would prefer Bioconductor, because of the regular release cycles, possibility to add annotation data and because other related packages are already in Bioc (e.g. xcms ChemmineR).

I would like to see PeakABro added to Bioconductor, with the package not containing compound data, but only the code to generate and use these. The compound data (being versioned!) could ideally be added to AnnotationHub.

Note that if it's going to be Bioconductor it has to fulfill some criteria (http://www.bioconductor.org/developers/package-guidelines/) and also conform (more or less) their coding style (http://bioconductor.org/developers/how-to/coding-style/ - specifically, make sure that the lines in the R sources, including comments and documentations, are not longer than 80 character).

stanstrup commented

I didn't have any concrete plans. I just made it for myself and then I was careless enough to post a screenshot on twitter 😁

I think bioconductor is the way to go, yes, and with the data going to AnnotationHub if you are up for helping out with this.
See also #6 (comment)

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jorainer commented

OK, I'll hack away and make some pull requests from time to time. It's perfect timing after all because I'll need peak annotations a lot in near future - and have a little more time, since xcms development slows down slightly.

jorainer commented

@stanstrup , do you see any chance to include some functionality from chemhelper and massageR into PeakABro? It would be just nice to:

  1. reduce the number of packages from which stuff is imported.
  2. all packages from which functionality is imported should be either on CRAN or Bioconductor (ideally), this might be an issue during Bioconductor's package review process...
stanstrup commented

Yes that was my plan.
I am importing the CAMERA adduct list form chemhelper. I am wondering if that belongs OK in this package or a separate package (or https://github.com/stanstrup/common_mz) could do.

from massageR it is only a tiny function that can be copied.

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