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MD-Anderson-Bioinformatics / NGCHM-R

An R package for creating Next-Generation Clustered Heat Maps (NG-CHM)

http://bioinformatics.mdanderson.org/main/NG-CHM-V2:Overview

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For cran #33

Closed bmbroom closed 2 years ago

bmbroom commented 2 years ago

Updates to NGCHM in support of future submission to CRAN.

marohrdanz commented 2 years ago

I had a look at CRAN's policies, https://cran.r-project.org/web/packages/policies.html, and there are at least a few things I think we need to address before actual submission:

Listing a designated 'Maintainer' in DESCRIPTION
I think CRAN will complain about tsvio in the 'Imports', because tsvio appears to only be in GitHub.
I think we have to specify where to get NGCHMSupportFiles and NGCHMDemoData because they are not (yet) in CRAN.

bmbroom commented 2 years ago

Giving the role "cre" to a person in the Authors@R field is equivalent to specifying a maintainer.
Plan to submit tsvio before NGCHM packages.
Plan to submit the two NGCHM support packages concurrently. Will include cross-references between them all.

bmbroom commented 2 years ago

P.S. Many, many, many other issues to address before we can make first CRAN submission attempt.

jmelott commented 2 years ago

Mary: If you're running R CMD check, you have to do so against the .tar.gz created by the build rather than against the source directory. The build process creates the maintainer and author tags correctly in the gz file from the authors@R tag. If you run the check against the source directory it will report authors and maintainer to be missing when using the authors@R in the description file.

bmbroom commented 2 years ago

I originally changed the examples in 8b4c33e0c9a40b483c58b5a9c442696f03cd745d back to TCGA.GBM.EXPR because I didn't know how to load TCGA.BRCA.ExpressionData explicitly. Now I do, so we could change some of them back. Nice to have variety.