[R-pkg-devel] I'm trying to include phyloseq as a CRAN package dependency and for the life of me I can't figure it out

[Martin Morgan]

CRAN knows about Bioconductor packages, so add phyloseq to Depends: , Imports:, or Suggests: as appropriate.

These CRAN packages seem to Import phyloseq, for instance

> db = available.packages(repos = "https://cloud.R-project.org")
> rownames(db)[grepl("phyloseq", db[,"Imports"])]
[1] "adaptiveGPCA"      "breakaway"         "chem16S"
[4] "HTSSIP"            "HybridMicrobiomes" "microbial"
[7] "MicrobiomeStat"    "mixKernel"         "SigTree"
[10] "SIPmg"             "treeDA"


From: R-package-devel <r-package-devel-bounces using r-project.org> on behalf of Sharon Bewick <sbewick using clemson.edu>
Date: Monday, December 4, 2023 at 6:17 AM
To: r-package-devel using r-project.org <r-package-devel using r-project.org>
Subject: [R-pkg-devel] I'm trying to include phyloseq as a CRAN package dependency and for the life of me I can't figure it out
I had this package included in a previous upload and it didn’t cause errors. However, now it is getting flagged as an error. I’ve included biocViews: phyloseq in the DESCRIPTION file, but that did not help. Unfortunately, I cannot make phyloseq a weak dependency. It can be installed through Bioconductor but not CRAN. Any advice, or examples would be appreciated. I have tried most of the ‘solutions’ I have found online without success.

Thanks!
Sharon

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