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LBMC / RAPToR

RAPToR (Real Age Prediction from Transcriptome staging on Reference) is a tool to accurately predict individual samples' developmental age from their gene expression profiles.
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Add BiocViews to description #1

Closed helenmiller16 closed 2 years ago

helenmiller16 commented 2 years ago

Hello,

My group is using this package in our analysis, as implemented in the ImmuneSignatures2 R package. I found that it could not install correctly when running R CMD Check via github actions because it could not figure out how to install the limma package. Because limma is a Bioconductor package, the DESCRIPTION file needs the biocViews tag so that R knows to install from Bioconductor. I also added pls as an import and GEOquery in suggests. With these small updates, a user can install this package and R should install all dependencies automatically, and R CMD Check passes on my package.

Helen

Romain-B commented 2 years ago

Hello, Thanks for your contribution! I was not aware one could include bioconductor packages this way, I will include this to the next update.

Maybe I have missed something, but why exactly did you add pls back as a dependency ? I removed it in the last update as I no longer used it for reference-building (since v1.1).

Best, Romain

helenmiller16 commented 2 years ago

RAPToR is still importing pls a couple places (eg https://github.com/LBMC/RAPToR/blob/master/R/plsr_interpol.R#L25) so the build was failing without it.

Romain-B commented 2 years ago

As mentioned above, I've fixed the dependency issues by removing the deprecated functions using pls, and included the biocViews trick to the DESCRIPTION file.

Thanks again :)