Hi Sergej, I sincerely don't know if the position of biocView really matters (I'll try it when preparing for the new CRAN release of pliman). I believe that biocView will not allow you to put limma in the imports field and automatically install it from Bioconductor, as you can see here in this discussion < https://stackoverflow.com/questions/54411495/bioconductor-packages-not-installing-with-biocviews-specification-in-description >
In my case, I had no errors when submitting pliman to CRAN using EBImage as suggests (I haven't yet tried to use biocView: and EBImage in the Imports section). Best regards, Olivoto Em qui., 16 de mar. de 2023 às 14:01, Ruff, Sergej < sergej.r...@tiho-hannover.de> escreveu: > thank you. > > > I see you added biocView: below your suggested Dependencies. Is it > necessary for CRAN to identify Bioconductor Dependencies and if so, should > I add it below or above the suggested packages? Do I also need BiocManager > among my Suggests? > > > Last question: How does CRAN work with Bioconductor Dependencies? Will > CRAN accept limma as a dependency or will my submission be rejected? > > > Best regards, > > Sergej > ------------------------------ > *Von:* Tiago Olivoto <tiagooliv...@gmail.com> > *Gesendet:* Donnerstag, 16. März 2023 17:36:47 > *An:* Ruff, Sergej > *Cc:* r-package-devel@r-project.org > *Betreff:* Re: [R-pkg-devel] How to declare Bioconductor Dependencies in > the Description File of my R Package > > Hi, > My package pliman depends on EBImage which is in Bioconductor. I have > created a function check_ebi() < > https://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534> > that is called in .onAttach() < > https://github.com/TiagoOlivoto/pliman/blob/master/R/zzz.R#L36> and > checks if EBImage is installed. If not, the function asks the user to > install it. Both EBImage and BiocManager are listed as suggests < > https://github.com/TiagoOlivoto/pliman/blob/master/DESCRIPTION#L22> > > I believe that this could be a possible solution > Best regards, > Olivoto > > > Em qui., 16 de mar. de 2023 às 11:18, Ruff, Sergej < > sergej.r...@tiho-hannover.de> escreveu: > >> I am currently building a package which uses the "limma"-package as a >> dependency. >> >> I want to submit my package to CRAN. >> >> Do I need to declare Bioconductor-dependencies such as Limma differently >> in the Description-File of my Package? >> >> The Check-Function in R shows no Notes, Warnings or Errors, but I am not >> sure if that means that limma will install when installing my package from >> CRAN. >> >> Currently I am declaring limma like this: >> >> Suggests: >> >> limma >> >> >> >> Can CRAN identify that limma is a Bioconductor-Package and will it Limma >> install, when installing my package from CRAN? >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
