Thanks for your response Martin,
I'm definitely thinking to use BiocManager::install("EBImage") since it is
the official suggestion of the Bioconductor community. Anyway, I've been
learning a lot from this discussion. Thanks all!!
Best,
TiagoEm sex., 3 de set. de 2021 às 12:58, Martin Morgan <mtmorgan.b...@gmail.com> escreveu: > The specific repository you've chosen is not what you want to do. This > will always install EBImage from Bioconductor version 3.13, but > Bioconductor version 3.13 is only relevant for R-4.1 (see > https://bioconductor.org/about/release-announcements/) > > Personally, I would encourage you to follow the Bioconductor community > best practice of BiocManager::install("EBImage"). In that way you will get > the version of EBImage that has been tested with other Bioconductor > packages in the same release, and on the version of R in use by your user. > > If you were to use a specific repository, it should the one that is as > good as base R can do (this can be different from the version that > BiocManager would choose because R's release cycle is different from > Bioconductor's). I think this is most easily accomplished by > utils::chooseBioCmirror(), and then selecting the 0-Bioconductor > repository. That's a lot to tell your users... Maybe others in the R > community have a better way (the key information is in > tools:::.BioC_version_associated_with_R_version(), but that is not an > exported function so not recommended for CRAN packages...) > > Martin Morgan > > On 9/1/21, 8:13 AM, "R-package-devel on behalf of Tiago Olivoto" < > r-package-devel-boun...@r-project.org on behalf of tiagooliv...@gmail.com> > wrote: > > Thank you, Duncan and Uwe for the suggestions. > I followed your instructions and created a function to check for > EBImage > that is only called in an interactive section and, if necessary, ask > the > user to install the package with install.packages("EBImage", repos=" > https://bioconductor.org/packages/3.13/bioc";) > > Best, > Tiago > > Em qua., 1 de set. de 2021 às 03:53, Uwe Ligges < > lig...@statistik.tu-dortmund.de> escreveu: > > > Two more comments. > > > > 1. Note that your code only works in interactice mode, not when > checking > > your package as it waits infinitely for the user's choice. > > > > 2. I do not see an advantage of installing BiocManager if EBImage is > > needed, the essential part is simply to select BioC as a repository > to > > install packages from. > > > > Best, > > Uwe Ligges > > > > > > On 31.08.2021 23:33, Duncan Murdoch wrote: > > > People shouldn't be able to install your package unless the "hard" > > > dependencies are available. > > > > > > If EBImage isn't essential to your package, you should make it a > "soft" > > > dependency by listing it in Suggests and checking for it every > time you > > > use it. > > > > > > Duncan Murdoch > > > > > > On 31/08/2021 3:20 p.m., Tiago Olivoto wrote: > > >> Dear all, > > >> I have a package called pliman > > >> <https://CRAN.R-project.org/package=pliman> > > >> which depends on the Bioconductor package EBImage. > > >> > > >> When running install.packages("pliman") I get the following > warning > > >> > > >> Warning in install.packages : dependency ‘EBImage’ is not > available > > >> > > >> and thus when loading the package with library(pliman), the > following > > >> error > > >> occurs > > >> > > >> Erro: package or namespace load failed for ‘pliman’ in > loadNamespace(i, > > >> c(lib.loc, .libPaths()), versionCheck = vI[[i]]): > > >> there is no package called ‘EBImage’ > > >> > > >> I created a check function to check if EBImage is available and if > > >> not, ask > > >> users if they want to install it > > >> > > >> --- > > >> check_ebi <- function(){ > > >> if(!requireNamespace("EBImage", quietly = TRUE)) { > > >> inst <- > > >> switch(menu(c("Yes", "No"), title = "Package {EBImage} > required > > >> but not > > >> available.\nDo you want to install it now?"), > > >> "yes", "no") > > >> if(inst == "yes"){ > > >> if (!requireNamespace("BiocManager", quietly = TRUE)){ > > >> install.packages("BiocManager") > > >> } > > >> BiocManager::install("EBImage", ask = FALSE, update = > FALSE) > > >> } else{ > > >> message("To use {pliman}, first install {EBImage} with > > >> 'BiocManager::install(\"EBImage\")'.") > > >> } > > >> } > > >> } > > >> --- > > >> > > >> Is there any way to run this function prior to namespace loading? > I > > tried > > >> putting check_ebi() into .onLoad() but the same error occurs. > > >> > > >> Thanks in advance for any suggestions. > > >> Tiago > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> ______________________________________________ > > >> R-package-devel@r-project.org mailing list > > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > >> > > > > > > ______________________________________________ > > > 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 > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
