I think the problem I was actually having was that BiocManager::install("githubuser/repo") will not install annotation or experimental data packages that are among the repo's dependencies. It is the same for devtools::install_github("githubuser/repo", repos = BiocManager::repositories(), dependencies = TRUE). Here is a minimal example from github.com/lwaldron/nothing, which depends on one software, one annotation, and one experimental data package - the software package will be installed, but the annotation and data packages are not available:
> remove.packages(c("TCGAutils", "mirbase.db", "curatedTCGAData")) Removing packages from ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ (as ‘lib’ is unspecified) > BiocManager::install("lwaldron/nothing") Bioconductor version 3.8 (BiocManager 1.30.1), R 3.5.1 (2018-07-02) Installing github package(s) 'lwaldron/nothing' Downloading GitHub repo lwaldron/nothing@master Skipping 3 packages not available: curatedTCGAData, GenomeInfoDbData, mirbase.db Installing 1 packages: TCGAutils ERROR: dependencies *‘mirbase.db’, ‘curatedTCGAData’* are not available for package ‘nothing’ On Mon, Jul 9, 2018 at 12:48 PM Levi Waldron <lwaldron.resea...@gmail.com> wrote: > Thanks Pariksheet and Martin! It seems that in fact both of these > approaches work, e.g. (I made a simpler test case to figure this out): > > devtools::install_github("lwaldron/nothing", repos = > BiocManager::repositories(), dependencies = TRUE) > remove.packages(c("nothing", "ABCp2")) > BiocManager::install("lwaldron/nothing", dependencies = TRUE) > > It's the dependencies of the Remotes: in Bioconductor/BiocWorkshops that > get skipped, but at this point it seems like trying to do dependency > management through GitHub and asking for trouble. I think the thing to do > is to copy all the dependencies of the Remotes: directly into the > DESCRIPTION file to streamline installation. > -- Levi Waldron http://www.waldronlab.io Assistant Professor of Biostatistics CUNY School of Public Health US: +1 646-364-9616 Skype: levi.waldron [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel