[Bioc-devel] BiocManager to install Depends/Imports/Suggests

[Martin Morgan]

I think it's a Mac thing, and it's decided to install binary (tgz), and 
the annotation packages are source (tar.gz).

Have you set options(pkgType = "both") ?

On 07/20/2018 08:40 AM, Levi Waldron wrote:
> 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 
> <http://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 using 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.research using gmail.com <mailto:lwaldron.research using 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 <http://www.waldronlab.io>
> Assistant Professor of Biostatistics CUNY School of Public Health
> US: +1 646-364-9616Skype: levi.waldron


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