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

Levi Waldron lw@ldron@re@e@rch @ending from gm@il@com
Fri Jul 20 14:40:22 CEST 2018

I think the problem I was actually having was that
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
(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,
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>

> 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
Assistant Professor of Biostatistics     CUNY School of Public Health
US: +1 646-364-9616                                           Skype:

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