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@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 <mailto: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 <http://www.waldronlab.io>
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616Skype: levi.waldron
This email message may contain legally privileged and/or...{{dropped:2}}
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