Dear all,
we recently observed a similar behavior due to a bug
in the remotes package which has been fixed in the github
version of the package:
https://github.com/r-lib/remotes/commit/d3a6766c0bcb456b82a0b06608f6149
fe4f5d83e
essentially, internally, somewhere, it would do something like:
On Fri, Jul 20, 2018 at 10:26 AM Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> 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") ?
>
Thanks Martin, and sorry for the slow
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")
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(),
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"))
I'm not able to confirm this, but since BiocManager::install() uses
remotes::install_github() when it sees a pattern "foo/bar", I think
BiocManager::install("foo/bar", dependencies = TRUE) will behave as
desired.
For local installs, I think we end up at utils::install.packages(),
where the
Hi Levi,
Why not use devtools which already does this? Setting `dependencies =
TRUE` installs the packages listed in Imports and Suggests, and
BiocManager::repositories() like BiocInstaller::biocinstallRepos() returns
a list of repositories. See inline below:
On Mon, Jul 9, 2018 at 4:51 AM,
It would be useful to be able to use BiocManager to install
the Depends/Imports/Suggests of a source package not on Bioconductor, e.g.:
BiocManager::install("Bioconductor/BiocWorkshops") #works but only if all
Depends/Imports are already installed
or:
