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 docs say
dependencies: logical indicating whether to also install uninstalled
packages which these packages depend on/link
to/import/suggest (and so on recursively). Not used if
'repos = NULL'.
where I think the repos has to be NULL for the local installation... I
don't want BiocManager::install() to deviate from base R behavior in
this case.
Martin
On 07/09/2018 11:39 AM, Pariksheet Nanda wrote:
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, Levi Waldron <lwaldron.resea...@gmail.com>
wrote:
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
devtools::install("Bioconductor/BiocWorkshops", repos =
BiocManager::repositories(), dependencies = TRUE)
Also from a local package, e.g.:
BiocManager::install("mypackage_0.1.tar.gz") # or,
BiocManager::install("mypackage")
devtools::install("mypackage_0.1.tar.gz", repos =
BiocManager::repositories(), dependencies = TRUE)
devtools::install("mypackage", repos = BiocManager::repositories(),
dependencies = TRUE)
devtools::install(".", repos = BiocManager::repositories(), dependencies =
TRUE)
Pariksheet
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