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

[Martin Morgan]

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.research using 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
> 
> 	[[alternative HTML version deleted]]
> 
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