[Bioc-devel] Installing Annotation Packages Matching a Pattern

[Hervé Pagès]

Hi Dario,

On 05/04/2014 08:00 PM, Dario Strbenac wrote:
> Hello,
>
> I would like to install all software packages and also all annotation packages containing the pattern Hsapiens or Mmusculus in their name. I know about biocLite(all_group()) to do the first task, but I'm not sure if it's possible to query the repository with a pattern. The installation guide simply advises "Visit the Workflows page and software package list to discover available packages."

Not all packages that contain or deal with human data contain the
pattern Hsapiens in them so I'm not sure what you are trying to achieve
with this.

Anyway, and FWIW, you could get the list of all BioC + CRAN packages
with:

   library(BiocInstaller)
   all_bioc_pkgs <- 
rownames(available.packages(contrib.url(biocinstallRepos())))

then use grep(..., value=TRUE) on 'all_bioc_pkgs' (character vector of
lenth > 7300) to keep only the packages that match a given regular
expression, then call biocLite() on that.

Cheers,
H.

>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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