[Bioc-devel] BiocInstaller: next generation

Martin Morgan m@rtin@morg@n @ending from ro@wellp@rk@org
Wed May 16 16:32:22 CEST 2018

On 05/16/2018 10:23 AM, Nicolas Descostes wrote:
> Dear Martin,
> I am starting using BiocInstaller. Regarding the BiocManager::valid(),
> would it be possible to retrieve a list with one element being a vector of
> the packages to update? or to run BiocManager() as  we do with biocLite()?

Running install() without any arguments will prompt to update old 
packages; install(ask=FALSE) will update packages without prompting.

I'm not sure if that was what you were asking...

> I would find it easier then copying/pasting the suggested command.
> As an opinion, I find it very useful to see the installed vs latest version
> in a table, can it be also printed by valid() as biocValid() does?

valid() returns an object that prints in a compact way, but the elements 
are visible with

 > v = valid()
 > names(v)
[1] "out_of_date" "too_new"
 > head(v$out_of_date)
     Package LibPath
bit "bit"   "/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.8"
ff  "ff"    "/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.5-Bioc-3.8"
     Installed Built   ReposVer Repository
bit "1.1-12"  "3.5.0" "1.1-13" "https://cran.rstudio.com/src/contrib"
ff  "2.2-13"  "3.5.0" "2.2-14" "https://cran.rstudio.com/src/contrib"

> Thanks,
> Nicolas
> 	[[alternative HTML version deleted]]
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