[Bioc-devel] BiocInstaller: next generation

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

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