[Bioc-devel] BiocInstaller: next generation
nicol@@@de@co@te@ @ending from gm@il@com
Wed May 16 16:34:54 CEST 2018
perfect! thanks a lot
2018-05-16 10:32 GMT-04:00 Martin Morgan <martin.morgan at roswellpark.org>:
> 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
>> 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)
>  "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"
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