[Bioc-devel] BiocInstaller: next generation

[Nicolas Descostes]

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
>> 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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>>
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>>
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