[Bioc-devel] BiocInstaller: next generation
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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