[BioC] Upgrading R

[Florian Hahne]

It sure is:
writeLines(installed.packages()[,1], con="packages.dump")

recompile R

packs <- readLines("packages.dump")
biocLite(packs)

Florian


On 11.05.2009, at 07:46, Michal Blazejczyk wrote:

> Hi everyone,
>
> I think an interesting feature in R would be "package list dump"  
> option.
> The way I see this working is the following: the user would issue
> a command on the source R installation (say, an older version), e.g.
>  packages.dump("~/R/packages.dump")
> Then the user would run the destination installation (say, a new  
> version)
> and recreate the environment by issuing a command like:
>  packages.load("~/R/packages.dump")
> This last command would go and download and install all packages that
> were listed in the dump.
>
> Or maybe this is already possible?
>
> Best,
> Michal
>
>
>> Hi Chintanu,
>>  Basically no, there is no such path. You should always upgrade R and
>> reinstall all packages. biocLite will help you to do that.
>>
>>  best wishes
>>    Robert
>>
>>
>> On Sat, May 9, 2009 at 4:33 PM, Sarmah, Chintanu Kumar
>> <Chintanu.Sarmah2 at lincolnuni.ac.nz> wrote:
>>> Hi,
>>> Wonder if there is a way to upgrade R.
>>> I?m currently using R 2.7.2, and wish to ?upgrade? to the latest  
>>> one via some process that doesn?t make me reinstall all the  
>>> packages again !! Please let me know.
>>> Thank you !
>>> Chintanu
>>>
>>> ? ? ? ?[[alternative HTML version deleted]]
>
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