[BioC] Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script

[Dan Tenenbaum]

Hello,

On Thu, Nov 24, 2011 at 6:32 PM, Firas Swidan <firas at biomatters.com> wrote:
> Hi,
>
> I used to be able to install Bioconductor packages from a script *without*
> having administrator rights (e.g., on Windows) by specifying the library
> location to where the packages are to be installed.
>
> However, with the new R (2.14.0) and Bioconductor releases, the command
>
>
>
> source("http://bioconductor.org/biocLite.R")
>
>
>
> would fail without administrator rights, because it tries to install
> packages to directories that require administrator rights.
>
> I checked the file biocLite.R and located the line where this problematic
> install happens (install.packages("BiocInstaller", repos=a["BioCsoft",
> "URL"]))
>
>
> Is there a safe way to avoid the requirement for administrator rights? I
> know that I could modify the above command and add a library location
> argument, but is that safe?
>
> In particular I am wondering why the r-script was modified to require the
> administrator right?
>

The script was not modified specifically to require administrator rights.

I tried to reproduce your situation, as I understand it, but perhaps I
don't have enough information. When I (as a Windows user without
administrative rights) ran the source() command above, I got a popup
asking me if I wanted to create a personal library directory. If I
said Yes, BiocInstaller installed itself just fine, and I was then
able to install packages with biocLite(). I did get some warnings
about packages that cannot be updated because they are installed in
directories that are not writeable. However, those are just warnings;
if you need to update any of those packages, you can install them
yourself with biocLite().

It would be helpful if you could send the complete output of your
session, including sessionInfo() and all the commands you tried, plus
any errors/warnings.

Thanks
Dan



> Thanks,
> Firas.
>
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>
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