[BioC] Warning message while trying to install Bioconductor

[Steve Lianoglou]

Hi,

On Sat, May 31, 2014 at 1:46 PM, Felix Francis [guest]
<guest at bioconductor.org> wrote:
> While trying to install Bioconductor, I get this warning message:
>
> installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'foreign', 'KernSmooth', 'lattice', 'MASS',
>   'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial'
>
> I do have the latest version of R. Please let me know how to resolve this.

It sounds like you do not have permissions to write into the installed
directory that R was installed in on the computer you are using.

Running the update/install as an administrator on the machine would
likely do the trick.

Also:

>  -- output of sessionInfo():
>
>> source("http://bioconductor.org/biocLite.R")
> Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
[/clip]

What you pasted is not the output of sessionInfo()

In the future, call the sessionInfo() function from within your R
session and paste what follows. For example, this is what mine looks
like in a session I have currently open:

R> sessionInfo()

R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] devtools_1.5

loaded via a namespace (and not attached):
[1] digest_0.6.4   evaluate_0.5.5 httr_0.3       memoise_0.2.1  parallel_3.1.0
[6] RCurl_1.95-4.1 stringr_0.6.2  tools_3.1.0    whisker_0.3-2

-- 
Steve Lianoglou
Computational Biologist
Genentech