[BioC] Warning message while trying to install Bioconductor
mtmorgan at fhcrc.org
Mon Jun 2 21:15:19 CEST 2014
On 06/02/2014 07:28 AM, Kasper Daniel Hansen wrote:
> And as a followup: what I do in a multi-user environment (and after some
> years of experience I think this is the best approach) is to immediately
> make a site-library directory where I install all packages. Basically we
> have groups like
> 1) me
> 2) people allowed to install R packages system-wide
> 3) most users
> I set the permissions of site-library to be 2), but the standard library is
> always 1) because it is installed as part of R. This mean any user in 2)
> who (say) tried to update all installed R packages system-wide will be told
> that the packages included with R cannot be updated; exactly the situation
> the OP described.
I went looking in the R-admin manual for best practices along these lines, and
was a little surprised not to see anything. Did I miss something?
The warning seems worth-while, even if the person receiving the message is not
in a position to do anything about it; maybe they'll hassle their sys admin? Is
there a better way of phrasing the message to make it more informative / tolerable?
> On Sun, Jun 1, 2014 at 8:19 AM, Wolfgang Huber <whuber at embl.de> wrote:
>> On 31 May 2014, at 23:53, Steve Lianoglou <lianoglou.steve at gene.com>
>>> On Sat, May 31, 2014 at 1:46 PM, Felix Francis [guest]
>>>> 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'
>>> 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.
>> Depending on how valuable the machine is, or how many users work with it,
>> it is preferable to install R as well as its libraries with an account with
>> limited rights; and then to use that account also for package updates and
>> the installation of additional packages, as what Felix is trying to do.
>> Doing it as administrator seems like leaving a hole for through which bad
>> things could be done (intentionally or unintentionally) . Iâ€™ve not yet seen
>> this actually happening, though.
>> Bioconductor mailing list
>> Bioconductor at r-project.org
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