The warning is appropriate.  Wolfgang and I are disagreeing with Steve's
suggestion that the OP should just update/install as administrator.

Best,
Kasper


On Mon, Jun 2, 2014 at 3:15 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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?
>
> Martin
>
>>
>> Best,
>> Kasper
>>
>>
>>
>>
>> On Sun, Jun 1, 2014 at 8:19 AM, Wolfgang Huber <whuber@embl.de> wrote:
>>
>>
>>> On 31 May 2014, at 23:53, Steve Lianoglou <lianoglou.steve@gene.com>
>>> wrote:
>>>
>>>> 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.
>>>
>>>          Wolfgang
>>>
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>>>
>>>
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>>
>>
>>
>>
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>>
>>
>
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