[BioC] Network install of packages

[Henrik Bengtsson]

Has anyone done any benchmarking on accessing the annotation packages
over a network vs. a local drive?  I can image (guess) that for some
annotation packages that are frequently used, it may pay of to have
the on a local drive, especially the SQLite based ones.  Correct me if
I'm wrong.

/Henrik

On Thu, Nov 6, 2008 at 12:00 PM, Wolfgang Huber <huber at ebi.ac.uk> wrote:
>
> Hi Anthony,
>
> I think it would be good sys-ad practice to install R and its packages
> (whether or not they're from Bioconductor) under a user-id that has been
> allowed to write to a shared directory, but that has otherwise restricted
> rights - but *not as root*.
>
>  Best wishes#
>        Wolfgang
>
> PS Like your. Creative. Use of Punctation.
>
> ----------------------------------------------------
> Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber
>
>
> Sean Davis ha scritto:
>>
>> On Thu, Nov 6, 2008 at 1:11 PM, Anthony Mullen <mullen1 at uiuc.edu> wrote:
>>
>>> Greetings -
>>>
>>> I am a Linux system administrator for the Department of Mathematics and
>>> the
>>> University of Illinois.  I installed R, perl-bioperl and perl-bioperl-run
>>> for a couple researchers who are doing collaboration using these tools.
>>>
>>> I was asked to install Bioconductor packages.  I took a quick look at the
>>> installation notes at the bioconductor.org page.  And I have a few
>>> questions.
>>>
>>> Where can I find the sizes of these standard/additional packages?  If I
>>> install these packages as root will they be available to other users? Or
>>> will each person have to install Bioconductor packages themselves?
>>>
>>
>>> I think I see what I need to do if I were to install these packages. But
>>> if
>>> Bioconductor packages are installed only in a local user-space. Then it
>>> doesn't make any sense for me to install them as root.
>>>
>>> It looks like the commands I may want to use are:
>>>
>>> #invoke R
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite()
>>> biocLite(groupName="all")
>>>
>>> But I see a note that states that selecting 'all' software packages will
>>> take up a lot of space.  But if the packages can be installed by root,
>>> such
>>> that other's can use the packages.  I can install all the Bioconductor
>>> packages on a local computer.  And the users network home directories
>>> won't
>>> have to support all the disk space.
>>>
>>
>>
>> Hi, Tony.  This is not a bioconductor issue, directly, since R deals with
>> this issue out-of-the-box.  If you install as root, then the users will
>> have
>> access to those packages.  If they need other packages, the packages will,
>> by default, be installed in the user's home folder.  So, you can use
>> exactly
>> the commands you mention above to install bioconductor and then, if
>> further
>> packages are necessary, the user can use biocLite() (and I would HIGHLY
>> RECOMMEND using biocLite() for all R package installation, if possible) to
>> install those other packages and R will "do the right thing" and install
>> them into the home directory.
>>
>> Sean
>>
>>        [[alternative HTML version deleted]]
>>
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