[BioC] Network install of packages
hb at stat.berkeley.edu
Thu Nov 6 21:05:10 CET 2008
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
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#
> 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
>>> 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
>>> 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
>>> 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
>>> 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,
>>> that other's can use the packages. I can install all the Bioconductor
>>> packages on a local computer. And the users network home directories
>>> 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
>> 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
>> the commands you mention above to install bioconductor and then, if
>> 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.
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