[BioC] Network install of packages

Wolfgang Huber huber at ebi.ac.uk
Thu Nov 6 21:00:12 CET 2008

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 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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