On Thu, Nov 6, 2008 at 3:05 PM, Henrik Bengtsson <hb@stat.berkeley.edu>wrote:

> 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.
>

The hit will depend on numerous hardware and computer environment factors,
particularly those which affect the ability to keep the SQLite database in
memory (cached).

Sean



>
> /Henrik
>
> On Thu, Nov 6, 2008 at 12:00 PM, Wolfgang Huber <huber@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@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]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

