[BioC] Installing beadarray

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Thu Nov 1 18:42:30 CET 2007

The space saving only really pops up when you do a
because that installs a "group" of packages, some of which you might  
not need. biocLite("SOMEPACKAGE") only installs what you need.

In your case everything went haywire because the packages you need  
are dependencies of dependencies. biocLite checks this, but since you  
just do "beadarray", biocLite just checks whether (pseudocode)
are installed - which they are. It never checks

If you had done this using biocLite from the beginning, you would not  
have had this problem. Having said that, perhaps the time is ripe to  
look into this second layer dependency issue.


On Nov 1, 2007, at 10:06 AM, Krys Kelly wrote:

> Dear Joern, Sean
> I did
>> biocLite("beadarray", dependencies=TRUE)
> As suggested by Joern, and lots of things got installed.
> But then I got:
>> library(beadarray)
> Loading required package: geneplotter
> Loading required package: annotate
> Loading required package: AnnotationDbi
> Error: package 'RSQLite' required by 'AnnotationDbi' could not be  
> found
> So I did:
>> biocLite("RSQLite")
> and it all seems to be OK now.
> I guess I liked installing packages and their dependencies myself  
> and never
> had a problem before, but I'll do as you suggest from now on to  
> save the
> headaches.
> Thanks
> Krys
> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent: 01 November 2007 16:57
> To: Krys Kelly
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Installing beadarray
> Krys Kelly wrote:
>> Hello
>> I have just installed R 2.6.0. To save space, I usually install  
>> packages
>> individually rather than using biocLite().  I installed beadarray and
> then,
>> when I typed library(beadarray), I got:
> Hi, Krys.
> You'll ALWAYS want to use biocLite.  It saves quite a few  
> headaches, in
> the end.  In addition to what you have done so far, you will need  
> to do:
> biocLite('beadarray')
> That should then install beadarray and the necessary accessory  
> packages,
> including DBI.  If that doesn't do it for you, let us know.
> Sean
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