[BioC] Library loading problem

[Steve Lianoglou]

Hi,

On Sun, Mar 23, 2014 at 1:11 AM, prabhakar ghorpade
<prabhakar_ghorpade at yahoo.co.in> wrote:
> Hello,
>         Thanks for reply. Isn't it possible to download all relevant packages for running particular package at once.

Yes, but it can be a huge pain as you will have to reverse engineer
the entire dependency graph for the packages that you want to use.

For instance, you got an error that you didn't have the "affyio"
package when you tried to load affy (I'm not sure how you got affy to
install this way, but let's forget that for now).

If you go to the page for the "affy" package:

http://bioconductor.org/packages/release/bioc/html/affy.html

You'll see that the "affyio" package is listed in the "Imports"
section for the package, and therefore required to use affy.

Minimally you will need the packages listed in the "Depends" and
"Imports". Most often you'll probably want what is in "Suggests" too,
but it's not strictly necessary.

Once you actually start analyzing data (it looks like you will be
using microarrays for now) you will need to download metadata for the
microarray you are using (which will not be installed by just
installing affy) as well as other things not explicitly listed
(probably the GO.db package and other organism-specific annotation
packages).

You could always bulk-download download all of the packages from the
appropriate version of bioconductor that you are using (hopefully it
is the latest one), and hope that would ease your pain, but many
packages also require functionality from CRAN, which you would miss.

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech