[Bioc-devel] Packaging a medium/large project

[Julian Gehring]

Hi Ushi,

> Thanks for your reply. I spoke to the original author. He has some
> concerns about wrapping everything into separate functions.

How you design the functions is in the end up to you.  Generally, in an
R package there should not be the need for calling 'source'.


> We are dealing with very large R objects. Is there a way to pass
> those objects by reference to avoid copies and to modify them inside the
> function?
> 
> Does R implement CopyOnWrite to avoid copies?

The way that R deals with objects in memory cannot be easily generalized
to my knowledge (at least I have trouble understanding in detail when
data actually gets copied).  Basic R functionality has the tendency to
copy data often.  Within Bioconductor, there are several solutions that
focus on a more efficient usage of the resources.  What may be suited
for you depends largely on what kind of data or its representation you
are using.

Best wishes
Julian