[Bioc-devel] parallel package generics

On Tue, Oct 23, 2012 at 12:13 PM, Steve Lianoglou <
mailinglist.honeypot at gmail.com> wrote:

In response to a question from yesterday, I pointed someone to the
ShortRead `srapply` function and I wondered to myself why it had to
necessarily by "burried" in the ShortRead package (aside from it
having a `sr` prefix).

I had thought it might be a good idea to move that (or something like
that) to BiocGenerics (unless implementations aren't allowed there)
but also realized that it would add more dependencies where someone
might not necessarily need them.

But, almost surely, a large majority of the people will be happy to do
some form of ||-ization, so in my mind it's not such an onerous thing
to add -- on the other hand, this large majority is probably enriched
for people who are doing NGS analysis, in which case, keeping it in
ShortRead can make some sense.

Taking one step back, I recall some chatter last week (or two) about
some better ||-ization "primitives" -- something about a pvec doo-dad,
and there being ideas to wrap different types of ||-ization behind an
easy to use interface (I think this was the convo), and then I took a
further step back and often wonder why we just don't bite the bullet
and take advantage of the `foreach` infrastructure that is already out
there -- in which case, I could imagne a "doSGE" package that might
handle the particulars of what Florain is referring to. You could then
configure it externally via some `registerDoSGE(some.config.object)`
and just have the package code happily run it through `foreach(...)
%dopar%` and be done w/ it.

IMHO it is relevant.  I have not looked for other abstractions, and this
one seems
to work.  Florian's objectives might be a good test case for adequacy.

... at least, I thought this is what was being talked about here (and
popped up a week or two ago) -- sorry if I completely missed the mark
...

-steve


On Tue, Oct 23, 2012 at 10:38 AM, Hahne, Florian
<florian.hahne at novartis.com> wrote:

Hi Martin,
I could define the generics in my own package, but that would mean that
those will only be available there, or in the global environment assuming
that I also export them, or in all additional packages that explicitly
import them from my name space. Now there already are a whole bunch of
packages around that all allow for parallelization via a cluster object.
Obviously those all import the parLapply function from the parallel
package. That means that I can't simply supply my own modified cluster
object, because the code that calls parLapply will not know about the
generic in my package, even if it is attached. Ideally parLapply would be
a generic function already in the parallel package. Not sure who needs to
be convinced in order for this to happen, but my gut feeling was that it
could be easier to have the generic in BiocGenerics.
Maybe I am missing something obvious here, but imo there is no way to
overwrite parLapply globally for my own class unless the generic is
imported by everyone who wants to make use of the special method.
Florian
--






On 10/23/12 2:20 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

On 10/17/2012 05:45 AM, Hahne, Florian wrote:

Hi all,
I was wondering whether it would be possible to have proper generics

for

some of the functions in the parallel package, e.g. parLapply and
clusterCall. The reason I am asking is because I want to build an S4
class
that essentially looks like an S3 cluster object but knows how to deal
with the SGE. That way I can abstract away all the overhead regarding
job
submission, job status and reducing the results in the parLapply method
of
that class, and would be able to supply this new cluster object to all
of
my existing functions that can be processed in parallel using a cluster
object as input. I have played around with the BatchJobs package as an
abstraction layer to SGE and that work nicely. As a test case I have
created the necessary generics myself in order to supply my own
SGEcluster
object to a function that normally deals with the "regular" parallel
package S3 cluster objects and everything just worked out of the box,
but
obviously this fails once I am in a name space and my generic is not
found
anymore. Of course what we would really want is some proper abstraction
of
parallelization in R, but for now this seem to be at least a cheap
compromise. Any thoughts on this?

Hi Florian -- we talked about this locally, but I guess we didn't
actually send
any email!

Is there an obstacle to promoting these to generics in your own package?
The
usual motivation for inclusion in BiocGenerics has been to avoid
conflicts
between packages, but I'm not sure whether this is the case (yet)? This
would
also add a dependency fairly deep in the hierarchy.

What do you think?

Martin

Florian

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Steve Lianoglou
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  | Memorial Sloan-Kettering Cancer Center
  | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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