[Bioc-devel] strange behavior on memory usage (fwd)

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Wed Aug 24 03:13:13 CEST 2005

> > should likewise be available without doing anything to the potentially
> > massive datastructures.
> >
> > A couple of other points:
> > 1) I noticed that a pdmapping environment has X and Y as vectors of integers.
> > These are pretty big.  Is it possible to use i2xy and xy2i software to get
> > rid of these completely?  these functions can be put into the environment,
> > and the necessary offsets can be updated whenever a subset is done using
> > a closure construct
> the problem here is nimblegen. its hard to explain, but there is no
> mapping for x,y to index.

ok, so we live with x and y as long as we can.

> > 2) installed package footprints with large .rda structures can be enormous, approaching
> > 1GB.  We can use save(...,compress=TRUE) to reduce the installed footprint
> > and the usage overhead at load time seems quite acceptable.  I got the
> > pdmapping50khind240.rda down from 440MB to 60MB with this method.  I understand
> > that compress=TRUE has no impact on the compressed preinstallation package size.
> > I am concerned about postinstall footprints.
> >
> how much longer does it take to load though? my thinking was that i rather
> have a large object and faster loads.

with this particular example i found only a few seconds clock time added
with compressed image and less CPU time, in one trial.  we need more data before
adopting this as a principle, probably, but the developers should do some
experiments and make a decision for their packages at this time.  a sevenfold
reduction in footprint is a serious consideration for these sizes.

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