[BioC] problem regarding runtime of pamr.cv

[James MacDonald]

Hi ALok,

I think you are mistaken. It is very unlikely that it would take R 60 seconds to print a number to stdout. Instead, what is happening is the printing of the numbers is from a for() loop (that is within another for() loop) that also runs the crossvalidation. So what takes the 60 seconds is the fitting of the pam model, not the printing of the fold index.

The authors have hard-coded this printing into their code, so unless you want to make modifications, you won't be able to stop it. 

Best,

Jim



James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662
>>> ALok <foralok at gmail.com> 02/26/09 4:04 PM >>>
Hi All

I am using  pamr.cv to cross validate the NSC classifier,
function runs smoothly with no error,
but unnecessarily it is printing each Fold index as

Fold 1 :123456789101112131415161718192021222324252627282930
Fold 2 :123456789101112131415161718192021222324252627282930

which takes approx *60 sec* for each *10 fold CV *runs with *4GB* memory
while runnning 10K simulations this factor will increase 10K times
i.e approx *1.6 hrs *

i have to do *10,000* iteration for each 10 fold CV for several datasets
and in each run it takes more than *15 hrs* just to print the Fold index ,
which is not needed by  any user in any case .

My question is that
Is there any way to stop printing Fold index on screen , so that simulation
time can be reduced


Thanks in advance

Regards
ALok

-- 
Ph.D scholar
Centre of Computational Biology and Bioinformatics
School of Information Technology
JNU New Delhi

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