Prof Brian Ripley <[EMAIL PROTECTED]> writes:
Any clue whether there is any benefit in using the FC3 versions over the versions that ships with R?
Yes: at least for earlier versions, none. (See the comments in the R-admin manual I quoted yesterday which no one else seems to have read.)
I did know about them. I was being mildly sarcastic and partly
curious.
In principle, having lapack/blas maintained as part of the distributions would be good, especially if they could sort out the (nontrivial) processor-specific tuning issues. Currently, the RPMs of R for both SuSE and Fedora ship with minimal tuning, and you need to compile your own version to take advantage of (say) an ATLAS blas. This is not hard to do, but you lose the niceties of the RPM system with respect to upgrades, dependencies and all that.
In practice, if the distributions also ship minimally tuned libs, and buggy ones too, the point gets rather moot.
Just to draw this particular thread to a close - I gave the FC3 lapack a run - as I'm stubborn and (like Peter) a little curious. The compilation proceeded without hangs, errors or warnings, but make check failed whilst running the examples from base. So looks like everything written in R Admin document holds for at least the current lapack distributed with FC3 (yes, I did read it!), so it looks like relying on distributions for lapack is not going to work just yet...
I provide the output from make check and base-Ex.Rout.fail just for illustration. I am quite happy with my R and the inbuilt lapack and FC3 provided blas - I was using the arrival of a new laptop as an excuse to try out a few things I had avoided previously and have learnt quite a lot in the process.
Thanks for everyone's input.
All the best,
Gav
Output from make check:
....
make[5]: Entering directory `/home/gavin/R/buildLapack/src/library'
>>> Building/Updating help pages for package 'base'
Formats: text html latex example
make[5]: Leaving directory `/home/gavin/R/buildLapack/src/library'
running code in 'base-Ex.R' ...make[4]: *** [base-Ex.Rout] Error 1
make[4]: Leaving directory `/home/gavin/R/buildLapack/tests/Examples'
make[3]: *** [test-Examples-Base] Error 2
make[3]: Leaving directory `/home/gavin/R/buildLapack/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/home/gavin/R/buildLapack/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/home/gavin/R/buildLapack/tests'
make: *** [check-devel] Error 2And from base-Ex.Rout.fail we have:
....
> ### Name: kappa
> ### Title: Estimate the Condition Number
> ### Aliases: kappa kappa.default kappa.lm kappa.qr kappa.tri
> ### Keywords: math
>
> ### ** Examples
>
> kappa(x1 <- cbind(1,1:10))# 15.71
[1] 15.70590
> kappa(x1, exact = TRUE) # 13.68
[1] 13.67903
> kappa(x2 <- cbind(x1,2:11))# high! [x2 is singular!]
[1] 8.351867e+16
>
> hilbert <- function(n) { i <- 1:n; 1 / outer(i - 1, i, "+") }
> sv9 <- svd(h9 <- hilbert(9))$ d
> kappa(h9)# pretty high!
[1] 728289254735
> kappa(h9, exact = TRUE) == max(sv9) / min(sv9)
Error in La.svd(x, nu, nv) : LAPACK routine 'DGEBRD' gave error code -10
Execution halted-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. & ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way [W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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