[Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3

Gavin Simpson gavin.simpson at ucl.ac.uk
Thu May 5 11:58:33 CEST 2005

Peter Dalgaard wrote:
> Prof Brian Ripley <ripley at stats.ox.ac.uk> 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
> 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,


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 2

And 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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