Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Sun 09 Apr 2006 - 21:24:25 GMT

Prof Brian Ripley <ripley@stats.ox.ac.uk> writes:

> >> Source directory: .
> >> Installation directory: /usr/local
> >>
> >> C compiler: gcc -g -O2 -std=gnu99
> >> Fortran 77 compiler: g77 -g -O2
> >>
> >> C++ compiler: g++ -g -O2
> >> Fortran 90/95 compiler: g77 -g -O2
> >>
> >> Interfaces supported: X11, tcltk
> >> External libraries: readline, BLAS(ATLAS)
> >> Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
> >> Options enabled: R profiling
> >>
> >> Recommended packages: yes
> >>
> >> 44 (0) $ make
> >> [...]
> >>
> >> 45 (0) $ make check
> >> [...]
> >> running code in 'd-p-q-r-tests.R' ... OK
> >> comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ...777,778d776
> >> < Warning message:
> >> < full precision was not achieved in 'qbeta'
> >> make[3]: *** [d-p-q-r-tests.Rout] Error 1
> >> [...]
> >>
> >> 46 (0) $ diff tests/d-p-q-r-tests.Rout.{save,fail}
> >> 3c3
> >> < Version 2.3.0 alpha (2006-04-03 r37628)
> >> ---
> >>> Version 2.3.0 alpha (2006-04-08 r37675)
> >> 791a792,793
> >>> Warning message:
> >>> full precision was not achieved in 'qbeta'
> >> 1073c1075
> >> < Time elapsed: 2.53 0.03 2.55 0 0
> >> ---
> >>> Time elapsed: 4.939 0.024 4.967 0 0
> >>
> >> The (hopefully) interesting part of tests/d-p-q-r-tests.Rout.fail:
> >>
> >>> ## Check q*(p* ( log ), log) = identity
> >>> All.eq(Rbeta, qbeta (log(Pbeta), shape1 = .8, shape2 = 2, log=TRUE))
> >> [1] TRUE
> >> Warning message:
> >> full precision was not achieved in 'qbeta'
> >>
> >> Please let me know if there is more I can provide to help trace this!

> >
> > I suspect that this is related to recent changes in the zero-finder,
> > and that it is relatively benign. (If it is the effect that I'm
> > thinking of, then the warning is spurious, and it is mainly a matter
> > of whether we want to try to get rid of the warning or update the
> > .Rout.save file.)
> 
> I am not seeing it on my platforms (FC3 x86_64 and i686 Linux with gcc
> 3.4.5 and 4.1.0, i386 Windows and Solaris, with various compilers) and
> the zero-finder changes postdate r37675 (and qbeta does not use it). I
> think several other people are testing i686 Debian, including the
> daiuly CRAN package checks ....
> 
> I suspect it is a real (and long-standing) problem of loss of accuracy
> (2.2.1 did a check but did not report the results: it seems to be a
> convergence failure looking at qbeta.c).  What compiler version is
> this?
> 
> ATLAS is not involved.  You'll need to trace qbeta.c.

I don't see it with a current version either. What happens if you reduce the optimization level? (I've tried both "-g" and -g "-O3"). Is that -std=gnu99 bit necessary?

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)                  FAX: (+45) 35327907

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Received on Mon Apr 10 07:51:53 2006

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