From p.dalgaard at biostat.ku.dk  Sun Apr  9 23:24:25 2006
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 09 Apr 2006 23:24:25 +0200
Subject: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta
In-Reply-To: <Pine.LNX.4.64.0604092050370.13534@gannet.stats.ox.ac.uk>
References: <m0wtdyanzp.fsf@bar.nemo-project.org>
	<x2y7yevjsp.fsf@turmalin.kubism.ku.dk>
	<Pine.LNX.4.64.0604092050370.13534@gannet.stats.ox.ac.uk>
Message-ID: <x23bgmmohi.fsf@turmalin.kubism.ku.dk>

Prof Brian Ripley <ripley at 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             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907



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