R devel - Mar 2006 - R 2.3.0 (alpha) on FreeBSD 6.1 fails make check-all

Hi Developers,

The alpha, compiles successfully, but it is failing make check-all (on
two seperate machines, both FreeBSD 6.1).

Here is the version string:

platform       i386-unknown-freebsd6.1
arch           i386
os             freebsd6.1
system         i386, freebsd6.1
status         alpha
major          2
minor          3.0
year           2006
month          03
day            27
svn rev        37584
language       R
version.string Version 2.3.0 alpha (2006-03-27 r37584)



Here is the error message from make check-all

comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save'
...706c706
< [1] "Mean scaled  difference: 0.08333333"
---
> [1] TRUE
gmake[3]: *** [d-p-q-r-tests.Rout] Error 1
gmake[3]: Leaving directory `/usr/local/beta/R-alpha/tests'
gmake[2]: *** [test-Specific] Error 2
gmake[2]: Leaving directory `/usr/local/beta/R-alpha/tests'
gmake[1]: *** [test-all-basics] Error 1
gmake[1]: Leaving directory `/usr/local/beta/R-alpha/tests'
gmake: *** [check-all] Error 2




I have checked d-p-q-r-tests.Rout.fail for any obvious problems - I
found some warnings, viz.


> pgamma(1,Inf,scale=Inf) == 0
[1] TRUE
> ## Also pgamma(Inf,Inf) == 1 for which NaN was slightly more
appropriate
> all(is.nan(c(pgamma(Inf,  1,scale=Inf),
+              pgamma(Inf,Inf,scale=Inf))))
[1] TRUE
Warning messages:
1: NaNs produced in: pgamma(q, shape, scale, lower.tail, log.p) 
2: NaNs produced in: pgamma(q, shape, scale, lower.tail, log.p) 



> x0 <- -2 * 10^-c(22,10,7,5)
> stopifnot(pbinom(x0, size = 3, prob = 0.1) == 0,
+           dbinom(x0, 3, 0.1) == 0) # d*() warns about non-integer
Warning messages:
1: non-integer x = -0.000000
2: non-integer x = -0.000020
> ## very small negatives were rounded to 0 in R 2.2.1 and earlier
>

I hope that this is helpful.  Thanks are due to Peter Dalgaard for
guidance.  So, thanks Peter :).

Cheers

Andrew
-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
Email: a.robinson at ms.unimelb.edu.au         http://www.ms.unimelb.edu.au

Thanks for checking.

Please look in d-p-q-r-tests.Rout.fail and see what immediately preceeds 
the line

[1] "Mean scaled  difference: 0.08333333"

Some experimentation suggests it is
> All.eq(Rhyper,	  qhyper   (Phyper, m = 40, n = 30, k = 20))
If so, we have

Rhyper <- scan()
16 11 11 15 11 13 13 12 13 10 10  7 11 14 13  9 14 13 13 11

Phyper	  <- phyper   (Rhyper, m = 40, n = 30, k = 20)

and those have been checked.  So the error would appear to be in

qhyper(Phyper, m = 40, n = 30, k = 20)

and indeed a mean scaled difference of 1/12 is plausible, since the mean 
of Rhyper is 12. So I deduce that your platform has a problem in qhyper, 
but please cross-check.

If so, this is strange as the only recent change to qhyper.c (or things I 
can see it uses such as lfastchoose) is cosmetic.

Can you confirm the diagnosis is correct so far?


On Tue, 28 Mar 2006, Andrew Robinson wrote:
> Hi Developers,
>
> The alpha, compiles successfully, but it is failing make check-all (on
> two seperate machines, both FreeBSD 6.1).
>
> Here is the version string:
>
> platform       i386-unknown-freebsd6.1
> arch           i386
> os             freebsd6.1
> system         i386, freebsd6.1
> status         alpha
> major          2
> minor          3.0
> year           2006
> month          03
> day            27
> svn rev        37584
> language       R
> version.string Version 2.3.0 alpha (2006-03-27 r37584)
>
>
>
> Here is the error message from make check-all
>
> comparing 'd-p-q-r-tests.Rout' to
'./d-p-q-r-tests.Rout.save'
> ...706c706
> < [1] "Mean scaled  difference: 0.08333333"
> ---
>> [1] TRUE
> gmake[3]: *** [d-p-q-r-tests.Rout] Error 1
> gmake[3]: Leaving directory `/usr/local/beta/R-alpha/tests'
> gmake[2]: *** [test-Specific] Error 2
> gmake[2]: Leaving directory `/usr/local/beta/R-alpha/tests'
> gmake[1]: *** [test-all-basics] Error 1
> gmake[1]: Leaving directory `/usr/local/beta/R-alpha/tests'
> gmake: *** [check-all] Error 2
>
>
>
>
> I have checked d-p-q-r-tests.Rout.fail for any obvious problems - I
> found some warnings, viz.
>
>
>
>> pgamma(1,Inf,scale=Inf) == 0
> [1] TRUE
>> ## Also pgamma(Inf,Inf) == 1 for which NaN was slightly more
> appropriate
>> all(is.nan(c(pgamma(Inf,  1,scale=Inf),
> +              pgamma(Inf,Inf,scale=Inf))))
> [1] TRUE
> Warning messages:
> 1: NaNs produced in: pgamma(q, shape, scale, lower.tail, log.p)
> 2: NaNs produced in: pgamma(q, shape, scale, lower.tail, log.p)
>
>
>
>
>> x0 <- -2 * 10^-c(22,10,7,5)
>> stopifnot(pbinom(x0, size = 3, prob = 0.1) == 0,
> +           dbinom(x0, 3, 0.1) == 0) # d*() warns about non-integer
> Warning messages:
> 1: non-integer x = -0.000000
> 2: non-integer x = -0.000020
>> ## very small negatives were rounded to 0 in R 2.2.1 and earlier
>>
>
>
> I hope that this is helpful.  Thanks are due to Peter Dalgaard for
> guidance.  So, thanks Peter :).
>
> Cheers
>
> Andrew
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

>>>>> "Andrew" == Andrew Robinson <A.Robinson at
ms.unimelb.edu.au>
>>>>>     on Tue, 28 Mar 2006 17:55:37 +1000 writes:
    Andrew> Hi Developers,
    Andrew> The alpha, compiles successfully, but it is failing make
check-all (on
    Andrew> two seperate machines, both FreeBSD 6.1).

    Andrew> Here is the version string:

    Andrew> platform       i386-unknown-freebsd6.1
    Andrew> arch           i386
    Andrew> os             freebsd6.1
    Andrew> system         i386, freebsd6.1
    Andrew> status         alpha
    Andrew> major          2
    Andrew> minor          3.0
    Andrew> year           2006
    Andrew> month          03
    Andrew> day            27
    Andrew> svn rev        37584
    Andrew> language       R
    Andrew> version.string Version 2.3.0 alpha (2006-03-27 r37584)



    Andrew> Here is the error message from make check-all

    Andrew> comparing 'd-p-q-r-tests.Rout' to
'./d-p-q-r-tests.Rout.save'
    Andrew> ...706c706
    Andrew> < [1] "Mean scaled  difference: 0.08333333"
    Andrew> ---
    >> [1] TRUE

So what we need to know is the ``neighborhood'' of the line
-----------------------------------------------
[1] "Mean scaled  difference: 0.08333333"
-----------------------------------------------

in your <builddir>/tests/d-p-q-r-tests.Rout

This will show which of the equality tests did not give TRUE.


    Andrew> gmake[3]: *** [d-p-q-r-tests.Rout] Error 1
    Andrew> gmake[3]: Leaving directory `/usr/local/beta/R-alpha/tests'
    Andrew> gmake[2]: *** [test-Specific] Error 2
    Andrew> gmake[2]: Leaving directory `/usr/local/beta/R-alpha/tests'
    Andrew> gmake[1]: *** [test-all-basics] Error 1
    Andrew> gmake[1]: Leaving directory `/usr/local/beta/R-alpha/tests'
    Andrew> gmake: *** [check-all] Error 2


    ......................