From ripley at stats.ox.ac.uk  Tue Oct 16 09:33:52 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 16 Oct 2007 08:33:52 +0100 (BST)
Subject: [Rd] package Geneland / Rgui under windows
In-Reply-To: <471373E9.90004@mail.nih.gov>
References: <37036.129.240.88.50.1192454949.squirrel@webmail.chalmers.se>
	<471373E9.90004@mail.nih.gov>
Message-ID: <Pine.LNX.4.64.0710160813060.19726@gannet.stats.ox.ac.uk>

On Mon, 15 Oct 2007, Sean Davis wrote:

> Gilles GUILLOT wrote:
>> Hi,
>> I experienced a problem with the package Geneland under R 2.6.0
>> with  windows XP professional.
>>
>> The commands below should simulate a dataset,
>> then make an MCMC simulation stored in tempdir().
>>
>> It works with R 2.5.1 (both GUI and command line)
>> It works with the command line of R 2.6.0
>> but not with the R GUI of 2.6.0: no output file is created in tempdir()
>> and R remains frozen.
>> I reported it as a bug
>> (PR#9964)  but did not get any feed back.
>
> I think the general rule-of-thumb is to contact the package author for
> problems with individual packages.  Many package authors read this list,
> but there are probably some that do not.  Sometimes problems with
> individual packages are actually bugs in R, but I would say that this is
> not usually the case.

Overwhelmingly so: I don't believe we know of any in the transition to 
2.6.0 that were not bugs in the packages concerned.

> However, the package author is probably the best person to make this 
> judgment.

In this case 'Gilles GUILLOT' completely failed to say that he is the 
maintainer, including in his bug report (and he is using a different email 
address from the one in the package: I only know this is the same person 
from a private reply).

I think he needs to run R under a debugger and find out what 'freezes' 
means.  If as I suspect this is in the compiled code of the package, it 
is not a bug in R.

Windows binaries for R 2.6.0 are built with a different compiler than 
3.4.5, and this has triggered a few package problems (note, not problems 
in R but in the packages concerned):

- a couple of packages infinite loop because the calculations are done in 
extended precision registers and so do not terminate, something we have 
had to work around for LAPACK, for example.

- I think three packages infinite-loop because they write outside array 
bounds.  In one case it always did, but used to get away with it.

None of these explain a Rgui/Rterm difference, if that is what is meant 
here (R has a 'command line' in both, and Rterm is a 'console application' 
in Windows-speak).  The main possible difference relates to I/O, and I see 
that Geneland uses Fortran I/O.  Fortran I/O to '*' (or units 5/6) is 
incompatible with a GUI application, and in gcc 4.2.1 Fortran I/O is 
pretty much incompatible with C I/O (initializing has been known to break 
C I/O).  So I suggest that Fortran I/O is removed and replaced by calls to 
realpr etc.

Filing a bug report on issues in your own package is not at all good form: 
R-bugs is not for 'feed back', but there *was* a comment filed on PR#9964.

-- 
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



[Rd] package Geneland / Rgui under windows
Prof Brian Ripley