Re: [Rd] package Geneland / Rgui under windows

From: Prof Brian Ripley <>
Date: Tue, 16 Oct 2007 08:33:52 +0100 (BST)

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):

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,        
Professor of Applied Statistics,
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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