I can confirm that if the Geneland is built under gcc 3.4.5 it works in R 2.6.0 in Rgui (modulo the output which is sent nowhere). So the issue is the Fortran code of the package, and very likely its use of Fortran I/O.
Since this confirms there is not a bug in R 2.6.0, I am filing this on R-bugs and closing the bug report. There is a bug in the package, but that is not a subject for R-bugs. I've put my build up on the CRANextras repository: Uwe might like to remove his so that users get that one until such a time as the I/O issues are resolved. On Tue, 16 Oct 2007, Prof Brian Ripley wrote: > 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, [EMAIL PROTECTED] 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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
