[Rd] make hanging during compile of r-patched/R-devel on Fedora Core 3

Gavin Simpson gavin.simpson at ucl.ac.uk
Wed May 4 17:58:46 CEST 2005

Marc Schwartz wrote:
> On Wed, 2005-05-04 at 13:56 +0100, Gavin Simpson wrote:
>>On a new Dell laptop, with a fresh FC3 installation (with latest updates 
>>applied) I am experiencing make hanging consistently after/during 
>>building grDevices. This happens when using the configure flag 
>>--with-lapack (I have the LAPACK rpm distributed with FC3 installed). 
>>The last two lines of output are:
>>make[5]: Leaving directory 
>>make[4]: Leaving directory 
>>hang here
>>There are no errors or warnings printed to the console.
>>The same thing happens with r-patched. Both source trees were checked 
>>out using subversion.
>>If I remove the configure flag for lapack, r-patches and r devel both 
>>build fine. I'm not sure where to look for error messages or to diagnose 
>>the problem. Has anyone experienced a similar problem? Where should I 
>>look for any errors/logs? Any other suggestions?
> Gavin,
> FWIW, I can duplicate this behavior on my Dell 5150 w/ FC3 using the r-
> patched tarball from 2005-05-03.
> I thought that perhaps this might be related to the use of the nVidia
> proprietary driver, but temporarily going back to the 'nv' driver did
> not resolve the problem.
> Thus, I am unable to provide more information as to the etiology of the
> problem other than to point to some of the references in the r-admin
> manual starting on page 19 regarding linear algebra.
> Perhaps there is a problem with the FC3 LAPACK.
> Best regards,
> Marc Schwartz

Cheers for this Mark,

I had a quick google search for this problem and found a discussion in 
the redhat mailing list archives that discusses the issue and points to 
the following bug:


Which describes the behaviour I am experiencing.

Basically, the LAPACK in FC3 is broken because it was compiled with 
gcc-3.4 and that introduced errors when -O2 optimisations were used to 
compile the rpm. That bug was recently reopened so there may be the 
possibility of the FC3 rpm being updated (the underlying problem has 
been fixed by compiling with lower optimisation).

I'll read more of the r-admin, and see about finding an alternative.

Also, note that lapack has been moved to Fedora Extras from FC4 so 
that's one more thing to remember to add after upgrading!

All the best,


Gavin Simpson                     [T] +44 (0)20 7679 5522
ENSIS Research Fellow             [F] +44 (0)20 7679 7565
ENSIS Ltd. & ECRC                 [E] gavin.simpsonATNOSPAMucl.ac.uk
UCL Department of Geography       [W] http://www.ucl.ac.uk/~ucfagls/cv/
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London.  WC1H 0AP.

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