Re: parcellfun test issue on Mac OS 10.8, was Re: problems installing openmpi_ext

[Alexander Hansen]

On 9/22/13 2:33 PM, Alexander Hansen wrote:
> On 9/11/13 9:54 AM, Alexander Hansen wrote:
> > On 9/11/13 9:28 AM, c. wrote:
> > > On 11 Sep 2013, at 17:06, Ben Abbott <address@hidden> wrote:
> > >
> > > > Ok.  That is easily fixed. First from a bash shell ...
> > > >
> > > >     sudo port uninstall octave-bim
> > > >
> > > > Then from macports octave-devel
> > > >
> > > > pkg install -forge bim
> > > > pkg load bim
> > > > parcellfun_example
> > > > Elapsed time is 11.1524 seconds.
> > > > parcellfun: child process 35648 created
> > > > parcellfun: child process 35649 created
> > > > parcellfun: 200/200 jobs done
> > > > parcellfun: waiting for child process 35648 to close
> > > > parcellfun: waiting for child process 35649 to close
> > > > Elapsed time is 5.37539 seconds.
> > > >
> > > > Ben
> > >
> > > Ben,
> > >
> > > Thanks for helping with this!
> > >
> > > Although Francis might be happy
> > > now with a working Octave installed
> > > from MacPorts, it would be great if
> > > we could also help Alexander fix the
> > > problems with the Octave package in Fink.
> > >
> > > c.
> >
> > I'd like that, too. :-)
> >
> > I've got an unresolved bug report on Savannah (#38280) which appears
> > also to be related to file I/O.
> >
> > I've just tried a build where the various *FLAGS variables are set to
> > what Carlo used, but that didn't change the results.  There didn't seem
> > to be substantial differences between his configure setup and Fink's
> > otherwise.  This was still using clang[++] as the C[++] compiler.
> >
> > I'm trying a build using (FSF) g++-4.8 now.
>
> Hi.  I've been a bit busy, but I'm still plugging away at this.  No
> success as of yet.
>
> I've got the following configure options right now:
>
>      config_opts = '--prefix=/sw' '--with-lapack=-L/sw/lib/lapack/3.4.2
> -lreflapack' '--with-blas=-L/sw/lib/lapack/3.4.2 -lrefblas'
> '--with-framework-carbon' '--with-x' '--x-libraries=/usr/X11/lib'
> '--x-includes=/usr/X11/include' '--with-magick=GraphicsMagick'
> '--with-qhull-includedir=/sw/include/libqhull'
> '--host=x86_64-apple-darwin' '--build=x86_64-apple-darwin'
> '--infodir=/sw/share/info' '--mandir=/sw/share/man'
> '--libexecdir=/sw/lib' '--enable-shared' '--enable-dl'
> '--disable-static' '--disable-docs' '--enable-dependency-tracking'
> 'build_alias=x86_64-apple-darwin' 'host_alias=x86_64-apple-darwin'
> 'CC=flag-sort -r gcc' 'CFLAGS=-D_THREAD_SAFE -pipe -O2 -MD -g'
> 'LDFLAGS=-Wl,-dead_strip_dylibs -L/sw/lib' 'CPPFLAGS=-D_THREAD_SAFE
> -I/sw/include' 'CXX=flag-sort -r g++' 'CXXFLAGS=-pipe -O2 -MD -g
> -I/usr/X11/include' 'F77=/sw/bin/gfortran-fsf-4.8' 'FFLAGS=-pipe -O2'
>
> and I've been trying to back out the various patches that I've applied.
>   If anybody's bored, those are visible via
>
> http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.7/stable/main/finkinfo/sci/
>
>
> in the files octave-3.6.4.info and the various octave*.patch files.

A little update:

I tried building Octave-3.6.4 manually with the default tuning, using 
Fink dependencies and the minimum patching that let the build proceed. 
Even with that, I'm still seeing errors with fload from the general 
package, as per 
https://mailman.cae.wisc.edu/pipermail/help-octave/2013-September/060375.html.

I saw some reports that Homebrew and Macports folks are now seeing the 
same thing with parcellfun (general):

http://octave.1599824.n4.nabble.com/parcellfun-pararrayfun-Malloc-Error-tp4658596.html

http://octave.1599824.n4.nabble.com/parcellfun-pararrayfun-Malloc-Error-tp4658596p4658876.html

--
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/