On Jul 10, 11:23 pm, David Philp <[EMAIL PROTECTED]> wrote:
Hi David,
> R does not work inside sage if LD_LIBRARY_PATH includes /sw/lib.
> (Which it ordinarily wouldn't, that was a mistake of mine.) That bug
> is pretty trivial and easily fixed.
Well, it is likely a problem that we do not ship our own libjpeg. We
will do so in the future (Tom Boothby has been poking me to review
that ticket for a while).
> But I found that R is the only component of sage that links to system
> frameworks. (Aside from python.) That seems to be a bit inconsistent
> for sage, i.e. R obviously does not link to Apple frameworks on other
> platforms.
Well, R is still somewhat in flux inside Sage and there have been
people who want Sage to become a framework, too.
> The aqua device is compiled in Mac-sage-R, though my feeling is that
> it wouldn't be a drama to remove it. There is plenty inside the R
> configure script about detecting CoreFoundation, though no simple
> option. I think it would be a good idea to switch off CF as well as
> Aqua.
>
> So the two questions are:
> * would switching off Aqua have any benefit, or inconvenience anyone?
> * would switching off CF be a good idea too?
I do not think it would matter if we turned them off, but other people
might have an opinion there, too. I am already turning off the Aqua
device in 64 bit mode on OSX for R anyway. But R 2.7.1 might have a
fix for those issues.
> D
>
> === BACKGROUND ===
> r.eval('1+1') fails
>
> The fail message includes the following:
> before (last 100 chars): ions/A/Frameworks/ImageIO.framework/Versions/
> A/ImageIO
> Expected in: /sw/lib/libJPEG.dylib
>
> sage -t r.devel/sage-main/sage/interfaces/py fails, or fails to complete
> sage -testall only gave problems with R, suggesting the fault lies
> there.
>
> === FIXES ===
> All of these work:
> * Renaming /sw so that the offending library can't be found.
> * Removing /sw/lib from LD_LIBRARY_PATH
It is generally discouraged to have Fink in $PATH or $LD_LIBRARY_PATH
when building or running Sage - too many thing could and have gone
wrong. In this specific case building our own libjpeg will fix your
problem.
> * Setting OSXFW="--enable-R-framework=no --with-aqua=no" inside R spkg-
> install
We should consider this, but other people should pipe in here before
we are making a decision.
Thanks for the detailed problem report and the solutions - I wish all
issues were that well reported and a potential fix attached :)
Cheers,
Michael
> ==================================
> David J Philp
> Postdoctoral Fellow
> National Centre for Epidemiology and Population Health
> Building 62, cnr Mills Rd & Eggleston Rd
> The Australian National University
> Canberra ACT 0200 Australia
>
> T: +61 2 6125 8260
> F: +61 2 6125 0740
> M: 0423 535 397
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>
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