On 12/7/12 2:04 PM, Greg Minshall wrote:
> Martin,
>
> thanks for the quick sleuthing. it is very weird. too bad the linker
> (in addition to preferring /opt/X11/lib) doesn't complain about
> duplicate symbols or some such.
>
> here's a bit more mystery (probably my ignorance of fink or R): if i
> build R (either 2.15.0 or 2.15.2) by hand (*), plotting works.
>
> what was the tool/options you used to find the duplicate libraries?
> (i'm afraid i've never really progressed beyond .o files and nm(1).)
Probably "otool -L" on the dylibs.
>
> cheers, Greg
>
> (*) "by hand" means, i download the tar file, untar, cd to the source
> directory, patch it with the r-base215.patch, then manually substitute
> for %p ["/sw"] and %c (from ConfigureParams) in CompileScript from
> r-base215.info, then copy and paste the resulting string into a bash
> shell, and let it run. here's the pasted string:
> ----
> #!/bin/sh -efv
>
> export F77=/sw/bin/gfortran-fsf-4.7
> export FC=/sw/bin/gfortran-fsf-4.7
>
> perl -pi -e "s|vecLib|Accelerate|g" src/modules/lapack/vecLibg95c.c
>
> unset R_HOME
> ./configure --libdir='/sw/lib' --mandir='${prefix}/share/man' \
> --with-blas="-framework vecLib -dylib_file
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib:/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib"
> \
> --with-lapack \
> --with-aqua --enable-R-framework=/sw/Library/Frameworks \
> --with-system-bzlib --with-system-pcre --with-system-zlib \
> --with-x --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib \
> --with-tcl-config=/sw/lib/tclConfig.sh --with-tk-config=/sw/lib/tkConfig.sh
> make
>
If I had to guess, I'd assume your hand build works because it uses
X11's cairo and libpng15 everywhere rather than Fink's, rather than
mixing them (or maybe it even just uses Fink').
You can check that with "otool -L <whatever.dylib>".
--
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/
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