On 1/9/13 1:19 AM, Josh Granek wrote:
> biopython-py27 seems to be missing a dependency on flex. Installing
> biopython-py27 ("fink install biopython-py27") failed with the error below
> when I did a clean install of Fink after upgrading to Mountain Lion. This
> was fixed by installing flex ("fink install flex").
>
> Best,
>
> Josh
>
> -------------------------------------
> gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib
> -L/sw/lib -I/sw/include
> build/temp.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/lex.yy.o
> build/temp.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/MMCIFlexmodule.o -lfl -o
> build/lib.macosx-10.8-x86_64-2.7/Bio/PDB/mmCIF/MMCIFlex.so
> ld: library not found for -lfl
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> error: command 'gcc' failed with exit status 1
> ### execution of /sw/bin/python2.7 failed, exit code 1
> ### execution of /tmp/fink.oKCSM failed, exit code 1
> Removing runtime build-lock...
> Removing build-lock package...
> /sw/bin/dpkg-lockwait -r fink-buildlock-biopython-py27-1.59-1
> (Reading database ... 128542 files and directories currently installed.)
> Removing fink-buildlock-biopython-py27-1.59-1 ...
> Failed: phase compiling: biopython-py27-1.59-1 failed
>
Yup.
Apparently Apple used to have a /usr/lib/libfl.a, but it went away on
Mountain Lion (though it's still in the 10.7 SDK). The package
potentially builds differently on 10.7 whether or not Fink's flex is
installed, and it needs to be coerced into using the same flex everywhere.
> . . .
>
> Also include the following system information:
> Package manager version: 0.34.4
> Distribution version: selfupdate-rsync Thu Jan 3 18:57:20 2013, 10.8, x86_64
> Trees: local/main stable/main
> Xcode.app: 4.5.2
> Xcode command-line tools: 4.5.0.0.1.1249367152
> Max. Fink build jobs: 1
> -------------------------------------
>
>
>
> P.S. Another problem I encountered when installing biopython-py27 is the need
> to deal with the fact that X11/Xlib.h is not where it used to be (since
> XQuartz puts it in a different place than Apple X11 had it). Unfortunately I
> didn't think to save the error message. This URL explains the problem and
> gives several solutions
> <http://stackoverflow.com/questions/11465258/xlib-h-not-found-when-building-graphviz-on-mac-os-x-10-8-mountain-lion>.
> Creating a symlink as follows worked for me:
>
> sudo ln -s /opt/X11/include/X11 /usr/local/include/X11
>
>
The error must have been in some other package. I don't see this with
biopython-py* on 10.8.
--
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/
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