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
>
> . . .
>
> 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
>
>
That symlink would be totally unacceptable in a Fink package, and we DO
NOT advocate doing that. Anybody who does voids their warranty for help
with build issues.
Unmotivated upstreams have been relying for a while on the deprecated
/usr/include/X11 -> /usr/X11/include/X11 symlink, which is now gone in
Xquartz, instead of looking explicitly for /usr/X11/include. And
sometimes packages even let you specify the X include path but they
still rely on that symlink.
Depending on the package, even something as simple as adding
/usr/X11/include (since that works on both 10.7 and 10.8) to the
CPPFLAGS may do the job.
--
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/
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