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
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