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 ------------------------------------------------------------------------------ Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much more. Keep your Java skills current with LearnJavaNow - 200+ hours of step-by-step video tutorials by Java experts. SALE $49.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122612 _______________________________________________ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users