On Apr 30, 2008, at 8:21 AM, Alexander Hansen wrote: > Gill Michelle wrote: >> Hello Finkers, >> >> I am having trouble compiling pymol-py25 on a fresh install of OS X >> Leopard. I have also tried to compile the most recent version of >> pymol (1.0r3) from SVN by hand against the required dependencies >> (from fink) and get the same error. >> >> Before the reinstall, I was running the same version of Leopard, >> though I had upgraded from Tiger rather than doing a fresh install. >> Under this old setup, I was able to successfully compile the same >> SVN version of pymol (using an identical rules makefile). A while >> back, I was also able to successfully install a version of pymol >> from fink, though I am not sure of the exact version number. >> >> Here is the error I am getting (the full install log was too big to >> post, but I can send it in a reply if needed): >> <snip> >> ././ExtensionClass.c:2876: warning: initialization from >> incompatible pointer type >> ././ExtensionClass.c:2988: warning: initialization from >> incompatible pointer type >> ././ExtensionClass.c: In function 'CopyMethods': >> ././ExtensionClass.c:3267: warning: passing argument 2 of >> 'PyDict_Next' from incompatible pointer type >> ./ExtensionClass.o -o ./ExtensionClass.so >> make[2]: execvp: ./ExtensionClass.o: Permission denied >> make[2]: *** [ExtensionClass.so] Error 127 >> make[1]: *** [make-modules] Error 2 >> make: *** [unix] Error 2 >> ### execution of make failed, exit code 2 >> >> >> Relevant info: >> Package manager version: 0.28.1 >> Distribution version: selfupdate-rsync Sun Apr 27 07:46:33 2008, >> 10.5, i386 >> Mac OS X version: 10.5.2, Intel (fresh install, not upgrade) >> Leopard Xcode >> i686-apple-darwin9 >> gcc version 4.0.1 >> make version 3.81 >> >> Fink sources: >> deb file:/sw/fink local main >> deb file:/sw/fink stable main crypto >> deb file:/sw/fink unstable main crypto >> deb http://sage.ucsc.edu/fink_intel_10.5_only stable main crypto >> deb http://sage.ucsc.edu/fink_intel_10.5_only unstable main crypto >> deb http://sage.ucsc.edu/fink_intel_10.5_only local main >> >> Please let me know if you need any other information. >> >> Thanks, >> Michelle Gill > Using my special moderator powers, I'll grab a snippet from the > full output for a bit more context. > > cd modules;make > gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include/ > python2.5 -I/sw/include/python2.5 -I/sw/include -c ././ > ExtensionClass.c -o ./ExtensionClass.o > ././ExtensionClass.c: In function 'initializeBaseExtensionClass': > ././ExtensionClass.c:1542: warning: passing argument 2 of > 'PyMapping_HasKeyString' discards qualifiers from pointer target type > ././ExtensionClass.c:1553: warning: passing argument 3 of > 'newCMethod' discards qualifiers from pointer target type > ././ExtensionClass.c:1553: warning: passing argument 6 of > 'newCMethod' discards qualifiers from pointer target type > ././ExtensionClass.c:1561: warning: passing argument 3 of > 'newCMethod' discards qualifiers from pointer target type > ././ExtensionClass.c:1561: warning: passing argument 6 of > 'newCMethod' discards qualifiers from pointer target type > ././ExtensionClass.c:1570: warning: passing argument 2 of > 'PyMapping_SetItemString' discards qualifiers from pointer target type > ././ExtensionClass.c:1580: warning: passing argument 2 of > 'PyMapping_GetItemString' discards qualifiers from pointer target type > ././ExtensionClass.c:1583: warning: assignment discards qualifiers > from pointer target type > ././ExtensionClass.c: At top level: > ././ExtensionClass.c:2870: warning: initialization from incompatible > pointer type > ././ExtensionClass.c:2872: warning: 'intargfunc' is deprecated > ././ExtensionClass.c:2872: warning: initialization from incompatible > pointer type > ././ExtensionClass.c:2873: warning: 'intargfunc' is deprecated > ././ExtensionClass.c:2873: warning: initialization from incompatible > pointer type > ././ExtensionClass.c:2874: warning: 'intintargfunc' is deprecated > ././ExtensionClass.c:2874: warning: initialization from incompatible > pointer type > ././ExtensionClass.c:2875: warning: initialization from incompatible > pointer type > ././ExtensionClass.c:2876: warning: initialization from incompatible > pointer type > ././ExtensionClass.c:2988: warning: initialization from incompatible > pointer type > ././ExtensionClass.c: In function 'CopyMethods': > ././ExtensionClass.c:3267: warning: passing argument 2 of > 'PyDict_Next' from incompatible pointer type > ./ExtensionClass.o -o ./ExtensionClass.so > make[2]: execvp: ./ExtensionClass.o: Permission denied > > It looks to me like there's some kind of compiler command missing on > that last line
Thanks, Alexander. It looks like I was a bit too aggressive with the trimming of my post. No coffee yet. *blush* As I mentioned, I was using an "upgraded" Leopard and, prior to upgrading, had installed the Tiger developer tools (including gcc) because I was running fink. I also installed the developer tools under Leoopard, but it's possible the old version remained installed and was being used even after I upgraded. If the compiler settings were different (I don't know), then this could explain the issue. I suspect a system setting (like a compiler setting or flag) could be the issue since I was able to successfully compile the SVN version under my previous system. As I mentioned, I get the same execvp error when compiling this EXACT same source code under my "new and improved" Leopard. Here is some info about my gcc compiler (output from gcc -v): Using built-in specs. Target: i686-apple-darwin9 Configured with: /var/tmp/gcc/gcc-5465~16/src/configure --disable- checking -enable-werror --prefix=/usr --mandir=/share/man --enable- languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/ $/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/ lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic -- host=i686-apple-darwin9 --target=i686-apple-darwin9 Thread model: posix gcc version 4.0.1 (Apple Inc. build 5465) Again, let me know if I can provide more info. I no longer have access to Tiger, but perhaps someone else can provide the necessary info here. Regards, Michelle Gill ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Fink-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/fink-users
