On Apr 30, 2008, at 9:09 AM, Gill Michelle wrote: > 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
OK, I think I have a temporary solution to the problem. I did some digging on the compilation directory (sw/src/fink.build/pymol- py25-1.0r2-1001/pymol-1.0r2). In the file "Rules.delsci", I changed the following line: PYTHON_EXE = python2.5 to: PYTHON_EXE = /sw/lib/python2.5 and then ran "make -f Makefile.delsci" in the directory and the compilation finished without errors. I then ran "./setup/setup/py" and did a little editing to the resulting pymol startup script ensure the proper python library was again being used. (Let me know if anybody needs this script.) I verified that I was able to run this version of pymol. I believe the omission of the explicit python path causes the system version of python2.5 (which I know is the default version included with Leopard) to be used instead of the fink version. I believe v2.4 is included with Tiger, so this wouldn't have been a problem. The following confirms my suspicion that Leopard's python was being called: ip30097% which python2.5 /usr/bin/python2.5 ip30097% ls -l /usr/bin/python2.5 lrwxr-xr-x 1 root wheel 75 Apr 26 16:46 /usr/bin/python2.5 -> ../../ System/Library/Frameworks/Python.framework/Versions/2.5/bin/python2.5 Perhaps the package could be updated to explicitly reference fink's python? 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
