Thank you for the suggestion. I tried editing the Rules.delsci, with no joy. i still get the same error:
./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 also, 'which python' returns /sw/bin/python I am also unable to compile from source: layer5/main.c: In function 'DrawBlueLine': layer5/main.c:304: error: 'GL_SHARED_TEXTURE_PALETTE_EXT' undeclared (first use in this function) layer5/main.c:304: error: (Each undeclared identifier is reported only once layer5/main.c:304: error: for each function it appears in.) error: command 'gcc' failed with exit status 1 Any help is appreciated. On Wed, Apr 30, 2008 at 10:38 AM, Gill Michelle <[EMAIL PROTECTED]> wrote: > > 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 > Fink-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/fink-users > ------------------------------------------------------------------------- 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 Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
