Hi Michael, For some reason, I'm not getting the emails from this listserve-- sorry. I'll have to look into that.
For the Fink compilation, I just noticed a typo in my suggestion. PYTHON_EXE should be set to "/sw/bin/python2.5" not "/sw/lib/ python2.5". I bet you can get the fink package to compile manually now. Unfortunately, I do not know how to correct the fink package and the maintainer's email does not seem to be active anymore. Hmm. For the source compilation, which version of the Rules.delsci file are you using? I am able to get a fink compilation (using Rules.delsci- fink as a basis) to work fine. However, when I attempt a framework installation, I get the same error as you report. I don't know the exact cause of it and googling didn't help, unfortunately. Since this is a non-fink compilation we're discussing here, it seems a little off topic for this mailing list. I also don't feel comfortable discussing the source code compilation (by this, I mean outside of fink) because I know Warren offers the incentive products for this exact reason. He has, understandably, also discouraged discussion of pymol compilation steps for other platforms on the pymol mailing list. We do however need to figure out how to get this corrected. Also, it should probably be corrected for all the other python versions of pymol. Hope this helps, Michelle Gill From: Michael Giffin <mijogiffin <at> gmail.com> Subject: Re: Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error Newsgroups: gmane.os.apple.fink.general Date: 2008-04-30 18:21:09 GMT (1 week, 7 hours and 26 minutes ago) 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 <michelle.lynn.gill <at> gmail.com> 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 <at> 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 ------------------------------------------------------------------------- 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. 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