Re: [Fink-users] cernlib won't install on my new MacBook Air
Hi Jess, sorry for the late reply. I was quite busy and traveling during the last months. On Apr 11, 2008, at 9:31 PM, Jess H. Brewer wrote: I have a brand new MacBook Air with Intel CPU, into which I've been loading up all my favorite linux tools from fink. I do a lot of data analysis using cernlib components (particularly minuit) and so, once I got fink set up (stable and unstable) and ran both # fink selfupdateand # fink update-all, I tried (several times) # fink install cernlib . It built stuff for an hour or so and terminated each time with a huge slew of can't find atom for N_GSYM stabs... messages, ending with the errors shown below (in admittedly excessive detail). I have tried to find some reference to similar problems in FAQ to no avail, and fink-beginners doesn't seem appropriate for this, so I'm appealing to wiser heads. I apologize for any gaffes or breahes of protocol or etiquette; please instruct me! -- Jess Brewer PS: I did successfully install pyminuit, so the problem is specific to the fortran cernlib. __ . . . can't find atom for N_GSYM stabs iqceta:G(0,6) in /sw/src/fink.build/ cernlib2005-gfortran-2005-2011/2005/src/cernlib/2005/lib/ libpacklib.a(izchav.o) can't find atom for N_GSYM stabs zkrakc:G(0,8)=u1288cqholk: (0,9)[EMAIL PROTECTED];ar(0,4);1;120;(0,10)[EMAIL PROTECTED];r(0,10);0;255;,0,960;iqholk: (0,11)=ar(0,4);0;119;(0,4),0,3840;iqkrak:(0,12)=ar(0,4);0;79;(0,4), 3840,2560;iqcetk:(0,13)=ar(0,4);0;121;(0,4),6400,3904;; in /sw/src/ fink.build/cernlib2005-gfortran-2005-2011/2005/src/cernlib/2005/lib/ libpacklib.a(izchav.o) can't find atom for N_GSYM stabs cqholk:G(0,9) in /sw/src/fink.build/ cernlib2005-gfortran-2005-2011/2005/src/cernlib/2005/lib/ libpacklib.a(izchav.o) can't find atom for N_GSYM stabs iqholk:G(0,11) in /sw/src/ fink.build/cernlib2005-gfortran-2005-2011/2005/src/cernlib/2005/lib/ libpacklib.a(izchav.o) rm -f /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/paw++ install -c paw++ /sw/src/fink.build/cernlib2005- gfortran-2005-2011/2005/src/cernlib/2005/bin/paw++ if [[ i386 == i386 gfortran == gfortran ]] ; then make patchy/Makefile (cd patchy; make install.bin) || exit 1 fi making Makefiles in /patchy... cd /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/;\ if [ -f ../../patchy/4.15/bin/ycompar ] ; then \ ln -s ../../patchy/4.15/bin/ycompar ycompar; \ else \ echo ycompar not linked, not existing;\ fi ycompar not linked, not existing cd /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/;\ if [ -f ../../patchy/4.15/bin/yedit ] ; then \ ln -s ../../patchy/4.15/bin/yedit yedit; \ else \ echo yedit not linked, not existing;\ fi yedit not linked, not existing cd /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/;\ if [ -f ../../patchy/4.15/bin/yfrceta ] ; then \ ln -s ../../patchy/4.15/bin/yfrceta yfrceta; \ else \ echo yfrceta not linked, not existing;\ fi yfrceta not linked, not existing cd /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/;\ if [ -f ../../patchy/4.15/bin/yindex ] ; then \ ln -s ../../patchy/4.15/bin/yindex yindex; \ else \ echo yindex not linked, not existing;\ fi yindex not linked, not existing cd /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/;\ if [ -f ../../patchy/4.15/bin/ylist ] ; then \ ln -s ../../patchy/4.15/bin/ylist ylist; \ else \ echo ylist not linked, not existing;\ fi ylist not linked, not existing cd /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/;\ if [ -f ../../patchy/4.15/bin/ypatchy ] ; then \ ln -s ../../patchy/4.15/bin/ypatchy ypatchy; \ else \ echo ypatchy not linked, not existing;\ fi ypatchy not linked, not existing cd /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/;\ if [ -f ../../patchy/4.15/bin/ysearch ] ; then \ ln -s ../../patchy/4.15/bin/ysearch ysearch; \ else \ echo ysearch not linked, not existing;\ fi ysearch not linked, not existing cd /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/ cernlib/2005/bin/;\ if [ -f ../../patchy/4.15/bin/yshift ] ; then \ ln -s ../../patchy/4.15/bin/yshift yshift; \ else \ echo yshift not linked, not existing;\ fi yshift not linked, not existing cd
Re: [Fink-users] Failed: phase compiling: imagemagick-6.4.0-1001 failed
I'm afraid that Martin Costabel accurately diagnosed your problem in his last message, and that the newest imagemagick-6.4.0-1001 is not compatible with the xquartz version of the X11 library. Nor is there any simple way that I can make it compatible. Your options are to either use the version of imagemagick in the stable tree (fink install imagemagick-6.2.8-1001), or to become a tester for the pangocairo branch, as described in the wiki: http:// wiki.finkproject.org/index.php/Fink:pangocairo_testing The latest imagemagick has not yet made it to the pangocairo branch, but when it does, it should hopefully work for you. -- Dave On Apr 30, 2008, at 5:12 AM, Jerry Fritschle wrote: On Apr 29, 2008, at 11:09 PM, David R. Morrison wrote: Can you please send me the output of fink list cairo ? Thanks in advance. Information about 6743 packages read in 2 seconds. cairo1.4.14-3 Vector graphics library cairo-shlibs 1.4.14-3 Vector graphics library cairomm1 1.4.8-1C++ interface for the cairo library cairomm1-shlibs 1.4.8-1C++ interface for the cairo library gerbv-cairo 2.0.1-10 Gerber (RS-274X) CAM file viewing tool pycairo-py24 1.2.6-1001 Python bindings for the cairo library pycairo-py24-dev 1.2.6-1001 Tools for compiling against pycairo pycairo-py25 1.2.6-1001 Python bindings for the cairo library pycairo-py25-dev 1.2.6-1001 Tools for compiling against pycairo i system-pkgconfig-cairo 1.4.14-1 [virtual pkgconfig package representing cairo] i system-pkgconfig-cairo- 1.4.14-1 [virtual pkgconfig package representing cairo-ft] i system-pkgconfig-cairo- 1.4.14-1 [virtual pkgconfig package representing cairo-pdf] i system-pkgconfig-cairo- 1.4.14-1 [virtual pkgconfig package representing cairo-png] i system-pkgconfig-cairo- 1.4.14-1 [virtual pkgconfig package representing cairo-ps] i system-pkgconfig-cairo- 1.4.14-1 [virtual pkgconfig package representing cairo-svg] i system-pkgconfig-cairo- 1.4.14-1 [virtual pkgconfig package representing cairo-xlib] i system-pkgconfig-cairo- 1.4.14-1 [virtual pkgconfig package representing cairo-xlib-xrender] - Drama is life with the dull bits cut out. -Alfred Hitchcock Jerry Fritschle [EMAIL PROTECTED] - 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
[Fink-users] Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error
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- 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
Re: [Fink-users] Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error
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
Re: [Fink-users] Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error
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 - 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
Re: [Fink-users] cernlib won't install on my new MacBook Air
Remi Mommsen wrote: [] /sw/src/fink.build/cernlib2005-gfortran-2005-2011/2005/src/patchy/ yexpand: line 30: fink-build-HOME.hbAUwGTKoq/nypatchy.cra.yexp: No such file or directory [] Do you know where the path 'fink-build-HOME.hbAUwGTKoq' comes from? Do you have any spaces in the path to the fink build directory? That directory is created by fink as a temporary HOME directory during fink builds, see /sw/lib/perl5/Fink/PkgVersion.pm, line 5835. On Leopard, it is a subdirectory of something like /var/folders/I5/I5XYEUYz2RWfpk+8ZKtEUTI/-Tmp-/ (random name created by the system, corresponding to the environment variable TMPDIR), so the whole path name would be /var/folders/I5/I5XYEUYz2RWfpk+8ZKtEUTI/-Tmp-/fink-build-HOME.hbAUwGTKoq/nypatchy.cra.yexp On Tiger this was simpler: There the directory would simply be created in /tmp/. -- Martin - 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
Re: [Fink-users] Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error
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
Re: [Fink-users] Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error
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:
Re: [Fink-users] Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error
Michael Giffin wrote: Thank you for the suggestion. I tried editing the Rules.delsci, with no joy. i still get the same error: You did that, and then followed Michelle's prescription exactly? You didn't try to do it in Fink, right? ./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 But what's more relevant is which python2.5 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 I assume you mean you're not able to compile pymol manually. Any help is appreciated. On Wed, Apr 30, 2008 at 10:38 AM, Gill Michelle [EMAIL PROTECTED] wrote: snip 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
Re: [Fink-users] Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error
Thanks for the reply, Alexander. On Wed, Apr 30, 2008 at 12:04 PM, Alexander Hansen [EMAIL PROTECTED] wrote: Michael Giffin wrote: Thank you for the suggestion. I tried editing the Rules.delsci, with no joy. i still get the same error: You did that, and then followed Michelle's prescription exactly? You didn't try to do it in Fink, right? that is correct: edit Rules.delsci: PYTHON_EXE = /sw/lib/python2.5 (maybe a dumb question, but this should not be /sw/bin/python2.5? anyway, tried that too, with same result) make with: $ sudo make -f Makefile.delsci fails with 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 But what's more relevant is which python2.5 $ which python2.5 /sw/bin/python2.5 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 I assume you mean you're not able to compile pymol manually. that is correct. if someone could find the source of my boneheadedness, that would be great. - 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
Re: [Fink-users] Failed: phase compiling: imagemagick-6.4.0-1001 failed
Jerry Fritschle wrote: On Apr 29, 2008, at 8:03 PM, Stan Sanderson wrote: Please run fink selfupdate and try again. I have added a BuildConflicts which should address this problem. Thank you Dave- it updated successfully. Not for me (on PPC.) Here is the error I get (hope this snip is enough.) [] coders/svg.c:97:32: error: librsvg/rsvg-cairo.h: No such file or I think this is another gift of the updated X11 that we will have to deal with. The latest xquartz X11 update comes with libcairo and cairo pkgconfig files and even cairo-svg.h, but not rsvg-cairo.h. Thus, even with Fink's cairo package removed, the imagemagick configure script find's X11's cairo, thinks cairo-svg is installed and crashes. On Jerry's compiler line, as on mine here with xquartz-2.2.0 installed, I see the evidence: -I/usr/X11/include/cairo We really need to get the pangocairo-branch out of the door ASAP, and we need to take care of the duplicate libraries in the new xquartz update. Besides freetype2 and fontconfig which we know how to deal with, there is now cairo, and also libpng that will cause trouble. On Jerry's compiler line I also see -I/usr/X11/include/libpng12 which is not there if one compiles on a machine with 10.5.2 X11, but without the latest xquartz update. -- Martin - 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
Re: [Fink-users] Compiling pymol-py25 under fresh install of OS X 10.5.2 fails with execvp error
Michael Giffin wrote: Thanks for the reply, Alexander. On Wed, Apr 30, 2008 at 12:04 PM, Alexander Hansen [EMAIL PROTECTED] wrote: Michael Giffin wrote: Thank you for the suggestion. I tried editing the Rules.delsci, with no joy. i still get the same error: You did that, and then followed Michelle's prescription exactly? You didn't try to do it in Fink, right? that is correct: edit Rules.delsci: PYTHON_EXE = /sw/lib/python2.5 (maybe a dumb question, but this should not be /sw/bin/python2.5? One would think so. anyway, tried that too, with same result) make with: $ sudo make -f Makefile.delsci fails with 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 But what's more relevant is which python2.5 $ which python2.5 /sw/bin/python2.5 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 I assume you mean you're not able to compile pymol manually. that is correct. if someone could find the source of my boneheadedness, that would be great. Just checking to see that we're making an apples-to-apples comparison. I'm not familiar with the build process of this particular package, but I can take a look at this issue on my own system once I can squeeze some room into my schedule. - 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
