oops meant to send this to fink-beginners also
---------- Forwarded message ----------
From: aaron bryden <[EMAIL PROTECTED]>
Date: Feb 27, 2007 2:59 PM
Subject: Re: [Fink-beginners] pymol, libpng problems
To: "Daniel E. Macks" <[EMAIL PROTECTED]>
Thanks for your help.
> I just compiled pymol-py24-0.99-4 and don't see any of my initial flag
> suspicions. So here are some pieces of info that could help us nail it
> down:
>
> What specific version of which pymol package are you using? What OS X
> version, what CPU type? Which x11 are you using (Apple's X11, Fink's
> xfree86, or Fink's x.org)?
pymol-py24 .99-1002
OS X version: 10.4.8
cpu type: 2GHz Intel Core Duo
Apple's X11 version = X11 1.1.3 - XFree86 4.4.0
I should add that I am using unstable because pymol is not available for intel
>
> Is this package being compiled on your machine or is it downloaded
> precompiled? If it's being compiled locally, could you tell us the
> command that created that _cmd.so file (it's the one that contains "-o
> modules/pymol/_cmd.so", about 6/7 of the way through the build
> output).
The package is being compiled on my machine. The output of the command
to build _cmd.so is
cc -bundle -bundle_loader /sw/bin/python2.4 -flat_namespace -undefined
suppress -o modules/pymol/_cmd.so */*.o ov/src/*.o -no-cpp-precomp
-Wmissing-prototypes -Wno-long-double -O3 -funroll-loops
-fomit-frame-pointer -ffast-math -I/sw/include
-I/sw/include/python2.4 -I/sw/include/python2.4/Numeric
-I/usr/X11R6/include -D_HAVE_LIBPNG -D_PYMOL_MODULE -D_PYMOL_NUMPY
-D_PYMOL_FINK -L/sw/lib -L/usr/X11R6/lib -lglut -lGL -lGLU -lpng
-lz -lm -lX11 -lXext
>
> Also, the output of these commands:
>
> otool -L /sw/lib/pymol-py24/modules/pymol/_cmd.
otool -L /sw/lib/pymol-py24/modules/pymol/_cmd.so
/sw/lib/pymol-py24/modules/pymol/_cmd.so:
/sw/lib/libfreeglut.3.dylib (compatibility version 12.0.0,
current version 12.0.0)
/usr/X11R6/lib/libGL.1.dylib (compatibility version 1.2.0,
current version 1.2.0)
/usr/X11R6/lib/libGLU.1.dylib (compatibility version 1.3.0,
current version 1.3.0)
/sw/lib/libpng.3.dylib (compatibility version 16.0.0, current
version 16.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current
version 1.2.3)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
current version 88.3.4)
/usr/X11R6/lib/libX11.6.dylib (compatibility version 6.2.0,
current version 6.2.0)
/usr/X11R6/lib/libXext.6.dylib (compatibility version 6.4.0,
current version 6.4.0)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0,
current version 1.0.0)
> otool -L /sw/lib/libpng.3.dylib
otool -L /sw/lib/libpng.3.dylib
/sw/lib/libpng.3.dylib:
/sw/lib/libpng.3.dylib (compatibility version 16.0.0, current
version 16.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current
version 1.2.3)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0,
current version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
current version 88.3.4)
> locate libpng.3.dylib
locate libpng.3.dylib
/Applications/Frozen-Bubble.app/Contents/Frameworks/libpng.3.dylib
/sw/lib/libpng.3.dylib
I then did deleted the application containing the earlier one and
rebuilt the pymol package, unfortunately this did not fix issues.
>
> Do you have any shell environment variables set in your personal shell
> config files?
Yes, but I don't think they should be affecting this. Pasting
.bash_profile anyway
sanitzed .bash_profile as follows:
echo is this working
export FLTK_HOME=/usr/local
alias xterm="xterm -sb"
export CVSROOT=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
export CVS_RSH=ssh
test -r /sw/bin/init.sh && . /sw/bin/init.sh
#export
PATH=/usr/local/bin:/usr/local/sbin:/usr/local/mysql/bin:$PATH:/Users/aaron/deps/feature
export FEATURE_DIR=/Users/aaron/deps/feature
export LOCAL_PDB_DIR=/Users/aaron/deps/structures
export LOCAL_DSSP_DIR=/Users/aaron/deps/structures
export PATH=$PATH
VMDMSMSUSEFILE=1
export VMDMSMSUSEFILE
>
> dan
>
> --
> Daniel Macks
> [EMAIL PROTECTED]
> http://www.netspace.org/~dmacks
>
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> Fink-beginners mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/fink-beginners
>
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Fink-beginners mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/fink-beginners
