I puzzled this one out. The culprit is the setup script for
NMPPipe (http://spin.niddk.nih.gov/NMRPipe/) which executes...
if ($?LD_LIBRARY_PATH) then
setenv LD_LIBRARY_PATH /usr/local/NMRPipe/nmrbin.mac/lib:${LD_LIBRARY_PATH}
else
setenv LD_LIBRARY_PATH /usr/local/NMRPipe/nmrbin.mac/lib
endif
if ($?DYLD_LIBRARY_PATH) then
setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:${LD_LIBRARY_PATH}
else
setenv DYLD_LIBRARY_PATH ${LD_LIBRARY_PATH}
endif
Do we have a convention on how to fix this sort of problem?
I would assume that since /usr/local/NMRPipe/nmrbin.mac/lib
contains...
ibBLT24.a libtcl8.4.dylib libxview.dylib tcl.timestamp
libolgx.dylib libtk8.4.dylib save xv.timestamp
that their tcltk is older than the 8.4.19 in fink and their
binaries should tolerate the newer tcltk shared libraries.
So far adding...
if ($?LD_LIBRARY_PATH) then
setenv LD_LIBRARY_PATH /sw/lib:$LD_LIBRARY_PATH
endif
if ($?DYLD_LIBRARY_PATH) then
setenv DYLD_LIBRARY_PATH /sw/lib:${LD_LIBRARY_PATH}
endif
to .cshrc seems to solve the issue in sparky but seems to
break pymol...
Traceback (most recent call last):
File "/sw/lib/pymol-py25/modules/pymol/__init__.py", line 184, in <module>
import pymol
File "/sw/lib/pymol-py25/modules/pymol/__init__.py", line 472, in <module>
import _cmd
ImportError: dlopen(/sw/lib/pymol-py25/modules/pymol/_cmd.so, 2): Symbol not
found: __cg_jpeg_CreateCompress
Referenced from:
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO
Expected in: /sw/lib/libJPEG.dylib
I find this last error rather strange. If I remove the proposed lines above
that reset
LD_LIBRARY_PATH and DYLD_LIBRARY_PATH then execute...
cd /usr/local/NMRPipe/nmrbin.mac/lib
mv libtcl8.4.dylib libtcl8.4.dylib.off
mv libtk8.4.dylib libtk8.4.dylib.off
I find pymol runs fine with .cshrc setting...
LD_LIBRARY_PATH=/usr/local/NMRPipe/nmrbin.mac/lib
DYLD_LIBRARY_PATH=/usr/local/NMRPipe/nmrbin.mac/lib
however if I execute...
setenv LD_LIBRARY_PATH /sw/lib
setenv DYLD_LIBRARY_PATH /sw/lib
pymol fails as above. It seems really weird that LD_LIBRARY_PATH and
DYLD_LIBRARY_PATH
can be set to a path outside of the fink lib directory and pymol runs fine but
when
pointed to /sw/lib, pymol crashes. Does anyone understand this error?
Jack
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