Hi Wayne,
I'm getting the same error as Claudia. I update from version 2.0.5 to
2.0.7. My version of 2.0.5 was NOT pre-compiled.
I've tried to recompile the c code but I have two issues.
By the way, there are two directories in $CCPN_TOP_DIR, ccpnmr2.0 and
ccpnmr2.0_2.0.5. I assume the former is version 2.0.7 and the later
is the old version.
If I navigate to $CCPN_TOP_DIR/c and type make clean I get the following:
cd memops/global; make clean
rm *.o
cd ccp/structure; make clean
rm *.o
rm: *.o: No such file or directory
make[1]: *** [clean] Error 1
make: *** [structure_clean] Error 2
Which I think is normal.
If I then type make, I get the following:
cd memops/global; make
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC utility.c
cc -c -I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/include/python2.5
-O -DDO_NOT_HAVE_MALLOC -fPIC python_util.c
python_util.c: In function 'valid_py_object':
python_util.c:54: warning: passing argument 1 of 'equal_strings'
discards qualifiers from pointer target type
python_util.c:54: warning: passing argument 2 of 'equal_strings'
discards qualifiers from pointer target type
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC hash_list.c
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC hash_table.c
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC mem_cache.c
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC mutex.c
cc -c -I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/include/python2.5
-O -DDO_NOT_HAVE_MALLOC -fPIC py_mem_cache.c
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC block_file.c
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC shape_file.c
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC int_array.c
cc -c -I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/include/python2.5
-O -DDO_NOT_HAVE_MALLOC -fPIC py_block_file.c
cc -c -I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/include/python2.5
-O -DDO_NOT_HAVE_MALLOC -fPIC py_shape_file.c
cc -L/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/lib
-bundle -bundle_loader /Users/justin/Documents/Programs/Software/an
alysis/ccpnmr/python2.5/bin/python2.5 -o BlockFile.so utility.o
python_util.o hash_list.o hash_table.o mem_cache.o mutex.o
py_mem_cache.o block
_file.o shape_file.o int_array.o py_block_file.o py_shape_file.o
cc -c -DNEED_GLUT_INIT -DGLUT_IN_OWN_DIR
-I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/include/python2.5
-I/usr/X11R6/i
nclude -I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/tcl8.5/include
-I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/tk
8.5/include -I/usr/X11R6/include
-I/System/Library/Frameworks/GLUT.framework/Headers -O
-DDO_NOT_HAVE_MALLOC -fPIC gl_handler.c
In file included from gl_handler.c:62:
/System/Library/Frameworks/GLUT.framework/Headers/glut.h:68:1:
warning: "APIENTRY" redefined
In file included from /usr/X11R6/include/GL/glx.h:45,
from gl_handler.c:56:
/usr/X11R6/include/GL/gl.h:104:1: warning: this is the location of the
previous definition
cc -c -DUSE_GL_TRUE
-I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/include/python2.5
-I/usr/X11R6/include -I/Users/justi
n/Documents/Programs/Software/analysis/ccpnmr/tcl8.5/include
-I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/tk8.5/include
-I/usr/X1
1R6/include -I/System/Library/Frameworks/GLUT.framework/Headers -O
-DDO_NOT_HAVE_MALLOC -fPIC py_gl_handler.c
cc -c -I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/include/python2.5
-I/usr/X11R6/include -I/Users/justin/Documents/Pro
grams/Software/analysis/ccpnmr/tcl8.5/include
-I/Users/justin/Documents/Programs/Software/analysis/ccpnmr/tk8.5/include
-O -DDO_NOT_HAVE_MALLOC
-fPIC py_tk_util.c
cc -c -O -DDO_NOT_HAVE_MALLOC -fPIC w32func.c
cc -L/Users/justin/Documents/Programs/Software/analysis/ccpnmr/python2.5/lib
-bundle -bundle_loader /Users/justin/Documents/Programs/Software/an
alysis/ccpnmr/python2.5/bin/python2.5 -o GlHandler.so -L/usr/X11R6/lib
-L/Users/justin/Documents/Programs/Software/analysis/ccpnmr/tcl8.5/lib
-L
/Users/justin/Documents/Programs/Software/analysis/ccpnmr/tk8.5/lib
-L/usr/X11R6/lib -framework GLUT \
utility.o python_util.o gl_handler.o py_gl_handler.o
py_tk_util.o w32func.o -framework GLUT -lGLU -lGL -ltk8.5 -ltcl8.5
-lX11 -l
Xext -lm
ld: cycle in dylib re-exports with /usr/X11R6/lib/libGL.dylib
collect2: ld returned 1 exit status
make[1]: *** [GlHandler.so] Error 1
make: *** [global] Error 2
By the way, I checked the environment.txt file and it seems to have
the correct paths to all appropriate directories.
Thanks,
Justin
On Thu, May 14, 2009 at 7:42 AM, Wayne Boucher <[log in to unmask]> wrote:
> Hello,
>
> So was the previous version a pre-compiled 2.0.6 Analysis? In 2.0.6 the
> update mechanism was such that even for the pre-compiled versions, when it
> does an update to 2.0.7 it will grab the source code version of that, not a
> pre-compiled version (that changed in 2.0.7). And in many cases, a
> compilation will fail just because you happen not to have some of the
> required (so called) header files. Hopefully there were some messages on
> the screen when this update happened, but they might well have been lost by
> now. If you go into ccpnmr/ccpnmr2.0/c and type "make" you should get those
> error messages. (Well, it's possible there is some other problem, but this
> is the most likely situation.)
>
> To avoid this issue, if you have a pre-compiled 2.0.6 Analysis we would
> recommend instead of using this auto-update mechanism that you download the
> 2.0.7 pre-compiled version from the website:
>
> http://www.ccpn.ac.uk/ccpn/software/downloads-v2
>
> You might want to rename the existing ccpnmr directory before unpacking the
> 2.0.7 file (just in case, but it ought to work).
>
> Wayne
>
> On Thu, 14 May 2009, claudia student wrote:
>
>> Hello,
>>
>> someone in the lab is running Analysis on a Mac and it auto-updated to
>> version 2.0.7 today. When he tried to open it he got the following
>> error message:
>>
>> Last login: Thu Feb 5 09:02:29 on console
>> /Users/bhaumikdave/Desktop/ccpnmr/bin/analysis2.0 ; exit;
>> bhaumik-daves-macbook:~ bhaumikdave$
>> /Users/bhaumikdave/Desktop/ccpnmr/bin/analysis2.0 ; exit;
>> Model read finished. Duration 1.24475502968
>> Model validity check skipped
>> Error, the Analysis module will not work, something is wrong with the C
>> code.
>> Traceback (most recent call last):
>> File
>> "/Users/bhaumikdave/Desktop/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisGui.py",
>> line 81, in <module>
>> from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
>> File
>> "/Users/bhaumikdave/Desktop/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisPopup.py",
>> line 87, in <module>
>> from ccpnmr.analysis.Analysis import Analysis
>> File
>> "/Users/bhaumikdave/Desktop/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/Analysis.py",
>> line 86, in <module>
>> from memops.c.MemCache import MemCache
>> ImportError: No module named MemCache
>>
>> Any suggestions as to how to fix this.
>>
>> Thank you,
>>
>> Claudia
>>
>
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