Wayne Boucher wrote:
>Hmmm, that looks like it was trying to start up the old (1.0.12) code.
>Which is not good! But it looks like that directory structure is
>non-standard. So the code should be in ccpnmr/ccpnmr1.0 and when the
>upgrade happens that directory should be renamed as
>ccpnmr/ccpnmr1.0_1.0.12, and the 1.0.13 version then gets to become the
>new ccpnmr/ccpnmr1.0. My guess is that the upgrade script got confused by
>the different directory structure and failed in parts, including that
>symbolic linking.
>
>
>
Hi Wayne
what I have is indeed named a little different. For historical and
organisational reasons I have a main ccpnmr directory and then one
directory per version below it (e.g. 1.0.12 1.0.13 etc) However
CCPNMR_TOP_DIR does correctly point to 1.0.12... is this something that
needs to be fixed? or is it me just being silly ;-)
regards
gary
>More about the symbolic linking. The C code is compiled as shared
>libraries, to give *.so files. This happens in the sub-directories of
>ccpnmr1.0/c. Because of the way Python works with imports (it's a long
>story), in order to get these to be importable into Analyhsis we create
>symbolic links to these shared libraries in ccpnmr1.0/python. There are
>three sub-directories to worry about, as you discovered, i.e. memops, ccp
>and ccpnmr. They each have a directory called c inside which the symbolic
>links live. There is a file called linkSharedObjs in each of those
>directories which can be run (executed) to create the symbolic links,
>should the installation script fail, which it seems to have done for you.
>
>Hope this makes sense.
>
>Wayne
>
>On Wed, 14 Feb 2007, gary thompson wrote:
>
>
>
>>---------- Forwarded message ----------
>>From: gary thompson <[log in to unmask]>
>>Date: 14-Feb-2007 11:56
>>Subject: memcache crash after upgrade a story
>>To: ccpnmr <[log in to unmask]>
>>
>>
>>Dear All
>>I have just done an automatic upgrade from 1.0.12 to 1.0.13 and get
>>the following on startup:
>>
>>Error, the Analysis module will not work, something is wrong with the C code.
>>Traceback (most recent call last):
>> File "/home/garyt/programs/ccpnmr/1.0.12/ccpnmr1.0/python/ccpnmr/analysis/AnalysisGui.py",
>>line 71, in ?
>> from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
>> File "/home/garyt/programs/ccpnmr/1.0.12/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py",
>>line 91, in ?
>> from ccpnmr.analysis.Analysis import Analysis
>> File "/home/garyt/programs/ccpnmr/1.0.12/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py",
>>line 83, in ?
>> from memops.c.MemCache import MemCache
>>ImportError: No module named MemCache
>>
>>this is under ubuntu now I have had a look in
>>ccpnmr1.0/python/memops/c and their is a file linkSharedObjs and
>>running this seems to sort this problem but then I got
>>
>>Error, the Analysis module will not work, something is wrong with the C code.
>>Traceback (most recent call last):
>> File "/home/garyt/programs/ccpnmr/1.0.12/ccpnmr1.0/python/ccpnmr/analysis/AnalysisGui.py",
>>line 71, in ?
>> from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
>> File "/home/garyt/programs/ccpnmr/1.0.12/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py",
>>line 91, in ?
>> from ccpnmr.analysis.Analysis import Analysis
>> File "/home/garyt/programs/ccpnmr/1.0.12/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py",
>>line 85, in ?
>> from ccpnmr.c.ContourFile import ContourFile, StoredContourFile
>>ImportError: No module named ContourFile
>>
>>so i went round and found all the linkSharedObjs scripts and ran them
>>and now everything seems to work ;-)
>>
>>so in ccpnmr1.0/python I ran 'find . -name '*linkS*' -print':
>>
>>./ccp/c/linkSharedObjs
>>./ccpnmr/c/linkSharedObjs
>>./memops/c/linkSharedObjs
>>
>>It seems there is something broken? ;-)
>>
>>regards
>>gary
>>
>>
>>
>
>.
>
>
>
--
-------------------------------------------------------------------
Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: [log in to unmask] Fax +44-113-2331407
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