Hello:
I've got the similar errors while installing Analysis1.0.15 from scratch
under a freshly installed CentOS 5.0. I have attached the log file with the
installation messages. Also, there is no the linkSharedObjs file inside
memops, ccp and ccpnmr as it is mentioned bellow.
I will appreciate your help.
Thank you,
Vitaliy
On Thu, 15 Feb 2007 11:49:42 +0000, Wayne Boucher <[log in to unmask]>
wrote:
>
>The symbolic linking failing is (probably) a separate issue, I'm not quite
>sure why that is happening. (It might be to do with the non-standard
>directory structure or it might be a problem with the "source" command in
>your Linux. On the latter point, in the next release the "make links"
>command will use "sh" instead of "source", since the former seems to
>be more standard.)
>
>Wayne
>
>On Thu, 15 Feb 2007, Gary S. Thompson wrote:
>
>> 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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