Another option (to get going again) is to backtrack to 2.1.3. So if you
are on a pre-compiled release then there should be a directory
ccpnmr_ccpnmr2.1.3 which is just the 2.1.3 directory renamed. And if you
are on a source code release then there should also be a backup (this time
inside ccpnmr/ but I forget how it's named).
Unfortunately we look set to have a 2.1.5 pretty damn soon (because it
turns out there is a small stupidity in the C code for printing windows),
but I'd like to understand this issue about the BayesPeakSeparator code
before we try and produce a 2.1.5.
Wayne
On Tue, 10 Aug 2010, Wayne Boucher wrote:
> Yes, if you update to 2.1.4 via the menu then you do get the C code coming
> down as well. If this is a pre-compiled release then one of them must be
> broken, so is this for 32-bit or 64-bit pre-compiled for Linux? I tested
> all the releases (I think) so it must be broken in some odd way. Our
> 32-bit computer is kaput right now (sod's law) so I can't easily check
> that, but I can see that the gzipped tar file contains the
> BayesPeakSeparator.so code so in theory that should be ok. And the 64-bit
> release starts up ok for me (at least on the computer that made it!).
>
> First of all can you check that there is a symbolic link in
> ccpnmr/ccpnmr2.1/python/cambridge/c:
>
> BayesPeakSeparator.so ->
> ../../../c/other/cambridge/bayes/BayesPeakSeparator.so
>
> Then check that
> ccpnmr/ccpnmr2.1/c/other/cambridge/bayes/BayesPeakSeparator.so actually
> exists.
>
> Both of these ought to be true. If so, can you add a script called python in
> the ccpnmr/bin directory which contains:
>
> #!/bin/csh
>
> setenv CCPNMR_BIN_DIR "$cwd/`dirname "$0"`"
> setenv CCPNMR_TOP_DIR "`dirname "${CCPNMR_BIN_DIR}"`"
> setenv PYTHONPATH ".:${CCPNMR_TOP_DIR}/ccpnmr2.1/python"
> setenv LD_LIBRARY_PATH
> "/usr/lib64:${CCPNMR_TOP_DIR}/tcl8.5/lib:${CCPNMR_TOP_DIR}/tk8.5/lib:${CCPNMR_TOP_DIR}/tcl8.5/lib/Tix8.4.3"
> setenv TCL_LIBRARY "${CCPNMR_TOP_DIR}/tcl8.5/lib/tcl8.5"
> setenv TK_LIBRARY "${CCPNMR_TOP_DIR}/tk8.5/lib/tk8.5"
> ${CCPNMR_TOP_DIR}/python2.6/bin/python2.6 -O $*
>
> (those setenv statements are one line each but email will mess it up). Make
> "chmod 755 python" (so that script) and then in the ccpnmr directory run:
>
>> bin/python
>>>> from cambridge.c import BayesPeakSeparator
>
> and see if you get a more sane error message.
>
> One other thing, to get this unbroken for now, you can comment out the line:
>
> from cambridge.bayes.PeakSeparatorGui import PeakSeparatorGui
>
> in ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisPopup.py (this will mean
> that the Peak Separator menu item will not work, of course, but should
> unbreak the rest of Analysis).
>
> Wayne
>
> On Tue, 10 Aug 2010, Marco Roeben wrote:
>
>> AWBN (Andrew James Benie) Andrew wrote:
>>> Actually I pretty certain that it does update the c code as well, as the c
>>> code for the bayes peak separator (under c/other/cambridge/bayes) was
>>> installed and compiled (and I've also recompiled that part). The bayes
>>> spearator was something that was added to 2.1.4 and isn't present in
>>> 2.1.3. Andy
>>
>> You are right. Upgrading by the menu command or simply by using 'updateAll'
>> from the bin directory should work. See also the mail from Wayne in reply
>> to
>> my message.
>>
>> I can confirm the described error message and I tried both, upgrading and
>> doing a complete new compilation.
>>
>>
>> best regards
>>
>> Marco
>>
>> --
>> Dipl. Chem. Marco Röben
>> Leibniz-Institut für Molekulare Pharmakologie (FMP)
>> dep.: Solution NMR
>> Robert-Rössle-Str. 10
>> D-13125 Berlin
>> +49-30-94793224 (phone)
>> +49-030-94793169 (fax)
>
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