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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