This was a release updated via the menu and I'm running it on a 32-bit linux installation. The error was that there was no symbolic link made in ccpnmr/ccpnmr2.1/python/cambridge/c to the .so file. A quick fix with ln -s was all that was needed and now it runs just fine. My guess is that the installation script doesn't make the symbolic link for some reason.
Andy
-----Original Message-----
From: CcpNmr software mailing list [mailto:[log in to unmask]] On Behalf Of Wayne Boucher
Sent: 10 August 2010 10:16
To: [log in to unmask]
Subject: Re: Problem after updating to 2.1.4
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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