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It's probably easiest to do the following: cd ccpnmr1.0/c make links That *should* remove the *.so files that are there and then create the symbolic links. But this is assuming that the linkSharedObjs scripts in ccpnmr1.0/python/memops/c, ccpnmr1.0/python/ccp/c and ccpnmr1.0/python/ccpnmr/c are the same as in the release (so do the above). Wayne On Thu, 1 Nov 2007, Murali Vadivelu wrote: > How do we fix that? Fixing the 'makefile' or so? > > Many thanks. > > On 1 Nov 2007, at 10:05, Wayne Boucher wrote: > > > Hello, > > > > We could do, only it should have been a symbolic link in the first > > place! > > (As should all the other *.so files in the Python c directories.) > > And if > > for some reason there are some systems where those symbolic links do > > not > > work then we ought to copy the *.so files over each time. But on > > your Mac > > I'm not sure why they were not symbolic links, Macs can cope with > > those > > perfectly well. > > > > Wayne > > > > On Thu, 1 Nov 2007, Murali Vadivelu wrote: > > > >> Dear Wayne, > >> > >> That fixed the issue. Is it possible for the update mechanism to > >> perform the task of replacing that physical file by a symbolic link, > >> and thus avoiding manual intervention. > >> > >> Many thanks. > >> > >> Best regards, > >> Murali. > >> > >> On 31 Oct 2007, at 20:27, Wayne Boucher wrote: > >> > >>> Hello, > >>> > >>> Someone else just had this problem and the underlying fault in that > >>> case > >>> was that the file ccpnmr1.0/python/memops/c/FitMethod.so was not a > >>> symbolic link to ccpnmr1.0/c/memops/global/FitMethod.so, but a > >>> copy of > >>> some previous version, so the latter was being updated by the update > >>> mechanism but not the former. (We have to have this symbolic link > >>> so that > >>> the Python picks up the C library.) It's possible this is what the > >>> problem below is, rather than a compilation issue. > >>> > >>> Wayne > >>> > >>> On Wed, 31 Oct 2007, Wayne Boucher wrote: > >>> > >>>> Hello, > >>>> > >>>> I think something must be going wrong with the update mechanism, > >>>> but I > >>>> don't know what. The function runFit was added recently, and I > >>>> just > >>>> checked and it is on the update server, so it should have been > >>>> installed > >>>> with your latest update, and it should have compiled. My guess > >>>> right now > >>>> is that it didn't compile for some reason. So first of all, let's > >>>> check > >>>> that runFit is there: > >>>> > >>>> cd /sw/lib/python2.5/site-packages/ccpnmr/ccpnmr1.0/c/memops/global > >>>> grep runFit py_fit.c > >>>> > >>>> And see if that gets any hits. If it's not there then somehow > >>>> py_fit.c > >>>> has not been downloaded. If it is there then my guess is that it's > >>>> not > >>>> being compiled. To do the latter do: > >>>> > >>>> cd /sw/lib/python2.5/site-packages/ccpnmr/ccpnmr1.0/c > >>>> make > >>>> > >>>> And then try again. > >>>> > >>>> Wayne > >>>> > >>>> On Wed, 31 Oct 2007, Murali Vadivelu wrote: > >>>> > >>>>> Dear Dan, > >>>>> > >>>>> I used the patch and the Fink package built properly. I was able > >>>>> to > >>>>> install and run the package. However, once I updated it, in > >>>>> spite of > >>>>> the proper compilation of the updated C code, I get the following > >>>>> error: > >>>>> Error, the DataAnalysisBasic module will not work, something is > >>>>> wrong > >>>>> with the C code. > >>>>> Traceback (most recent call last): > >>>>> File "/sw/lib/python2.5/site-packages/ccpnmr/ccpnmr1.0/python/ > >>>>> ccpnmr/analysis/AnalysisGui.py", line 72, in <module> > >>>>> from ccpnmr.analysis.AnalysisPopup import AnalysisPopup > >>>>> File "/sw/lib/python2.5/site-packages/ccpnmr/ccpnmr1.0/python/ > >>>>> ccpnmr/analysis/AnalysisPopup.py", line 103, in <module> > >>>>> from ccpnmr.analysis.CalcHeteroNoePopup import > >>>>> CalcHeteroNoePopup > >>>>> File "/sw/lib/python2.5/site-packages/ccpnmr/ccpnmr1.0/python/ > >>>>> ccpnmr/analysis/CalcHeteroNoePopup.py", line 69, in <module> > >>>>> from ccpnmr.analysis.DataAnalysisBasic import matchHnoePeaks > >>>>> File "/sw/lib/python2.5/site-packages/ccpnmr/ccpnmr1.0/python/ > >>>>> ccpnmr/analysis/DataAnalysisBasic.py", line 63, in <module> > >>>>> from memops.c.FitMethod import runFit > >>>>> ImportError: cannot import name runFit > >>>>>>>> > >>>>> > >>>>> I tried to manually recompile the C code after a 'make clean', and > >>>>> still get the same error. > >>>>> > >>>>> Many thanks. > >>>>> > >>>>> Best regards, > >>>>> Murali. > >>>>> > >>>>> On 29 Oct 2007, at 19:37, Murali Vadivelu wrote: > >>>>> > >>>>>> There is a new patch file fixing this issue on the tracker - https://sourceforge.net/tracker/index.php?func=detail&aid=1822306&group_id=17203&atid=414256 > >>>>>> > >>>>>> A description of the problem is here - http://wiki.finkproject.org/index.php/Fink:Packaging:Preparing_for_10.5#OpenGL_Bug > >>>>>> > >>>>>> On 29 Oct 2007, at 10:43, Daniel O'Donovan wrote: > >>>>>> > >>>>>>> ** ONLY OF INTEREST TO APPLE USERS ** > >>>>>>> > >>>>>>> Dear all, > >>>>>>> > >>>>>>> We've been testing the new OS X release, leopard (10.5) and it's > >>>>>>> compatibility with CCPN Analysis here in the lab. Thanks to the > >>>>>>> fink people acting sprightly almost everything seems to be > >>>>>>> running > >>>>>>> happily. Unfortunately though, there is an issue with the GL > >>>>>>> libraries which will prevent Analysis from compiling an running. > >>>>>>> We're working on a fix for this which should be out soon, but a > >>>>>>> word of warning to any adventurous users - tread carefully! > >>>>>>> (It is > >>>>>>> possible to run Analysis without these libraries) > >>>>>>> > >>>>>>> Of course, if anyone has already tried compiling with Leopard > >>>>>>> and > >>>>>>> had success please let us know! Many thanks, > >>>>>>> > >>>>>>> Dan > >>>>>>> > >>>>>>> Daniel O'Donovan CCPN PhD Student > >>>>>>> Dept. of Biochemistry > >>>>>>> University of Cambridge > >>>>>>> +44 1223 766 018 > >>>>> > >>>> > >> >