Right, I'll change the release to take this into account. Hopefully this
will work for the other people who've been having trouble as well.
Wayne
On Wed, 19 Nov 2008, Michael Latham wrote:
> I removed the original LD_LIBRARY_PATH from analysis2.0 and updated
> DYLD_LIBRARY_PATH to be
>
> export
> DYLD_LIBRARY_PATH=/Users/michaellatham/PROGRAMS/ccpnmr/tcl8.5/lib:/Users/michaellatham/PROGRAMS/ccpnmr/tk8.5/lib
>
> which removes the /usr/X11R6/lib from the path as you also suggested.
> Analysis2.0 starts without warning and opens a spectrum without any
> complaints.
>
> -Mike
>
> On Wed, Nov 19, 2008 at 9:51 AM, Wayne Boucher <[log in to unmask]>wrote:
>
> > Interesting. I just found the following page via google:
> >
> > [log in to unmask]" target="_blank">http:[log in to unmask]
> >
> > and on the DY issue he claims:
> >
> > "Even though Apple's current docs say they would
> > honour LD_LIBRARY_PATH (probably due to their promise to be more
> > Linux-friendly), in actuality we've never seen it work. Instead
> > we must set DYLD_LIBRARY_PATH for Darwin/OSX systems."
> >
> > On this other, warning, issue, he claims it's some kind of bug (well,
> > Apple might say "feature") and also:
> >
> > "The only way to fix this for real is to remove /usr/X11R6/lib from
> > the DYLD_ path entirely."
> >
> > So it sounds like you can remove the LD_LIBRARY_PATH and also
> > /usr/X11R6/lib from the DYLD_LIBRARY_PATH. Does that then make it work
> > without the warning?
> >
> > Wayne
> >
> > On Wed, 19 Nov 2008, Michael Latham wrote:
> >
> > > Hi guys,
> > >
> > > I duplicated the LD_LIBRARY_PATH line in bin/analysis2.0 and added DY (so
> > > now have a DYLD_LIBRARY_PATH line). When I run analysis2.0 I get the
> > > following out in the terminal along with the rest of the version and
> > > reference information.
> > >
> > > Model read finished. Duration 2.52180099487
> > > Model validity check skipped
> > > dyld: warning DYLD_ setting caused circular dependency in
> > > /usr/X11R6/lib/libGL.1.dylib
> > >
> > > WARNING: Python NumPy module not installed or accessible.
> > > NumPy is required for CcpNmr automatic assignment routines.
> > >
> > > Analysis then starts, and I was able to open a spectrum without any
> > > additional error messages. I am a little confused about the dyld
> > warning.
> > > And is this a Mac thing or something in my setup? Let me know if there
> > is
> > > anything else you want me to try.
> > >
> > > Thanks for the help,
> > > Mike
> > >
> > >
> > > On Wed, Nov 19, 2008 at 8:29 AM, Wayne Boucher <[log in to unmask]
> > >wrote:
> > >
> > > > This seems to be not a problem with configRelease but a problem with
> > the
> > > > environment variable setting. So the scripts set LD_LIBRARY_PATH, not
> > > > DYLD_LIBRARY_PATH. Please edit (for example) bin/analysis and add the
> > DY
> > > > in front, and then try again. (Or duplicate the line and add DY in
> > front
> > > > to one of them.) We've come across another issue related to a png
> > library
> > > > so let us know how you get on (I don't yet know how that's going to be
> > > > resolved).
> > > >
> > > > Wayne
> > > >
> > > > On Wed, 19 Nov 2008, Daniel O'Donovan wrote:
> > > >
> > > > > Nope, sorry, scrub that - after re-reading your email it seems that
> > > > > configRelease.py has failed
> > > > > ( the path in dyld: Library not loaded:
> > /Users/wb104/ccpnmr/tcl8.5/lib/
> > > > > libtcl8.5.dylib should not contain Wayne's directories - the wb104
> > > > > part ).
> > > > >
> > > > > In configRelese.py could you add
> > > > >
> > > > > print newDir, fullfile
> > > > >
> > > > > at line 25 and re-run the script - and then we might be able to tell
> > > > > which paths aren't being corrected!
> > > > >
> > > > > Dan
> > > > >
> > > > > On 19 Nov 2008, at 07:11, Daniel O'Donovan wrote:
> > > > >
> > > > > > Hello Mike,
> > > > > >
> > > > > > I've just tried a fresh install on my mac (previously with no CCPN
> > > > > > code) and I had no problems. To recap, I
> > > > > >
> > > > > > 1. I downloaded analysis2.0.5_tiger.tgz
> > > > > > 2. Untar $ tar zxvf analysis2.0.5_tiger.tgz
> > > > > > 3. Change to the new directory and run
> > > > > > $ python configRelease.py
> > > > > > 4. Check and set my CCPN_TOP_DIR (for bash not csh)
> > > > > > $ export CCPNMR_TOP_DIR=/Users/indiedan/Downloads/ccpnmr
> > > > > > 4. Run bin/analysis
> > > > > >
> > > > > > If that's still not working then we need to look deeper. I note
> > that
> > > > > > your using a .cshrc rather than .bashrc (default for Mac OSX)
> > Wayne;
> > > > > > does the binary release depend on bash?
> > > > > > Your tcl libraries are obviously not being picked up, to fix this
> > we
> > > > > > need to add libtcl8.5.dylib to the dynamic library path. Could you
> > > > > > try running from your terminal
> > > > > >
> > > > > > with cshell
> > > > > > $ setenv DYLD_LIBRARY_PATH /Users/michaellatham/PROGRAMS/ccpnmr/
> > > > > > tcl8.5/lib
> > > > > >
> > > > > > or bash
> > > > > > $ export DYLD_LIBRARY_PATH=/Users/michaellatham/PROGRAMS/ccpnmr/
> > > > > > tcl8.5/lib
> > > > > >
> > > > > > and then to make sure it's correctly set
> > > > > > $ env | grep DYLD_LIBRARY_PATH
> > > > > > and make sure it looks correct, then try re-running analysis.
> > > > > >
> > > > > > I hope that's of some help, maybe Wayne has a clearer view of
> > what's
> > > > > > going wrong!
> > > > > >
> > > > > > Dan
> > > > > >
> > > > > > On 19 Nov 2008, at 00:53, Michael Latham wrote:
> > > > > >
> > > > > >> Hi Wayne,
> > > > > >>
> > > > > >> I ran the configRelease.py script (>python configRelease.py) and
> > > > > >> did not receive any messages. When I try to run analysis2.0, I
> > get
> > > > > >> the following error message.
> > > > > >>
> > > > > >> dyld: Library not loaded: /Users/wb104/ccpnmr/tcl8.5/lib/
> > > > > >> libtcl8.5.dylib
> > > > > >> Referenced from: /Users/michaellatham/PROGRAMS/ccpnmr/python2.5/
> > > > > >> bin/python2.5
> > > > > >> Reason: image not found
> > > > > >> ./PROGRAMS/ccpnmr/bin/analysis2.0: line 8: 11936 Trace/BPT
> > > > > >> trap /Users/michaellatham/PROGRAMS/ccpnmr/python2.5/bin/
> > > > > >> python2.5 -i -O
> > ${CCPNMR_TOP_DIR}/ccpnmr2.0/python/ccpnmr/analysis/
> > > > > >> AnalysisGui.py $1 $2 $3 $4 $5 $6
> > > > > >>
> > > > > >> In my .cshrc, I have CCPNMR_TOP_DIR set to /Users/michaellatham/
> > > > > >> PROGRAMS/ccpnmr.
> > > > > >>
> > > > > >> Thanks for your help,
> > > > > >> Mike
> > > > > >>
> > > > > >> On Tue, Nov 18, 2008 at 4:22 PM, Wayne Boucher <
> > > > [log in to unmask]
> > > > > >> > wrote:
> > > > > >> Ah, Tim convinced me to rename that script from updateHome.py to
> > > > > >> configRelease.py. It's the same script, just a different name.
> > > > > >> (Apparently one of our users here found the first name a bit
> > > > > >> worrying, so
> > > > > >> hopefully this new name is less so.)
> > > > > >>
> > > > > >> One other thing I probably forgot to mention. The Linux
> > pre-compiled
> > > > > >> versions do not have the OpenGL option enabled, but the OSX one
> > does,
> > > > > >> since I know that Mac has a standard way of doing it (but be
> > warned
> > > > > >> that
> > > > > >> sometimes the glut libraries seem not to be installed by default
> > on
> > > > > >> OSX).
> > > > > >>
> > > > > >> Wayne
> > > > > >>
> > > > > >> On Tue, 18 Nov 2008, Michael Latham wrote:
> > > > > >>
> > > > > >> > Hi Wayne,
> > > > > >> >
> > > > > >> > I think I must be missing something here. I downloaded the pre-
> > > > > >> compiled
> > > > > >> > 64-bit Linux and Mac OS 10.4 versions of Analysis v2, for two
> > > > > >> different
> > > > > >> > installations, from the website. After unpacking the tgz file,
> > I
> > > > > >> do not see
> > > > > >> > the updateHome.py script in the ccpnmr/ directory. The contents
> > > > > >> of the
> > > > > >> > ccpnmr/ directory are
> > > > > >> >
> > > > > >> > bin doc tk8.5
> > > > > >> > ccpnmr2.0 python2.5
> > > > > >> > configRelease.py tcl8.5
> > > > > >> >
> > > > > >> > Thanks for your help,
> > > > > >> > Mike
> > > > > >> >
> > > > > >> >
> > > > > >> > On Thu, Nov 6, 2008 at 8:43 AM, Wayne Boucher <
> > > > [log in to unmask]
> > > > > >> >wrote:
> > > > > >> >
> > > > > >> > > Hello,
> > > > > >> > >
> > > > > >> > > I guess I haven't mentioned this (or perhaps I have) but if
> > > > > >> people get in
> > > > > >> > > a pickle with their Python/Tcl/Tk installation (or even if you
> > > > > >> don't),
> > > > > >> > > then we have just this week released a 64-bit Linux pre-
> > > > > >> compiled version
> > > > > >> > > of Analysis v2, available at:
> > > > > >> > >
> > > > > >> > > http://www.ccpn.ac.uk/ccpn/software/downloads-v2
> > > > > >> > >
> > > > > >> > > (just below the source-code-only version). This pre-compiled
> > > > > >> version
> > > > > >> > > includes Python (2.5) and Tcl/Tk (8.5) in it.
> > > > > >> > >
> > > > > >> > > After you unpack the tgz file, you have to run a script,
> > > > > >> updateHome.py, in
> > > > > >> > > the top (ccpnmr) directory in order to change variables from
> > > > > >> pointing at
> > > > > >> > > where the code was compiled to where it now resides. Other
> > > > > >> than this, you
> > > > > >> > > are supposed to be able to use it "out of the box". (Well, it
> > > > > >> assumes you
> > > > > >> > > have the X11 libraries installed.)
> > > > > >> > >
> > > > > >> > > (It does not yet include numpy, which is used in certain
> > > > > >> Analysis v2
> > > > > >> > > funtionality.)
> > > > > >> > >
> > > > > >> > > We're experimenting a bit here, so would be interested in
> > > > > >> hearing how
> > > > > >> > > people get on with this. It was compiled on a SUSE 10
> > computer
> > > > > >> and seemed
> > > > > >> > > to work ok on an Ubuntu 8 machine.
> > > > > >> > >
> > > > > >> > > We will probably offer a Mac variant as well (10.4 and 10.5)
> > at
> > > > > >> some
> > > > > >> > > point.
> > > > > >> > >
> > > > > >> > > Wayne
> > > > > >> > >
> > > > > >> >
> > > > > >>
> > > > > >
> > > > > > Daniel O'Donovan
> > > > > > [log in to unmask]
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > Daniel O'Donovan
> > > > > [log in to unmask]
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
>
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