Running

Q: Why is OSX complaining that it cannot connect to the display?

A: In OSX the error message:

    _tkinter.TclError: this isn't a Tk applicationcouldn't connect to display ":0.0"

probably means that the X server is either not running or appears to be running but has become knackered.  The solution is to start the X server (after stopping it, if it already appears to be running).  The X server application is Applications/Utilities/X11 (in the Finder).

Q: Why is OSX complaining about the $DISPLAY environment variable?

A: In OSX the error message:

    _tkinter.TclError: no display name and no $DISPLAY environment variable

probably means that the DISPLAY environment variable has not been set.  In bash this should be set by:

    export DISPLAY=:0.0

(possibly placed in .bashrc) and in csh/tcsh (and similar variants) this should be set by:

    setenv DISPLAY :0.0

(possibly placed in .cshrc).

Q: Why is the text of the menus coming out as unreadable gibberish?

A: It probably means that the font that Analysis is trying to use is not available on the computer and some messed up variant is being substituted instead.  This is not easy to fix in Analysis because it is impossible to read the menus, so unless you remember which menu is which, you will have a hard time changing the font to something else.

The best way to deal with this is to change the font in the relevant XML file.  Check for the two files:

    PROJECT_DIR/ccpnmr/AnalysisProfile/*.xml

and

    ~/.ccpn/data/ccpnmr/AnalysisProfile/*.xml

Here PROJECT_DIR is the project directory, ~ is the user's home directory, and the * represents some long semi-meaningful string which depends on the project, the user and the time the file was created.

One or other of these files might not exist, but check whichever does.  In the file check for lines like:

  <ANAP.AnalysisProfile.font>

    <IMPL.Line>Lucida 12</IMPL.Line>

  </ANAP.AnalysisProfile.font>

These lines might not occur but if they do then the font that is named is likely to be the font that is causing the trouble.  Try changing it to "Helvetica 12", then save the file.

Start up Analysis again and hopefully the problem will be solved.

Q: What do I do if Analysis will not start up because of a coding error?

A: This probably means that something has been uploaded to the update server that has fundamentally broken Analysis.  Notify the Analysis developers (e.g. via the JISCMAIL mailing list at http://www.jiscmail.ac.uk/lists/CCPNMR.html).  When they have fixed the problem run the script ccpnmr/bin/updateAll and it should then allow you to start up Analysis again.

Q: What can I do to speed Analysis up?

A: Analysis caches a certain amount of spectrum data and contours. But with large data sets this caching starts to be ineffective, as it keeps getting refreshed.  By default Analysis works with 128 Megawords (so 512 megabytes) as the limit of the amount of memory allocated for the cache.  If your computer has more memory then it's worth increasing the cache size.  But note that this is the memory just of the cache, and Analysis also uses lots of memory for Python objects.  To set the cache size to be something other than the default, you use the optional -m flag when starting up Analysis.  For example, to set the cache to be 256 Megawords (so 1 Gb) do:

    analysis -m 256

Q: What do the following error messages and warnings say and how can I go further when they occur?

First loading attempt failed - compatibility problem? / Some files unfindable - has project moved? In either case followed by "Re-trying, skipping cached TopObjects:"

As long as the project loads, all should actually be OK. For efficiency the Project XML file contains small shell objects for all known TopObjects. When files are moved or the project is upgraded the cached information may point to files that can no longer can be found. The program will then erase the cache and look directly at the available files. If there are no other error messages, everything is fine and you can ignore this message. If other things go wrong, you should report this in a bug report, as it might help pinpoint the problem.

Cannot downgrade to older version: “memops.general.Implementation.ApiError: Could not import memops.format.compatibility.downgrade.v_2_3_b3 Forwards compatibility from 2.1.b3 to 2.0.b3 missing. Trying to load new-version data with old-version code?”

This happens if you are trying to read a file that is produced by a newer version of the CCPN than your program. In the example above your program version is 2.0.b3 and your data file version is 2.1.b3. Note that these are NOT the same as the Analysis version you see when you open the program. The common reasons are:

Project Not Valid, cannot load: “File "/home/rhf22/cvsroots/stable/all/python/memops/xml/Implementation.py", line 4391, in loadFromStream for event, elem in ElementTree.iterparse(stream, events=("start", "end")): File "<string>", line 68, in __iter__SyntaxError: no element found: line 271278, column 0”

1. This can happen if your computer crashes or the disk is full mid-save. Can also occur

    if a project was saved inside / on top of an existing project; two

    projects sharing same files.

2. Consider trying to load from a backup.

3. Usually best to send to the CCPN developers (email the JISC list:(CCPNMR@JISCMAIL.AC.UK) rather than to fix by                yourself. Editing XML files is “dangerous” unless you know what you're doing.

Key already in use: "Read topObj with guid conflicts with existing topObj: <topObjectGuid>"

1. This can happen if your computer crashes or the disk is full mid-save. Can also occur

  if a project was saved inside / on top of an existing project; two

  projects sharing same files.

2. Consider trying to load from a backup.

3. Usually best to send to the CCPN developers rather than to fix by yourself. Editing XML files is “dangerous” unless you know what you're doing.

Fitting Error

Tcl/OpenGL errors

If there is a long error trace send this to CCPN developers (email the JISC list: (CCPNMR@JISCMAIL.AC.UK), otherwise restart Analysis and try again. Some failures are sporadic and only indirectly related to CCPN, so they may not happen again.