ERROR: plot.enma() example

Issue #75 resolved
Barry Grant created an issue

Running the example in plot.enma.Rd gives the error below.

Also, the internal call to dssp() could lead to an error if dssp is not available (or if a user has an old version - like I do on my laptop). Perhaps we can just proceed with a warning and without sse annotation if this happens?

> example(plot.enma)
Error in plot.window(xlim, ylim, ...) : need finite 'ylim' values

> plot.enma(all.modes, pdbs)
Hit <Return> to see next plot:
Error in plot.window(xlim, ylim, ...) : need finite 'ylim' values
In addition: Warning message:
In if (y == "deformations") yval <- x$deform else yval <- x$fluctuations :
  the condition has length > 1 and only the first element will be used
> plot.enma(all.modes, pdbs=pdbs)
Hit <Return> to see next plot:
Error in plot.window(xlim, ylim, ...) : need finite 'ylim' values

Comments (6)

  1. Barry Grant reporter

    I enclosed this example section in the Rd file with a donturn for now but the issue remains open.

  2. Lars Skjærven

    funny I haven't noticed this before. fixed now by including na.rm=TRUE when setting the ylim.

    For the dssp - isnt this OK?

    > plot.enma(all.modes, pdbs=pdbs)
    Error in dssp(pdb.ref) : Launching external program 'DSSP' failed
      make sure 'dssp' is in your search path
    
  3. Barry Grant reporter

    Will dssp errors such as this result in no plot being produced?

    If so, why not just make the plot without dssp annotation - it should not be the limiting factor here in my view. By the way do you have a recent dssp build for mac. My build process is messed up with the update to OS X 10.9...

  4. Lars Skjærven

    Included a try() on the dssp() function call with some improved messaging.

    > plot.enma(all.modes, pdbs=pdbs)
    Warning message:
    In plot.enma(all.modes, pdbs = pdbs) : SSE cannot be drawn
      Launching external program 'DSSP' failed
    

    I only have OSX 10.8.5 at the moment.

  5. Log in to comment