Entangled graph TikZ improvement in manual + TikZ update
Merge branch 'entangled'
Code review while adding/adjusting/enhancing java doc.
Fixes #3. List of user defined power functions doesn't need to have
names. If the list has no names, the functions will be referenced as
"func1", "func2", etc. in the output.
Updated NEWS.
Git should ignore logs from Java.
Ignore warning from chol.
More robust function call with named arguments.
Fixes regression introduced with commit acaee497 if f is missing, i.e. has a default value =list().
Fixed typo in calcPower.Rd
We can no longer use the Cholesky decomposition given by R's chol function since it returns "meaningless results" if matrices are not non-negative definite (even for minimal negative eigen values which are essentially zero):

     If ‘pivot = TRUE’ and ‘x’ is not non-negative definite then there
     will be a warning message but a meaningless result will occur.  So
     only use ‘pivot = TRUE’ when ‘x’ is non-negative definite by
     construction.

Therefore we now use the singular value decomposition.
Moved vignettes from gMCP/inst/doc to gMCP/vignettes.
NEWS for version 0.8-4
Ignoring files.
New jar file.
Updated checklist since extended RUnit test would have found the change in chol earlier.
Next version: 0.8-5.
Moving MASS, PolynomF, multcomp and lattice from the "Depends:" field to "Imports:". Therefore imports have to be done in the NAMESPACE, also startGUI and RUnit tests are loading (some of) these packages.
R CMD check finishes but the whole package has still to be checked manually. Now is a good time to write RUnit tests for _every_ function we have in the package.
Further RUnit tests.
Two new TODO items.