updating nexus files, not sure if needed

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@849 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
new ignore for pdf files.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@850 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
updates to formatting and updates tests to reflect new checks.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@851 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
updates to checkPhylo4Cpp (removed unncessary functions), fixed case of non-rooted tree for node generation, fixed test for NA edge lengths, fixed edge length must be a named vector (even if empty), fixed omission of test on valid ordering.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@852 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
update NAMESPACE with new Rcpp requirements.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phylobase@853 edb9625f-4e0d-4859-8d74-9fd3b1da38cb