Visualize stuff on the master branch

[Lars Skjærven]

Looks like there are currently quite a bit of unfinished functions on the the master branch. I think its mainly related to the visualize functionality:

cna:
  function(cij, ...)
cna.dccm:
  function(cij, cutoff.cij, cm, vnames, cluster.method,
           collapse.method, cols, minus.log)

Missing link or links in documentation object 'identify.cna.Rd':
  ‘plot.igraph’ ‘plot.communities’ ‘igraph.plotting’

Codoc mismatches from documentation object 'layout.pdb':
layout.pdb
  Code: function(pdb, membership, renumber = TRUE, k = 3, full = FALSE)
  Docs: function(pdb, membership, renumber = TRUE, k = 3)

Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE
  there is no package called ‘rgl’
Error in visualize.default(pdb$xyz, ele.symb = ele.symb, con, cell, type,  : 
  Please install the rgl package from CRAN
Calls: visualize -> visualize.pdb -> visualize.default
Execution halted

anyone wants to filter this out unless it's ready for release?

[Barry Grant]

Yes, thats a shame. These are indeed old 'visualize' related droppings that were present on the feature-cna branch and now have made there way into master - unfortunately.

Xinqiu and I can look after cleaning these up. Please don't delete the feature-cna branch until we are done cleaning. Have you checked the various atom mass datasets have not been messed up with these?

[Lars Skjærven]

I've gone over the mass related functions. These should now be fine and working properly with the NMA related stuff.

[Xinqiu Yao]

Hi,

I've made a commit to delete these functions. Let me if you have any problem!

[Barry Grant]

Appears to be fixed now - thanks Xinqiu!