R CMD check warnings on feature_visualize_dataframe branch

[Barry Grant]

There are currently 5 warnings and 1 note (see below) as well as some function bloat on this branch (e.g. addABC() function is not there or required probably) .

Also there is also some Rd examples that still need to be enclosed in dontrun blocks so rgl windows won't pop up whilst checking and testing.

> $ R CMD check bio3d
* using log directory ‘/Users/barry/tmpwork/Rpackage/GIT/bio3d/bio3d/ver_devel/bio3d.Rcheck’
* using R version 3.1.2 (2014-10-31)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘bio3d/DESCRIPTION’ ... OK
* this is package ‘bio3d’ version ‘2.2-2.9000’
* checking package namespace information ... OK
* checking package dependencies ... OK

<...trim..>

* checking replacement functions ... WARNING
  ‘connectivity<-.pdb’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... OK

* checking R code for possible problems ... NOTE
addPBCBox: no visible global function definition for ‘cell.coords’
visualize.xyz: no visible binding for global variable ‘elements’
visualize.xyz: no visible global function definition for ‘addABC’

<...trim..>

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘addPBCBox’ ‘addXYZ’ ‘connectivity<-’ ‘connectivity<-.pdb’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'connectivity':
connectivity<-.pdb
  Code: function(object, value, ...)
  Docs: function(object, value)
  Argument names in code not in docs:
    ...

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'connectivity':
  ‘connectivity<-’ ‘connectivity<-.pdb’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK

<...trim...>

* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignette without corresponding PDF/HTML:
   ‘bio3d_vignettes.Rmd’

* checking running R code from vignettes ...
   ‘bio3d_vignettes.Rmd’ using ‘UTF-8’ ... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 5 warnings.
NOTE: There was 1 note.

[Barry Grant]

OTHER: Edits for R CMD check on the visualize devel branch

There are still 4 warnings and 1 note related to Julien's functions. There is also some Rd examples that still need to be enclosed in dontrun blocks so rgl windows won't pop up whilst testing.

See Issue #244 on bitbucket for more on remaining warnings.

→ <<cset 77c3066419c2>>

[Idé Julien]

Hey Barry. I will have a look at these warnings today.

[Barry Grant]

Thanks for fixing these Julien.

Side-note: I was wondering if visualize() could have centre=FALSE as a default or is there a reason you prefer to have things non centered? I end up re-setting this in all the view functions.

Note also that the logic of this flag is reverse for me: I think of centering initially as centering the molecule in the display so for me centre=TRUE should have the molecule in the center of the screen but I guess you are thinking of the center of the coordinate frame? What do you think?

[Idé Julien]

At some point I have added the center parameter because the view is not center on the molecule when we display the Cartesian reference (xyz.axes = TRUE). The easiest way to center the view was to simply center the structure at the origin of the Cartesian reference. This is what the function does actually when center = TRUE. The problem is that if you center the structure by default, what you visualize by default doesn't correspond to the original pdb but to a translated version of the pdb. It is not a big problem, I guess. If you prefer, by default we can set center to TRUE but in the future I should find a better way to center the rgl view without translating the structure to the reference.

[Barry Grant]

Thanks for the explanation Julien.

I end up always setting centre=FALSE as we are most often looking at superposed protein molecules and re-centering each time can be misleading in these cases. I don't often use the xyz.axes=TRUE, but I see that this a useful feature.

For me centre=FALSE should be the default and we can perhaps think about a better center=TRUE or axes placement approach for the next version.

These are really cool functions. Thanks again!