cna branch R CMD check errors

There are lots of R CMD check problems reported on the feature-cna branch that need to be solved before we can merge to master.
E.g:
* installing *source* package ‘bio3d’ ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bio3d)
pico:ver_devel barry$ R CMD check bio3d
* using log directory ‘/Users/barry/tmpwork/Rpackage/GIT/bio3d/ver_devel/bio3d.Rcheck’
* using R version 3.0.2 (2013-09-25)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘bio3d/DESCRIPTION’ ... OK
* this is package ‘bio3d’ version ‘2.0-1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bio3d’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
‘library’ or ‘require’ call not declared from: ‘rgl’
‘library’ or ‘require’ call to ‘igraph’ which was already attached by Depends.
  Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addABC: no visible global function definition for ‘segments3d’
addABC: no visible global function definition for ‘text3d’
addPBCBox: no visible global function definition for ‘segments3d’
addXYZ: no visible global function definition for ‘segments3d’
addXYZ: no visible global function definition for ‘text3d’
visualize.default: no visible global function definition for ‘open3d’
visualize.default: no visible global function definition for ‘par3d’
visualize.default: no visible global function definition for ‘bg3d’
visualize.default: no visible global function definition for ‘rgl.ids’
visualize.default: no visible global function definition for
  ‘segments3d’
visualize.default: no visible global function definition for
  ‘spheres3d’
visualize.default: no visible global function definition for ‘points3d’
visualize.pdb: no visible binding for global variable ‘pdb’
* checking Rd files ... WARNING
atom2ele.Rd: non-ASCII input and no declared encoding
cna.Rd: non-ASCII input and no declared encoding
prepare_Rd: identify.cna.Rd:35-36: Dropping empty section \references
prepare_Rd: layout.pdb.Rd:32-33: Dropping empty section \references
problems found in ‘atom2ele.Rd’, ‘cna.Rd’
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘make.name.tree’ ‘unlist2’
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 'cna':
cna
  Code: function(cij, cutoff.cij = 0.4, cm = NULL, vnames =
                 colnames(cij), cluster.method = "btwn",
                 collapse.method = "max", cols = vmd.colors(),
                 minus.log = TRUE)
  Docs: function(cij, vnames = colnames(cij), cutoff.cij = 0.4, cm =
                 NULL, method = "btwn")
  Argument names in code not in docs:
    cluster.method collapse.method cols minus.log
  Argument names in docs not in code:
    method
  Mismatches in argument names (first 3):
    Position: 2 Code: cutoff.cij Docs: vnames
    Position: 3 Code: cm Docs: cutoff.cij
    Position: 4 Code: vnames Docs: cm

Codoc mismatches from documentation object 'nma.pdbs':
nma.pdbs
  Code: function(pdbs, fit = TRUE, full = FALSE, defa = FALSE, rm.gaps
                 = TRUE, outpath = "pdbs_nma", ...)
  Docs: function(pdbs, fit = TRUE, full = FALSE, rm.gaps = TRUE, defa =
                 FALSE, outpath = "pdbs_nma", ...)
  Mismatches in argument names:
    Position: 4 Code: defa Docs: rm.gaps
    Position: 5 Code: rm.gaps Docs: defa

Codoc mismatches from documentation object 'pca.xyz':
pca.xyz
  Code: function(xyz, subset = rep(TRUE, nrow(as.matrix(xyz))), use.svd
                 = FALSE)
  Docs: function(xyz, subset = rep(TRUE, nrow(as.matrix(xyz)), use.svd
                 = FALSE))
  Argument names in code not in docs:
    use.svd
  Mismatches in argument default values:
    Name: 'subset' Code: rep(TRUE, nrow(as.matrix(xyz))) Docs: rep(TRUE, nrow(as.matrix(xyz)), use.svd = FALSE)

Codoc mismatches from documentation object 'plot.cna':
plot.cna
  Code: function(x, weights = NULL, layout = NULL, col = NULL, ...)
  Docs: function(x, weights = E(x$community.network)$weight * 10,
                 layout = NULL, col = NULL, ...)
  Mismatches in argument default values:
    Name: 'weights' Code: NULL Docs: E(x$community.network)$weight * 10

Codoc mismatches from documentation object 'prune.cna':
prune.cna
  Code: function(x, edges.min = 1, size.min = 1)
  Docs: function(x, edges.min = 1, size.min = 1, cluster.method =
                 "btwn")
  Argument names in docs not in code:
    cluster.method

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'cna'
  ‘method’

Undocumented arguments in documentation object 'print.cna'
  ‘object’

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.
S3 methods shown with full name in documentation object 'identify.cna':
  ‘identify.cna’

S3 methods shown with full name in documentation object 'plot.cna':
  ‘plot.cna’

S3 methods shown with full name in documentation object 'print.cna':
  ‘print.cna’ ‘summary.cna’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
‘library’ or ‘require’ call not declared from: ‘abind’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘bio3d-Ex.R’ failed
The error most likely occurred in:

> ### Name: cmap.filter
> ### Title: Contact Map Consensus Filtering
> ### Aliases: cmap.filter
> ### Keywords: analysis
>
> ### ** Examples
>
> ## load example data
> data(pdb)
Warning in data(pdb) : data set ‘pdb’ not found
> data(trj.1)
Warning in data(trj.1) : data set ‘trj.1’ not found
> data(trj.2)
Warning in data(trj.2) : data set ‘trj.2’ not found
> data(trj.3)
Warning in data(trj.3) : data set ‘trj.3’ not found
>
> ## Lets work with Calpha atoms only
> library(bio3d)
> ca.inds <- atom.select(pdb, "calpha")

Build selection from input string

Error in unique(pdb$atom[, "resid"]) : object 'pdb' not found
Calls: atom.select -> parse.string -> unique
Execution halted
Comments (1)
