R CMD check WARNINGS

[Barry Grant]

On master branch as of Thu Nov 20 13:33:48 EST 2014 Lets try to run and solve R CMD check after each major edit to avoid these building up in the future. Thanks!

* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘ggplot2’
'loadNamespace' or 'requireNamespace' call not declared from: ‘ggplot2’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... WARNING
as.pdb:
  function(...)
as.pdb.prmtop:
  function(prmtop, crd, inds, inds.crd, ncore)

print:
  function(x, ...)
print.cnapath:
  function(pa, ...)

summary:
  function(object, ...)
summary.cnapath:
  function(pa, ..., pdb, label, col, plot, concise, cutoff, normalize)

See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
atom.select.prmtop: no visible global function definition for ‘amb2pdb’
cnapath : <anonymous>: no visible global function definition for ‘%--%’
summary.cnapath: no visible binding for global variable ‘Length’
summary.cnapath: no visible binding for global variable ‘State’
summary.cnapath: no visible binding for global variable ‘bw’
summary.cnapath: no visible binding for global variable ‘..density..’
summary.cnapath: no visible binding for global variable ‘Node’
summary.cnapath: no visible binding for global variable ‘..count..’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'read.crd.amber.Rd':
  ‘amb2pdb’

Missing link or links in documentation object 'read.prmtop.Rd':
  ‘amb2pdb’

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘print.prmtop’
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 'as.pdb':
as.pdb.prmtop
  Code: function(prmtop, crd = NULL, inds = NULL, inds.crd = inds,
                 ncore = NULL)
  Docs: function(pdb, crd, inds = NULL, inds.crd = inds, ncore = NULL,
                 ...)
  Argument names in code not in docs:
    prmtop
  Argument names in docs not in code:
    pdb ...
  Mismatches in argument names:
    Position: 1 Code: prmtop Docs: pdb
  Mismatches in argument default values:
    Name: 'crd' Code: NULL Docs:

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

[Lars Skjærven]

updated! sorry about the mess

now it should only be the cnapath issues left

[Lars Skjærven]

by the way, is there a reasons for why printseq=TRUE in print.pdb() and FALSE in summary.pdb()

print.pdb <- function(x, ...) {
  ## Print a summary of basic PDB object features
  y <- summary.pdb(x, printseq=TRUE, ...)
}

summary.pdb <- function(object, printseq=FALSE, ...) {

documentation says printseq=FALSE

[Barry Grant]

I believe my intention was to have print.pdb() be more verbose (with the sequence) but summary() be more concise along the lines of other R summary functions. Is there a miss-math with the documentation?

[Lars Skjærven]

from the documentation I get the impression that the default of printseq is FALSE:

summary(object, printseq=FALSE, ...)

but in the code of print.pdb() it is specified to be TRUE. thus, if I want to use print I will get:

> print(pdb, printseq=F)
Error in summary.pdb(x, printseq = TRUE, ...) : 
  formal argument "printseq" matched by multiple actual arguments

I would set the default to TRUE in summary.pdb(), and remove the argument from inside print.pdb() ?

[Barry Grant]

Ahh I see, so we can't currently turn printseq off in print.pdb(). Your suggestion would lead to the sequence being printed with both summary.pdb() and print.pdb(), which is what I wanted to avoid. I think the summary should by default be shorter and without the sequence. Therefore, I would suggest the following change to print.pdb() although I have not checked if this will cause some inconsistency and thus complaints with the parent print function:

# new print function
print.pdb2 <- function(x, printseq=TRUE, ...) {
  ## Print a summary of basic PDB object features
  y <- summary.pdb(x, printseq=printseq, ...)
}

> print.pdb2(pdb, print=F)

 Call:  read.pdb(file = "4AKE")

   Total Models#: 1
     Total Atoms#: 3459,  XYZs#: 10377  Chains#: 2  (values: A B)

     Protein Atoms#: 3312  (residues/Calpha atoms#: 428)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 147  (residues: 147)
     Non-protein/nucleic resid values: [HOH (147) ]

+ attr: atom, helix, sheet, seqres, xyz,
        calpha, call

What do you think?

[Lars Skjærven]

Sounds good !

[Barry Grant]

Ok I will commit this now, thanks!