Fix documentation-related warnings displayed by R CMD check

[matthuska]

See below, it's mostly just missing rdoxygen2 docstrings:

* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘exactgevparams’ ‘jaspar’ ‘R_affinity_multi’ ‘R_affinity_sum_multi’
Undocumented data sets:
‘exactgevparams’ ‘jaspar’
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 ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'get.affinity.cutoff'
‘cutoff’
Documented arguments not in \usage in documentation object 'get.affinity.cutoff':
‘pvalue.cutoff’
Documented arguments not in \usage in documentation object 'read.transfac':
‘dir’
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 ... WARNING
Argument items with no description in Rd object 'evaluate.ranking':
‘ranking’ ‘seq.name2matrix’ ‘roc.plot’ ‘add’ ‘col’ ‘predictors’
Argument items with no description in Rd object 'local.paffinity':
‘affnt’ ‘pwm’ ‘seq’ ‘Rmax’ ‘lambda’ ‘pseudo.count’ ‘gc.content’
‘window.size’ ‘window.offset’

[matthuska]

Fixed them with the exception of these two in e7cf0d9:

* checking Rd contents ... WARNING
Argument items with no description in Rd object 'evaluate.ranking':
  'ranking' 'seq.name2matrix' 'roc.plot' 'add' 'col' 'predictors'

Argument items with no description in Rd object 'local.paffinity':
  'affnt' 'pwm' 'seq' 'Rmax' 'lambda' 'pseudo.count' 'gc.content'
  'window.size' 'window.offset'

@matthiasheinig can you add this documentation sometime? no rush.