debugging package

I am trying to debug a package to submit it to CRAN and am getting a bunch
of error messages.  Most of the errors are because of the Rd files which
were automatically populated by the package.skeleton function.  I find the
section on documentation to be pretty confusion in the R Extensions manual.
Any help on getting these errors fixed would be hugely appreciated.  Thanks.
--Markus

* checking for working pdflatex ... OK
* using log directory '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck'
* using R version 2.9.2 Patched (2009-09-24 r50179)
* using session charset: UTF-8
* checking for file 'NFIRS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NFIRS' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package 'NFIRS' can be installed ... WARNING
Found the following significant warnings:
        missing link(s):  ~~fun~~ CLASSNAME-class

See '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... ERROR
Rd files with likely Rd problems:
Unaccounted top-level text in file 'NFIRS-class.Rd':
Following section 'note':
"\n\n ~Make other sections like Warning with \\section{Warning }{....}
~\n\n"

Unaccounted top-level text in file 'NFIRS-package.Rd':
Following section 'references':
"\n~~ Optionally other standard keywords, one per line, from file KEYWORDS
in the R documentation directory ~~\n"

Rd files with missing or empty '\title':
   NFIRS.summary.Rd
   read.NFIRS.Rd

Rd files without 'description':
   NFIRS.summary.Rd
   read.NFIRS.Rd
Rd files without 'title':
   NFIRS.summary.Rd
   read.NFIRS.Rd
These entries are required in an Rd file.

Rd files with non-standard keywords:
   as.data.frame-methods.Rd: ~~ other possible keyword(s)
   head-methods.Rd: ~~ other possible keyword(s)
   NFIRS.summary.Rd: ~kwd1 ~kwd2
   read.NFIRS.Rd: ~kwd1 ~kwd2
   summary-methods.Rd: ~~ other possible keyword(s)
   tail-methods.Rd: ~~ other possible keyword(s)
Each '\keyword' entry should specify one of the standard keywords (as
listed in file 'KEYWORDS' in the R documentation directory).

Rd files with duplicated alias 'as.data.frame,NFIRS-method':
   as.data.frame-methods.Rd NFIRS-class.Rd
Rd files with duplicated alias 'head,NFIRS-method':
   head-methods.Rd NFIRS-class.Rd
Rd files with duplicated alias 'summary,NFIRS-method':
   NFIRS-class.Rd summary-methods.Rd
Rd files with duplicated alias 'tail,NFIRS-method':
   NFIRS-class.Rd tail-methods.Rd

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.

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 * checking whether package 'NFIRS' can be installed ... WARNING
 Found the following significant warnings:
       missing link(s):  ~~fun~~ CLASSNAME-class
 See '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck/00install.out' for details.

 * checking Rd files ... ERROR
 Rd files with likely Rd problems:
 Unaccounted top-level text in file 'NFIRS-class.Rd':
 Following section 'note':
 "\n\n ~Make other sections like Warning with \\section{Warning }{....}
 ~\n\n"

 Unaccounted top-level text in file 'NFIRS-package.Rd':
 Following section 'references':
 "\n~~ Optionally other standard keywords, one per line, from file KEYWORDS
 in the R documentation directory ~~\n"

 Rd files with missing or empty '\title':
  NFIRS.summary.Rd
  read.NFIRS.Rd

 Rd files without 'description':
  NFIRS.summary.Rd
  read.NFIRS.Rd

 Rd files without 'title':
  NFIRS.summary.Rd
  read.NFIRS.Rd
 These entries are required in an Rd file.

 Rd files with non-standard keywords:
  as.data.frame-methods.Rd: ~~ other possible keyword(s)
  head-methods.Rd: ~~ other possible keyword(s)
  NFIRS.summary.Rd: ~kwd1 ~kwd2
  read.NFIRS.Rd: ~kwd1 ~kwd2
  summary-methods.Rd: ~~ other possible keyword(s)
  tail-methods.Rd: ~~ other possible keyword(s)
 Each '\keyword' entry should specify one of the standard keywords (as
 listed in file 'KEYWORDS' in the R documentation directory).

 Rd files with duplicated alias 'as.data.frame,NFIRS-method':
  as.data.frame-methods.Rd NFIRS-class.Rd
 Rd files with duplicated alias 'head,NFIRS-method':
  head-methods.Rd NFIRS-class.Rd
 Rd files with duplicated alias 'summary,NFIRS-method':
  NFIRS-class.Rd summary-methods.Rd
 Rd files with duplicated alias 'tail,NFIRS-method':
  NFIRS-class.Rd tail-methods.Rd

 See the chapter 'Writing R documentation files' in manual 'Writing R
 Extensions'.

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