[R] debugging package

[Uwe Ligges]

On 06.01.2010 02:15, Markus Weisner wrote:
> 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


You are supposed to fill in documentation and delete the examples such 
as "~~fun~~" while filling in appropriate things.


> 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"

Well this tells *you* how to make other sections. Just delete that part.


>
> 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"


Same as above.

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

 From here the messages are quite self explaining, I think.

Uwe Ligges



> 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'.
>
> 	[[alternative HTML version deleted]]
>
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