debugging package
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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