[Rd] R CMD CHECK problem

[Uwe Ligges]

Joerg van den Hoff wrote:
> I tried two times to get some help for this from the help list but to no avail. I hope,
> it's OK to post this here (once...). if not, please ignore (the rest of) this
> mail:
> 
> for one of my private packages R CMD CHECK {package} givves me annoying warnings
> due to 'missing links' in the manpages for functions from another private
> package mentioned in the manpages. specifically, I have two packages, the first
> (named `pkc') depending on the second one (named `roiutils'). The source code
> and DESCRIPTION files describes the dependency as it should be, I think
> ('Imports', `require'). but if I run
> 
> R CMD CHECK pkc 
> 
> I get "significant warnings" related to missing links (refering to functions
> from the second package) in the manpages of the first package as can be
> seen below. despite the warnings, after installing the two packages the help
> system works just fine including the cross-references.
> 
> my question:
> why is it, that R CMD CHECK is complaining?  what am I doing wrong?
> how have I to specify the links in the manpages to tell CHECK that
> everything is basically OK? 


Specify links in the form \link[roiutils]{readroi} as the Writing R 
Extension manual suggests.

Uwe Ligges


> ========================CUT====================================
> * checking for working latex ... OK
> * using log directory '/Users/vdh/rfiles/Rlibrary/.check/pkc.Rcheck'
> * using R version 2.4.0 (2006-10-03)
> * checking for file 'pkc/DESCRIPTION' ... OK
> * this is package 'pkc' version '1.1'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'pkc' can be installed ... WARNING
> Found the following significant warnings:
>        missing link(s):  readroi readroi readroi figure readroi conv3exmodel readroi
>        missing link(s):  figure readroi
> * 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 syntax errors ... OK
> * checking R files for non-ASCII characters ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies ... OK
> * checking whether the name space can be loaded with stated dependencies ... 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 ... WARNING
> Rd files with unknown sections:
>   /Users/vdh/rfiles/Rlibrary/pkc/man/fitdemo.Rd: example
> 
> See the chapter 'Writing R documentation files' in manual 'Writing R
> Extensions'.
> * checking Rd cross-references ... WARNING
> Missing link(s) in documentation object 'compfit.Rd':
>   readroi readroi readroi figure readroi conv3exmodel readroi
> 
> Missing link(s) in documentation object 'exp3fit.Rd':
>   figure readroi
> ========================CUT====================================
> 
> 
> any hints appreciated,
> 
> joerg
> 
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