From j.van_den_hoff at fzd.de  Mon Mar 19 13:56:45 2007
From: j.van_den_hoff at fzd.de (Joerg van den Hoff)
Date: Mon, 19 Mar 2007 13:56:45 +0100
Subject: [Rd] R CMD CHECK problem
Message-ID: <20070319125645.GA15395@marco.fz-rossendorf.de>


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? 

========================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



[Rd] R CMD CHECK problem
Joerg van den Hoff