From D.Strbenac at garvan.org.au  Wed Apr  6 02:00:08 2011
From: D.Strbenac at garvan.org.au (Dario Strbenac)
Date: Wed,  6 Apr 2011 10:00:08 +1000 (EST)
Subject: [Rd] R CMD check for 2.13 rc
Message-ID: <20110406100008.BLL11522@gimr.garvan.unsw.edu.au>

Hi,

I have a couple of new errors in our package when I check it on R 2.13-rc (r55310). The first one that's mystifying me is

* checking R code for possible problems ... NOTE
Error : object normalizePath is not exported by 'namespace:utils'
Error : object normalizePath is not exported by 'namespace:utils'

Firstly, it's strange to see NOTE and Error being used interchangeably here. The package is being developed by a couple of us, so I checked that there were no calls to normalizePath in any of our code, and there aren't:

darstr at clark-lab:~/Repitools_github/pkg$ grep -r normalizePath .
./Repitools.Rcheck/00check.log:Error : object normalizePath is not exported by 'namespace:utils'
./Repitools.Rcheck/00check.log:Error : object normalizePath is not exported by 'namespace:utils'
./Repitools.Rcheck/tests/tests.Rout.fail:Error : object 'normlizePath' is not exported by 'namespace:utils'

I haven't got a clue where to look next.

My second concern is that I have used the code:

setOldClass("AffymetrixCelSet")

to make an S3 class be S4 dispatchable on. But R 2.13 wants me to document this class that I don't own:

* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  AffymetrixCelSet

Is this truly necessary ?

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia



[Rd] R CMD check for 2.13 rc
Dario Strbenac