From hb at biostat.ucsf.edu  Wed Apr  6 02:21:55 2011
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Tue, 5 Apr 2011 17:21:55 -0700
Subject: [Rd] R CMD check for 2.13 rc
In-Reply-To: <20110406100008.BLL11522@gimr.garvan.unsw.edu.au>
References: <20110406100008.BLL11522@gimr.garvan.unsw.edu.au>
Message-ID: <BANLkTimjpYPE+Gd2XQJMuj7uX6Eb8SuE1Q@mail.gmail.com>

I think normalizePath() has been moved to 'base' very++ recently.  /H

On Tue, Apr 5, 2011 at 5:00 PM, Dario Strbenac <D.Strbenac at garvan.org.au> wrote:
> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] R CMD check for 2.13 rc
Henrik Bengtsson