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
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 >
---- Original message ---->Date: Tue, 5 Apr 2011 17:21:55 -0700 >From: henrik.bengtsson at gmail.com (on behalf of Henrik Bengtsson <hb at biostat.ucsf.edu>) >Subject: Re: [Rd] R CMD check for 2.13 rc >To: D.Strbenac at garvan.org.au >Cc: r-devel at r-project.orgYes, I think the warning about normalizePath will be fine when packages ours depends on get updated. Has anyone got a comment yet, about why setOldClass() classes must now be documented ? - Dario.