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.