From |@wrence@m|ch@e| @end|ng |rom gene@com  Tue Feb  8 17:52:56 2022
From: |@wrence@m|ch@e| @end|ng |rom gene@com (Michael Lawrence)
Date: Tue, 8 Feb 2022 08:52:56 -0800
Subject: [Rd] S4 class name conflicts
In-Reply-To: <CABtg=KmbgbS7rxQyTn++ytLD8S+apAv3zCC1rz3eYtqPPo-thw@mail.gmail.com>
References: <CABtg=KmbgbS7rxQyTn++ytLD8S+apAv3zCC1rz3eYtqPPo-thw@mail.gmail.com>
Message-ID: <CAOQ5Nyd5mJFo6yYHVh8X1OTQNh2u3GHQtTVaUuOxbwBTc3XcGA@mail.gmail.com>

Hi Gabor,

Thanks for reporting this issue. Would you be able to help me
reproduce it? I'm guessing this depends on some combination of git
checkouts, so it would be helpful to know which.

Michael

On Tue, Feb 8, 2022 at 6:32 AM G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:
>
> The RNeXML CRAN package currently has some check warnings, originating
> from an S4 class name conflict.
>
> RNeXML sets the S4 class "tree". A dependency of the package now
> depends on the cli package, which calls setOldClass() on an S3 "tree"
> class.
>
> This causes two potential issues. One is that RNeXML maybe ends up
> using cli's class internally, because this is what we see at install
> time:
>
> ** byte-compile and prepare package for lazy loading
> Found more than one class "tree" in cache; using the first, from namespace 'cli'
> Also defined by ?RNeXML?
>
> The second issue is an error when RNeXML is unloaded:
>
> ? unloadNamespace("RNeXML")
> Error in .mergeMethodsTable(generic, mtable, tt, attach) :
>   trying to get slot "defined" from an object of a basic class
> ("environment") with no slots
>
> This makes R CMD check fail as well.
>
> Is cli doing something wrong here? Or is this a bug in base R? Or is
> it a known limitation? If the latter, would it make sense for the
> RNeXML installation to fail instead of creating a broken package. (If
> it is a broken package at all.)
>
> Gabor
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



-- 
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

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[Rd] S4 class name conflicts
Michael Lawrence