[R-SIG-Mac] R dock icon bug, OSX10.11.5, upgrade from incomplete uninstall of R3.2 to 3.3.1

[Simon Urbanek]

Julian,

I'm not sure I understand your question - can elaborate on "listing functions long since deleted"? Are you referring to R functions, your code or something like that? Your operation of R will create many artifacts depending on what you do, run and use - none of which is under our control.

As for applications, OS X has no central repository, the presence of an application is enough to get it registered. You can use mdfind to locate all instances of an application, for example to search the R GUI you can use

mdfind "kMDItemCFBundleIdentifier == 'org.R-project.R'"

For the framework you would use

mdfind "kMDItemCFBundleIdentifier == 'org.r-project.R-framework'"

The other thing to consider is the metadata registered which you can check with pkgutil via

pkgutil --pkgs | grep ^org.r-project

Finally, as Carl pointed out, OS X may be caching the the files association - I don't know if there is a way to force dis-asociation or if it will keep it in case you decide to re-install the application.

Cheers,
Simon
 


> On Jul 4, 2016, at 8:57 PM, Audrey Julian <a.l.julian at gmail.com> wrote:
> 
> Hi,
> 
> I ran into a situation where a complete deletion of all R resources
> and a fresh install was needed with the upgrade to R 3.3.1. I've found
> that despite following the manuals uninstall guidance, it appears
> "something" R related is remaining somewhere on the hard drive. The
> error presents if I right click the R icon from the Mac dock. The icon
> is listing functions long since deleted from hard drive. This suggests
> that the uninstall of R3.2 is perhaps incomplete. I can't tell if the
> "something" extends a simple representation of old deleted files, or
> perhaps there is something going on that's more significant. I've gone
> down this path to clear up environment variable issues so I'm eager to
> ensure I've removed .
> 
> Environment specs:
> OSX 10.11.5
> R3.3.1
> 
> Investigation steps taken: I've through the manuals, rseek.org
> searches on this topic but haven't been able to find a solution. Also
> pestered people in an R user group locally. 1 person confirmed they
> see the same weird behavior on their machine. No details on their
> specs however.
> 
> Remediation steps attempted:
> 
> - Trashed R.app and Rstudio.app, emptied trash
> - Followed guidance on
> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Uninstalling-under-OS-X,
> ran sudo rm from terminal and visually confirmed directories deleted.
> - For some reason the official guide didn't mention directory, found
> and manually deleted ~/library/application support/R/
> - Icons were still in the dock, manually removed them.
> - Unhid files, deleted all .RData, .Rhistory, etc files anywhere found
> on harddrive
> - Ran from terminal: defaults delete com.apple.dock, then killall Dock
> - Arranged Finder "All My Files" view by application, confirmed
> garbage .R files indeed weren't on hard drive
> - In above step noted .R files associated with Xcode, opened Xcode and
> confirmed no recent files displayed by app.
> - Deleted all recently opened files by Apple > Recent Items > Clear Menu
> - Rebooted and reinstalled R / Rstudio and check what happens, no change.
> - Opened R, opened a different .R file. This new .R file is listed if
> right clicking the icon but separated from the garbage .Rs file by a
> line. Closed the test .R file, garbage still there.
> - Created icon from both Launchpad and from ~/Applications/R.app,
> garbage there in both methods
> 
> 
> 
> Regards, A. Julian
> 
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