From kevinushey at gmail.com  Wed Jul 20 19:19:33 2016
From: kevinushey at gmail.com (Kevin Ushey)
Date: Wed, 20 Jul 2016 10:19:33 -0700
Subject: [Rd] package installation fails when symlink of same name exists
In-Reply-To: <22415.22504.313987.661421@stat.math.ethz.ch>
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On Wed, Jul 20, 2016 at 3:52 AM, Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
>>>>>> Jeroen Ooms <jeroenooms at gmail.com>
>>>>>>     on Wed, 20 Jul 2016 10:26:19 +0200 writes:
>
>     > On Tue, Jul 19, 2016 at 6:46 PM, Kevin Ushey <kevinushey at gmail.com> wrote:
>     >> R fails to install a package from source over a pre-existing package
>     >> when the path to that package is a symlink, rather than a directory.
>     >> ...
>     >> I don't think anyone's reported this being an issue before
>
>     > I ran into this as well a while back:
>     >   https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16725
>
> I've now at least "acknowledged" that bug report.
> and have looked into changing the  is_subdir() function so it
> returns TRUE in the case of a symlink [on those platforms where
> Sys.readlink() "works", i.e., supposedly not on Windows; however
> that maybe sufficient to close that bug report and also Kevin's
> issue, right ?]
>
> However, Kevin, in his posting, continues
>
>     > I guess my wish here would be that R would check if any file already
>     > existed at the 'instdir' path, and if it existed and was a symlink, R
>     > would remove that symlink before install.
>
> are you sure?
> I think ... and from what you mention below ("packrat") it would
> rather be important to *keep* the symlink, and install to
> whereever the symlink is pointing,  no ?

For packrat's case at least, removing the symlink and installing to a
newly-created directory within the library would be fine -- later,
when a user wants to 'save the state' of their library, they would
call 'packrat::snapshot()', and that call would take care of moving
the newly-installed package to the cache and restoring the symlink as
required.

That said, installing within the symlinked directory would definitely
be nice :-) I just thought the request might be out of scope.

>     > It could happen before creating the directory, e.g. here:
>
>     > https://github.com/wch/r-source/blob/62f5acbdbdf36e1fc618510312125d1677d79941/src/library/tools/R/install.R#L277-L281
>
>     > One thing that was a bit surprising to me -- R does not remove a
>     > pre-existing package installation if it exists (when installing from
>     > source), it merely installs over it, so files / artifacts from a
>     > previous package installation could be left over after installing a
>     > new package. It seems this is not a problem in practice since I don't
>     > think anyone's reported this being an issue before, but for hygiene it
>     > seems like a pre-existing directory could / should be removed when
>     > installing a new package. (It appears that R does clear out a
>     > pre-existing directory when downloading and installing a package
>     > binary directly from CRAN.)
>
> Well, at least with  update.packages()  it seems natural to me
> that R would not just remove all previous parts there ..
>
>     > For motivation: I bumped into this when attempting to implement a
>     > package caching feature with packrat. A packrat project using a global
>     > cache will have a (private) R library containing symlinks to R package
>     > installations in a separate, global library. This allows projects to
>     > effectively be isolated from one another, while avoiding duplication
>     > of packages used across multiple projects.
>
> Yes, I found this a nice feature when I heard about packrat.
>
> But then, really R should *not* remove the symlink and create a
> regular subdirectory in that library there !

I agree this would be ideal, I just thought this request might be out
of scope, since the typical use case for R libraries is a
directory-of-directories, not a directory-of-symlinks-to-directories
(although packrat has had a lot of success with the second scenario!)

Thanks, Martin!

>     > Unfortunately, some packrat
>     > users bump into this when attempting to update a package that has
>     > entered the cache (and so is a symlink in their R library).
>
>     > Thanks for your time,
>     > Kevin
>



[Rd] package installation fails when symlink of same name exists
Kevin Ushey