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

Martin Maechler maechler at stat.math.ethz.ch
Thu Jul 21 18:03:34 CEST 2016

>>>>> Kevin Ushey <kevinushey at gmail.com>
>>>>>     on Wed, 20 Jul 2016 10:19:33 -0700 writes:

    > 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!

You are welcome.
I have committed a change (svn rev 70955) which no longer "errors out" on
symlinks {{and the same change improves debugging: you can turn
	  off the "dreaded" q(), and that's done by default if(interactive())}}

However, that change indeed was mainly to  is_subdir()
and indeed the code later *does* replace the package-name symlink by a newly
created directory <lib>/<package>  rather than leaving the
symlink.. where I continue to find the latter *the* correct
action, but that would need changes in other places of the code.

 [tested (and "minimal")  patches are welcome for that other goal ..]


    >> > 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

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