>>>>> Kevin Ushey <kevinus...@gmail.com>
>>>>> on Wed, 20 Jul 2016 10:19:33 -0700 writes:
> On Wed, Jul 20, 2016 at 3:52 AM, Martin Maechler
> <maech...@stat.math.ethz.ch> wrote:
>>>>>>> Jeroen Ooms <jeroeno...@gmail.com>
>>>>>>> on Wed, 20 Jul 2016 10:26:19 +0200 writes:
>>
>> > On Tue, Jul 19, 2016 at 6:46 PM, Kevin Ushey <kevinus...@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 ..]
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
>>
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