[Rd] Possible bug when finding shared libraries during staged installation

[Simon Urbanek]

I'll have a look at the code - I don't think I actually reviewed all those macOS modifications - I wasn't even aware that they were added to the code.


> On May 24, 2019, at 08:52, Martin Maechler <maechler using stat.math.ethz.ch> wrote:
> 
>>>>>> Kara Woo 
>>>>>>    on Thu, 23 May 2019 14:24:26 -0700 writes:
> 
>> Hi all,
>> With the new staged installation, it seems that R CMD INSTALL sometimes
>> fails on macOS due to these lines [1] when sapply() returns a list. The
>> x13binary package has an example [2], reproducible with the following steps:
> 
>> $ git clone git using github.com:x13org/x13binary.git && cd x13binary
>> $ git checkout 663ad7122
>> $ R CMD INSTALL .
> 
>> (We've also run into it in an internal package, but it's easier to
>> reproduce with x13binary)
> 
>> In this case the file command returns multiple results for one of the
>> dynamic libraries, so are_shared looks like this:
> 
>>> are_shared
>> $`/Users/Kara/projects/forks/x13binary/inst//lib/libgcc_s.1.dylib`
>> [1] TRUE TRUE TRUE
> 
>> $`/Users/Kara/projects/forks/x13binary/inst//lib/libgfortran.3.dylib`
>> [1] TRUE
> 
>> $`/Users/Kara/projects/forks/x13binary/inst//lib/libquadmath.0.dylib`
>> [1] TRUE
> 
> Thank you, Kara.
> 
> Just for curiosity, what does
> 
> file /Users/Kara/projects/forks/x13binary/inst//lib/libgcc_s.1.dylib
> 
> produce on your Mac?
> 
>> slibs[are_shared] then fails with invalid subscript type 'list'.
> 
> yes, "of course".
> 
>> I believe this may be a bug and I have included a patch that uses any() and
>> vapply() to ensure that only one value is returned for each library and the
>> result is an atomic vector. This is my first time submitting a bug report
>> or patch here; I'm happy to make any changes if needed.
> 
> Your patch was not attached with MIME type   text/plain  and so
> was filtered out by the mailing list software.
> OTOH, I could relatively easily guess how to fix the bug,
> notably when seeing the above "file ...dylib" result.
> 
> What we *meant* to say in  https://www.r-project.org/bugs.html 
> is that in such a situation
> 1) you send your finding / suspicion / diagnosis
>   to the R-devel mailing list,  in order to get confirmation etc
>   if what you see is a bug;
> 2) then ideally, you'd do a formal bug report at
>   https://bugs.r-project.org/
> 	(for which you need to get an "account" there to be created
> 	 once only by a bugzilla admin, typically an R core member).
> 
> In this case, that (2) may not be necessary, but you may want
> that anyway (and let some of us know).
> 
>> Thanks for considering,
>> Kara
> 
> Thank *you* indeed for the report,
> Martin
> 
>> [1]
>> https://github.com/wch/r-source/blob/3fe2bb01e9ec1b268803a437c308742775c2442d/src/library/tools/R/install.R#L594-L597
>> [2] https://github.com/x13org/x13binary/issues/46
> 
>> R version 3.6.0 Patched (2019-05-22 r76579)
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> Running under: macOS Mojave 10.14.4
> 
> --
> Martin Maechler
> ETH Zurich  and  R Core Team
> 
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