From tom@@@k@||ber@ @end|ng |rom gm@||@com  Fri May 24 14:58:44 2019
From: tom@@@k@||ber@ @end|ng |rom gm@||@com (Tomas Kalibera)
Date: Fri, 24 May 2019 14:58:44 +0200
Subject: [Rd] Possible bug when finding shared libraries during staged
 installation
In-Reply-To: <23783.59686.93067.483632@stat.math.ethz.ch>
References: <CAEvqV34wSchVg+YW57khWh7NffGOyCeYd5PbmC+1x5OUZk-jRQ@mail.gmail.com>
 <23783.59686.93067.483632@stat.math.ethz.ch>
Message-ID: <b0dc0646-50fd-9f27-62c7-ff1e3a4e925c@gmail.com>

On 5/24/19 2:52 PM, Martin Maechler 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 at 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?

I can reproduce, it is something like

/usr/lib/libgcc_s.1.dylib: Mach-O universal binary with 2 architectures: 
[x86_64:Mach-O 64-bit dynamically linked shared library x86_64] 
[i386:Mach-O dynamically linked shared library i386]
/usr/lib/libgcc_s.1.dylib (for architecture x86_64):??? Mach-O 64-bit 
dynamically linked shared library x86_64
/usr/lib/libgcc_s.1.dylib (for architecture i386):??? Mach-O dynamically 
linked shared library i386

Thanks for the report, I will fix.

Tomas

>
>      > 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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