From woo@k@r@ @end|ng |rom gm@||@com  Fri May 24 18:56:37 2019
From: woo@k@r@ @end|ng |rom gm@||@com (Kara Woo)
Date: Fri, 24 May 2019 09:56:37 -0700
Subject: [Rd] Possible bug when finding shared libraries during staged
 installation
In-Reply-To: <b0dc0646-50fd-9f27-62c7-ff1e3a4e925c@gmail.com>
References: <CAEvqV34wSchVg+YW57khWh7NffGOyCeYd5PbmC+1x5OUZk-jRQ@mail.gmail.com>
 <23783.59686.93067.483632@stat.math.ethz.ch>
 <b0dc0646-50fd-9f27-62c7-ff1e3a4e925c@gmail.com>
Message-ID: <CAEvqV37y6VqWh_v_rGjH2+BzN3QieNS+Xv36cUe24x4o2Bp1sQ@mail.gmail.com>

Yes, that's the same result that I see as well.

If you still want the formal report I can create one if someone adds me to
bugzilla, but it sounds like that may not be necessary. Thanks for looking
into this!

On Fri, May 24, 2019 at 5:58 AM Tomas Kalibera <tomas.kalibera at gmail.com>
wrote:

> 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
>
>
>

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