Possible bug when finding shared libraries during staged installation

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?

     > 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