[R-SIG-Mac] Cannot compile Fortran on macOS

[Kevin Ushey]

The main thing that stands out to me in that error:

  Referenced from: /usr/local/lib/libquadmath.0.dylib
  Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib

R bundles its own copies of libquadmath and libgcc:

kevinushey using Kevins-MBP:/Library/Frameworks/R.framework/Resources/lib
$ ls -la
total 19120
drwxrwxr-x  11 root  admin      352 Apr 24 03:23 .
drwxrwxr-x  18 root  admin      576 Apr 29 11:46 ..
-rwxrwxr-x   1 root  admin  4070896 Apr 24 03:23 libR.dylib
drwxrwxr-x   3 root  admin       96 Apr 24 03:22 libR.dylib.dSYM
-rwxrwxr-x   1 root  admin   201472 Apr 24 03:23 libRblas.dylib
drwxrwxr-x   3 root  admin       96 Apr 24 03:22 libRblas.dylib.dSYM
-rwxrwxr-x   1 root  admin  2181472 Apr 24 03:23 libRlapack.dylib
drwxrwxr-x   3 root  admin       96 Apr 24 03:22 libRlapack.dylib.dSYM
-rw-rw-r--   1 root  admin   160624 Apr 24 03:23 libgcc_s.1.dylib
-rwxrwxr-x   1 root  admin  2851008 Apr 24 03:23 libgfortran.5.dylib
-rwxrwxr-x   1 root  admin   309648 Apr 24 03:23 libquadmath.0.dylib

 which should normally be used during the link step. However, versions in
/usr/local/lib are being discovered instead, which presumably aren't
compatible.

The simplest fix is (likely) to move those files out of the way. Otherwise,
you'd likely have to muck around with Makevars / Makeconf to adjust the
linker flags so the correct versions of these libraries are found.

Best,
Kevin

On Tue, May 19, 2020 at 6:46 AM Adelchi Azzalini <azzalini using stat.unipd.it>
wrote:

> Hi.
> In essence, my problem is that I cannot install a package which requires
> Fortran-77 compilation on my Mac.
>
> More in detail, this is my own package 'mnormt' which exists on CRAN since
> 2006; it is currently at version 1.5-7. It has been developed in successive
> versions on a Linux machine, where it compiles with no problems. The macOS
> and MS-windows versions are created on CRAN, where it passes all pertaining
> checks.
>
> Now, in the new pandemic world, I need create a new version of the
> package, but working from home, hence using my Mac laptop instead of the
> Linux desktop as in the past. Unfortunately, compilation or loading does
> not work. If I run
>
>  R CMD check mnormt_1.5-7.tar.gz
>
> first I get a bunch of warning messages such as
>
> Warning: Possible change of value in conversion from REAL(8) to INTEGER(4)
> ....  [-Wconversion]
> Warning: ‘lxchng’ may be used uninitialized in this function
> [-Wmaybe-uninitialized]
> Warning: Label 10 at (1) defined but not used [-Wunused-label]
>
> and finally it crashes with
>
> Error: package or namespace load failed for ‘mnormt’:
>  .onLoad failed in loadNamespace() for 'mnormt', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object
> '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so':
>
> dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so,
> 6): Symbol not found: ___addtf3
>   Referenced from: /usr/local/lib/libquadmath.0.dylib
>   Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
>  in /usr/local/lib/libquadmath.0.dylib
> Error: loading failed
>
> Needless to say, I have no idea what this "addtf3" is or it should be.
> There is no such a symbol in the Fortran code.
>
> I believe to have installed all ingredients indicated at
> https://mac.r-project.org/tools/
> See the list below with details about my system and other installed tools.
>
> Any suggestions for sorting this out?
>
> Adelchi Azzalini
>
>
> ---------------------------------------------------
> Installation info:
>
> R> R.version
>                _
> platform       x86_64-apple-darwin17.0
> arch           x86_64
> os             darwin17.0
> system         x86_64, darwin17.0
> status
> major          4
> minor          0.0
> year           2020
> month          04
> day            24
> svn rev        78286
> language       R
> version.string R version 4.0.0 (2020-04-24)
> nickname       Arbor Day
>
> --- macOS Mojave 10.14.6
>
> --- Xcode version 11.3.1
>
> --- Fortran
>
> [aa using mac-2013:~] gfortran -v
> Using built-in specs.
> COLLECT_GCC=gfortran
>
> COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper
> Target: x86_64-apple-darwin18
> Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran
> --with-gmp=/Users/fx/devel/gcc/build_package/deps
> --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18
> --disable-multilib --with-native-system-header-dir=/usr/include
> --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> Thread model: posix
> gcc version 8.2.0 (GCC)
>
> [aa using mac-2013:~] echo $PATH
>
> .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin
>
> -- other tools indicated at https://mac.r-project.org/tools/
>    xz-5.2.5/  is installed
>    PCRE2 10.34 built with --disable-jit
>    bzip2 Version 1.0.6 is installed
>
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