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

[David Winsemius]

On 5/19/20 1:54 PM, Kevin Ushey wrote:
> 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.


Kevin;


Is that the sort of situation that might be cause by mixing 
homebrew-compiled and R.Framework-compiled packages?


David.

>
> 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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac using r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac