Thanks to everyone that provided suggestions. I was about to follow the recommended step of renaming /usr/local and reinstall a bunch of programs. However, that renaming is blocked, presumably by Apple System Integrity Protection. Is there any alternative to disabling this Apple "feature"? Do you recommend to re-instate it after the re-construction of /usr/local/ ? As you see, I am not familiar with Apple tricks.
Thanks again, Adelchi > On 20 May 2020, at 05:50, Simon Urbanek <simon.urba...@r-project.org> wrote: > > > Adelchi, > > as pointed out you have conflicting libraries in /usr/local - likely from > some conflicting package manager. I would recommend re-naming /usr/local to > remove the issue and installing a clean GNU Fortran (see > http://mac.r-project.org/tools/ or from the official GNU Fortran pages which > use the same binary), that's all you really need. > > Cheers, > Simon > > > >> On 20/05/2020, at 1:45 AM, Adelchi Azzalini <azzal...@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@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@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@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
