> On 20 May 2020, at 08:44, Adelchi Azzalini <azzal...@stat.unipd.it> wrote:
>
> 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
Please ignore the message above.
Right after sending it, I realized that the simple workaround was to move
everything in
/usr/local/
to
/usr/local/local-2020520/
After reinstalling R, TeX, etc... compilation now works fine!
Thanks for your effective help.
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
>>
>
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