Hi
You can try
export MACOSX_DEPLOYMENT_TARGET=10.14
and “make install” again.
Hai
On Thu, Apr 18, 2019 at 4:20 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> So, today I came to the office just to find that my laptop had
> autoupdated, amongst other things, XCode which is now Version 10.2.1
> (10E1001).
>
> Having a moment of honest panic I tried to recompile the AmberTools18
> package and yes, once again I cannot compile… This is not using the gnu gcc
> (which still, however, does not work and fails with the “_Atomic” error).
> This issue is still persistent and has not been fixed by the developers or
> by apple and diskussions are seemingly ongoing on how to handle this
> problem. I did exactly what worked on the last version and what is outlined
> in the latest confirmed install procedure on the website though it fails
> with the same parmed error as last time.
>
> …
> …
> copying parmed/modeller/data/standard_residues.lib ->
> build/lib.macosx-10.7-x86_64-2.7/parmed/modeller/data
> UPDATING build/lib.macosx-10.7-x86_64-2.7/parmed/_version.py
> set build/lib.macosx-10.7-x86_64-2.7/parmed/_version.py to
> '3.0.0+57.g74a84d30'
> running build_ext
> building 'parmed.amber._rdparm' extension
> creating build/temp.macosx-10.7-x86_64-2.7
> creating build/temp.macosx-10.7-x86_64-2.7/src
> clang -fno-strict-aliasing
> -I/Users/guolaa/SOFTWARE/amber18/miniconda/include -arch x86_64 -DNDEBUG -g
> -fwrapv -O3 -Wall -Wstrict-prototypes
> -I/Users/guolaa/SOFTWARE/amber18/AmberTools/src/parmed/src
> -I/Users/guolaa/SOFTWARE/amber18/miniconda/include/python2.7 -c
> src/_rdparm.cpp -o build/temp.macosx-10.7-x86_64-2.7/src/_rdparm.o
> warning: include path for stdlibc++ headers not found; pass
> '-stdlib=libc++' on the command line to use the libc++ standard library
> instead [-Wstdlibcxx-not-found]
> In file included from src/_rdparm.cpp:17:
> /Users/guolaa/SOFTWARE/amber18/AmberTools/src/parmed/src/readparm.h:5:10:
> fatal error: 'locale' file not found
> #include <locale>
> ^~~~~~~~
> 1 warning and 1 error generated.
> error: command 'clang' failed with exit status 1
> make[2]: *** [parmed] Error 1
> make[1]: *** [serial] Error 2
> make: *** [install] Error 2
>
> I have commented out the libstdc++ lines as described and done a
> search/replace (:%s/libstdc++/libc++/g) to make sure I did not miss a new
> line or something else however it still does not work and fails with the
> same error. These are the files modified:
> $AMBERHOME/AmberTools/src/configure2
> $AMBERHOME/AmberTools/src/pytraj/setup.py
>
> Are there any more files referencing the now deprecated c++ stuff from
> Xcode that I am unaware of?
>
> (( Maybe it’s just time to give up and dual-boot as it at least seems that
> Apple is hellbent on breaking cross platform compatibility ))
>
> Best regards
> // Gustaf
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 18 2019 - 07:00:02 PDT
