First and foremost, thank you for implementing this Python CUTEst interface! I am very

Thanks for your help! When I run gcc -v , I see <code

Encountering error when importing problem on Mac OS X 10.13,about jfowkes/pycutest

Comments (16)

jfowkes commented on August 18, 2024

Glad that you find it helpful!

It appears that the Apple supplied gcc compiler on your system is out of date, please install the latest version of Command Line Tools (macOS High Sierra version 10.13), see here for detailed instructions:
http://railsapps.github.io/xcode-command-line-tools.html

When you run gcc -v you want to see Target: x86_64-apple-darwin17.5.0 or higher number in the output.

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hjmshi commented on August 18, 2024

Thanks for your help! When I run gcc -v, I see Target: x86_64-apple-darwin17.7.0, so the GCC version doesn't seem to be the issue. Could it be that CUTEst (not PyCUTEst) is not compatible with 10.13?

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jfowkes commented on August 18, 2024

In that case do you have MACOSX_DEPLOYMENT_TARGET=10.7 environment variable set or -mmacosx-version-min=10.7 somewhere in your CFLAGS? For some reason your system is trying to compile C code for MacOS 10.7 (Lion) instead of 10.13 (High Sierra).

I’m using CUTEst and PyCUTEst on 10.13 no problem (although I am using gcc from homebrew). What is the full output of gcc -v? And does brew list contain multiple versions of gcc by any chance?

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jfowkes commented on August 18, 2024

Actually having thought more about this, I think it is an issue with how PyCUTEst detects which version of GCC to link against on MacOS. What is the output of ls -lh /usr/local/Cellar/gcc/*/lib/gcc/*/ ? And what does the following python code (from pycutest/install_scripts.py) return:

import os
from glob import glob
print(max(glob('/usr/local/Cellar/gcc/*/lib/gcc/*/'),key=os.path.getmtime))

It’s supposed to find the same GCC version as that returned by gcc -v.

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hjmshi commented on August 18, 2024

Thanks for helping with the debugging.

The full output of gcc -v is:

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/c++/4.2.1
Apple LLVM version 9.1.0 (clang-902.0.39.2)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

There does appear to be multiple versions of gcc installed: 7.2.0, 8.1.0, and 8.2.0.

The output of ls -lh/usr/local/Cellar/gcc/*/lib/gcc/*/ is

/usr/local/Cellar/gcc/7.2.0/lib/gcc/7/:
total 83504
drwxr-xr-x   3 hjmshi  admin    96B Aug 14  2017 gcc
drwxr-xr-x  43 hjmshi  admin   1.3K Aug 30  2017 i386
-r--r--r--   1 hjmshi  admin   1.0M Aug 30  2017 libasan.4.dylib
lrwxr-xr-x   1 hjmshi  admin    15B Aug 14  2017 libasan.dylib -> libasan.4.dylib
-r--r--r--   1 hjmshi  admin    11K Aug 14  2017 libasan_preinit.o
-r--r--r--   1 hjmshi  admin    50K Aug 30  2017 libatomic.1.dylib
-r--r--r--   1 hjmshi  admin   220K Aug 14  2017 libatomic.a
lrwxr-xr-x   1 hjmshi  admin    17B Aug 14  2017 libatomic.dylib -> libatomic.1.dylib
-r--r--r--   1 hjmshi  admin   1.9M Aug 14  2017 libcc1.0.so
lrwxr-xr-x   1 hjmshi  admin    11B Aug 14  2017 libcc1.so -> libcc1.0.so
-r--r--r--   1 hjmshi  admin   212K Aug 30  2017 libcilkrts.5.dylib
-r--r--r--   1 hjmshi  admin   758K Aug 14  2017 libcilkrts.a
lrwxr-xr-x   1 hjmshi  admin    18B Aug 14  2017 libcilkrts.dylib -> libcilkrts.5.dylib
-r--r--r--   1 hjmshi  admin   173B Aug 14  2017 libcilkrts.spec
-r--r--r--   1 hjmshi  admin    15K Aug 14  2017 libgcc_ext.10.4.dylib
-r--r--r--   1 hjmshi  admin    15K Aug 14  2017 libgcc_ext.10.5.dylib
-r--r--r--   1 hjmshi  admin   250K Aug 30  2017 libgcc_s.1.dylib
lrwxr-xr-x   1 hjmshi  admin    16B Aug 14  2017 libgcc_s_ppc64.1.dylib -> libgcc_s.1.dylib
lrwxr-xr-x   1 hjmshi  admin    16B Aug 14  2017 libgcc_s_x86_64.1.dylib -> libgcc_s.1.dylib
-r--r--r--   1 hjmshi  admin   2.0M Aug 30  2017 libgfortran.4.dylib
-r--r--r--   1 hjmshi  admin   7.8M Aug 14  2017 libgfortran.a
lrwxr-xr-x   1 hjmshi  admin    19B Aug 14  2017 libgfortran.dylib -> libgfortran.4.dylib
-r--r--r--   1 hjmshi  admin   198B Aug 14  2017 libgfortran.spec
-r--r--r--   1 hjmshi  admin   251K Aug 30  2017 libgomp.1.dylib
-r--r--r--   1 hjmshi  admin   1.2M Aug 14  2017 libgomp.a
lrwxr-xr-x   1 hjmshi  admin    15B Aug 14  2017 libgomp.dylib -> libgomp.1.dylib
-r--r--r--   1 hjmshi  admin   169B Aug 14  2017 libgomp.spec
-r--r--r--   1 hjmshi  admin   247K Aug 30  2017 libitm.1.dylib
-r--r--r--   1 hjmshi  admin   1.6M Aug 14  2017 libitm.a
lrwxr-xr-x   1 hjmshi  admin    14B Aug 14  2017 libitm.dylib -> libitm.1.dylib
-r--r--r--   1 hjmshi  admin   162B Aug 14  2017 libitm.spec
-r--r--r--   1 hjmshi  admin   148K Aug 30  2017 libobjc-gnu.4.dylib
-r--r--r--   1 hjmshi  admin   533K Aug 14  2017 libobjc-gnu.a
lrwxr-xr-x   1 hjmshi  admin    19B Aug 14  2017 libobjc-gnu.dylib -> libobjc-gnu.4.dylib
-r--r--r--   1 hjmshi  admin   279K Aug 30  2017 libquadmath.0.dylib
-r--r--r--   1 hjmshi  admin   977K Aug 14  2017 libquadmath.a
lrwxr-xr-x   1 hjmshi  admin    19B Aug 14  2017 libquadmath.dylib -> libquadmath.0.dylib
-r--r--r--   1 hjmshi  admin   290B Aug 14  2017 libsanitizer.spec
-r--r--r--   1 hjmshi  admin    18K Aug 30  2017 libssp.0.dylib
-r--r--r--   1 hjmshi  admin    57K Aug 14  2017 libssp.a
lrwxr-xr-x   1 hjmshi  admin    14B Aug 14  2017 libssp.dylib -> libssp.0.dylib
-r--r--r--   1 hjmshi  admin   2.0K Aug 14  2017 libssp_nonshared.a
-r--r--r--   1 hjmshi  admin   2.5M Aug 30  2017 libstdc++.6.dylib
-r--r--r--   1 hjmshi  admin    13M Aug 14  2017 libstdc++.a
-r--r--r--   1 hjmshi  admin   2.4K Aug 30  2017 libstdc++.a-gdb.py
lrwxr-xr-x   1 hjmshi  admin    17B Aug 14  2017 libstdc++.dylib -> libstdc++.6.dylib
-r--r--r--   1 hjmshi  admin   4.6M Aug 14  2017 libstdc++fs.a
-r--r--r--   1 hjmshi  admin   855K Aug 14  2017 libsupc++.a
-r--r--r--   1 hjmshi  admin   358K Aug 30  2017 libubsan.0.dylib
lrwxr-xr-x   1 hjmshi  admin    16B Aug 14  2017 libubsan.dylib -> libubsan.0.dylib

/usr/local/Cellar/gcc/8.1.0/lib/gcc/8/:
total 111296
drwxr-xr-x   3 hjmshi  admin    96B May  3 12:44 gcc
drwxr-xr-x  39 hjmshi  admin   1.2K May  3 12:47 i386
-r--r--r--   1 hjmshi  admin   1.1M May  3 12:47 libasan.5.dylib
lrwxr-xr-x   1 hjmshi  admin    15B May  3 12:47 libasan.dylib -> libasan.5.dylib
-r--r--r--   1 hjmshi  admin    11K May  3 12:47 libasan_preinit.o
-r--r--r--   1 hjmshi  admin    50K May  3 12:47 libatomic.1.dylib
-r--r--r--   1 hjmshi  admin   225K May  3 12:45 libatomic.a
lrwxr-xr-x   1 hjmshi  admin    17B May  3 12:45 libatomic.dylib -> libatomic.1.dylib
-r--r--r--   1 hjmshi  admin   2.3M May  3 12:44 libcc1.0.so
lrwxr-xr-x   1 hjmshi  admin    11B May  3 12:44 libcc1.so -> libcc1.0.so
-r--r--r--   1 hjmshi  admin    15K May  3 12:44 libgcc_ext.10.4.dylib
-r--r--r--   1 hjmshi  admin    15K May  3 12:44 libgcc_ext.10.5.dylib
-r--r--r--   1 hjmshi  admin   268K May  3 12:47 libgcc_s.1.dylib
lrwxr-xr-x   1 hjmshi  admin    16B May  3 12:44 libgcc_s_ppc64.1.dylib -> libgcc_s.1.dylib
lrwxr-xr-x   1 hjmshi  admin    16B May  3 12:44 libgcc_s_x86_64.1.dylib -> libgcc_s.1.dylib
-r--r--r--   1 hjmshi  admin   2.7M May  3 12:47 libgfortran.5.dylib
-r--r--r--   1 hjmshi  admin    11M May  3 12:45 libgfortran.a
lrwxr-xr-x   1 hjmshi  admin    19B May  3 12:45 libgfortran.dylib -> libgfortran.5.dylib
-r--r--r--   1 hjmshi  admin   198B May  3 12:45 libgfortran.spec
-r--r--r--   1 hjmshi  admin   254K May  3 12:47 libgomp.1.dylib
-r--r--r--   1 hjmshi  admin   1.4M May  3 12:45 libgomp.a
lrwxr-xr-x   1 hjmshi  admin    15B May  3 12:45 libgomp.dylib -> libgomp.1.dylib
-r--r--r--   1 hjmshi  admin   169B May  3 12:44 libgomp.spec
-r--r--r--   1 hjmshi  admin   249K May  3 12:47 libitm.1.dylib
-r--r--r--   1 hjmshi  admin   1.8M May  3 12:45 libitm.a
lrwxr-xr-x   1 hjmshi  admin    14B May  3 12:45 libitm.dylib -> libitm.1.dylib
-r--r--r--   1 hjmshi  admin   162B May  3 12:45 libitm.spec
-r--r--r--   1 hjmshi  admin   165K May  3 12:47 libobjc-gnu.4.dylib
-r--r--r--   1 hjmshi  admin   625K May  3 12:45 libobjc-gnu.a
lrwxr-xr-x   1 hjmshi  admin    19B May  3 12:45 libobjc-gnu.dylib -> libobjc-gnu.4.dylib
-r--r--r--   1 hjmshi  admin   283K May  3 12:47 libquadmath.0.dylib
-r--r--r--   1 hjmshi  admin   1.0M May  3 12:44 libquadmath.a
lrwxr-xr-x   1 hjmshi  admin    19B May  3 12:44 libquadmath.dylib -> libquadmath.0.dylib
-r--r--r--   1 hjmshi  admin   290B May  3 12:47 libsanitizer.spec
-r--r--r--   1 hjmshi  admin    19K May  3 12:47 libssp.0.dylib
-r--r--r--   1 hjmshi  admin    63K May  3 12:44 libssp.a
lrwxr-xr-x   1 hjmshi  admin    14B May  3 12:44 libssp.dylib -> libssp.0.dylib
-r--r--r--   1 hjmshi  admin   2.1K May  3 12:44 libssp_nonshared.a
-r--r--r--   1 hjmshi  admin   3.0M May  3 12:47 libstdc++.6.dylib
-r--r--r--   1 hjmshi  admin    15M May  3 12:46 libstdc++.a
-r--r--r--   1 hjmshi  admin   2.4K May  3 12:46 libstdc++.a-gdb.py
lrwxr-xr-x   1 hjmshi  admin    17B May  3 12:46 libstdc++.dylib -> libstdc++.6.dylib
-r--r--r--   1 hjmshi  admin    11M May  3 12:46 libstdc++fs.a
-r--r--r--   1 hjmshi  admin   963K May  3 12:46 libsupc++.a
-r--r--r--   1 hjmshi  admin   369K May  3 12:47 libubsan.1.dylib
lrwxr-xr-x   1 hjmshi  admin    16B May  3 12:47 libubsan.dylib -> libubsan.1.dylib

/usr/local/Cellar/gcc/8.2.0/lib/gcc/8/:
total 111320
drwxr-xr-x   3 hjmshi  admin    96B Aug 18 12:00 gcc
drwxr-xr-x  39 hjmshi  admin   1.2K Aug 18 12:03 i386
-r--r--r--   1 hjmshi  admin   1.1M Aug 18 12:03 libasan.5.dylib
lrwxr-xr-x   1 hjmshi  admin    15B Aug 18 12:02 libasan.dylib -> libasan.5.dylib
-r--r--r--   1 hjmshi  admin    11K Aug 18 12:02 libasan_preinit.o
-r--r--r--   1 hjmshi  admin    50K Aug 18 12:03 libatomic.1.dylib
-r--r--r--   1 hjmshi  admin   225K Aug 18 12:00 libatomic.a
lrwxr-xr-x   1 hjmshi  admin    17B Aug 18 12:00 libatomic.dylib -> libatomic.1.dylib
-r--r--r--   1 hjmshi  admin   2.3M Aug 18 12:00 libcc1.0.so
lrwxr-xr-x   1 hjmshi  admin    11B Aug 18 12:00 libcc1.so -> libcc1.0.so
-r--r--r--   1 hjmshi  admin    15K Aug 18 12:00 libgcc_ext.10.4.dylib
-r--r--r--   1 hjmshi  admin    15K Aug 18 12:00 libgcc_ext.10.5.dylib
-r--r--r--   1 hjmshi  admin   268K Aug 18 12:03 libgcc_s.1.dylib
lrwxr-xr-x   1 hjmshi  admin    16B Aug 18 12:00 libgcc_s_ppc64.1.dylib -> libgcc_s.1.dylib
lrwxr-xr-x   1 hjmshi  admin    16B Aug 18 12:00 libgcc_s_x86_64.1.dylib -> libgcc_s.1.dylib
-r--r--r--   1 hjmshi  admin   2.7M Aug 18 12:03 libgfortran.5.dylib
-r--r--r--   1 hjmshi  admin    11M Aug 18 12:00 libgfortran.a
lrwxr-xr-x   1 hjmshi  admin    19B Aug 18 12:00 libgfortran.dylib -> libgfortran.5.dylib
-r--r--r--   1 hjmshi  admin   198B Aug 18 12:00 libgfortran.spec
-r--r--r--   1 hjmshi  admin   254K Aug 18 12:03 libgomp.1.dylib
-r--r--r--   1 hjmshi  admin   1.4M Aug 18 12:00 libgomp.a
lrwxr-xr-x   1 hjmshi  admin    15B Aug 18 12:00 libgomp.dylib -> libgomp.1.dylib
-r--r--r--   1 hjmshi  admin   169B Aug 18 12:00 libgomp.spec
-r--r--r--   1 hjmshi  admin   249K Aug 18 12:03 libitm.1.dylib
-r--r--r--   1 hjmshi  admin   1.8M Aug 18 12:00 libitm.a
lrwxr-xr-x   1 hjmshi  admin    14B Aug 18 12:00 libitm.dylib -> libitm.1.dylib
-r--r--r--   1 hjmshi  admin   162B Aug 18 12:00 libitm.spec
-r--r--r--   1 hjmshi  admin   165K Aug 18 12:03 libobjc-gnu.4.dylib
-r--r--r--   1 hjmshi  admin   626K Aug 18 12:00 libobjc-gnu.a
lrwxr-xr-x   1 hjmshi  admin    19B Aug 18 12:00 libobjc-gnu.dylib -> libobjc-gnu.4.dylib
-r--r--r--   1 hjmshi  admin   283K Aug 18 12:03 libquadmath.0.dylib
-r--r--r--   1 hjmshi  admin   1.0M Aug 18 12:00 libquadmath.a
lrwxr-xr-x   1 hjmshi  admin    19B Aug 18 12:00 libquadmath.dylib -> libquadmath.0.dylib
-r--r--r--   1 hjmshi  admin   290B Aug 18 12:02 libsanitizer.spec
-r--r--r--   1 hjmshi  admin    19K Aug 18 12:03 libssp.0.dylib
-r--r--r--   1 hjmshi  admin    64K Aug 18 12:00 libssp.a
lrwxr-xr-x   1 hjmshi  admin    14B Aug 18 12:00 libssp.dylib -> libssp.0.dylib
-r--r--r--   1 hjmshi  admin   2.1K Aug 18 12:00 libssp_nonshared.a
-r--r--r--   1 hjmshi  admin   3.0M Aug 18 12:03 libstdc++.6.dylib
-r--r--r--   1 hjmshi  admin    15M Aug 18 12:01 libstdc++.a
-r--r--r--   1 hjmshi  admin   2.4K Aug 18 12:01 libstdc++.a-gdb.py
lrwxr-xr-x   1 hjmshi  admin    17B Aug 18 12:01 libstdc++.dylib -> libstdc++.6.dylib
-r--r--r--   1 hjmshi  admin    11M Aug 18 12:01 libstdc++fs.a
-r--r--r--   1 hjmshi  admin   964K Aug 18 12:01 libsupc++.a
-r--r--r--   1 hjmshi  admin   369K Aug 18 12:03 libubsan.1.dylib
lrwxr-xr-x   1 hjmshi  admin    16B Aug 18 12:02 libubsan.dylib -> libubsan.1.dylib

The code you provided gives /usr/local/Cellar/gcc/8.2.0/lib/gcc/8/.

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jfowkes commented on August 18, 2024

Thanks for the output! So PyCUTEst is finding the latest homebrew version of GCC (8.2.0) as intended but the gcc command is using the Apple GCC compiler (which is actually LLVM/clang) and I believe that is where the incompatibility is arising. I assumed that installing GCC via homebrew would automatically point gcc to the homebrew version but that appears not to be the case.

You see the way PyCUTEst works is that for each CUTEst problem it compiles an external C library in the PYCUTEST_CACHE folder (i.e. it caches the problem) and that is the stage at which your issue is arising.

Could you clear out your PYCUTEST_CACHE folder and try setting gcc to point to the latest homebrew GCC version (8.2.0) to see if that fixes your issue? There are a number of ways of doing this, see:
https://stackoverflow.com/questions/28970935/osx-replace-gcc-version-4-2-1-with-4-9-installed-via-homebrew

If not then we’ll have to dig deeper into PyCUTEst’s external C library compilation process.

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hjmshi commented on August 18, 2024

Thanks! This fixed the linker warnings. Unfortunately, even after changing the gcc command to the latest version from homebrew, my kernel still crashes, leading to a Segmentation fault: 11. The crash occurs at the same line as before, so the bug is probably occurring in the external C library compilation.

Thanks again for all of your help!

EDIT: Weirdly enough, in Spyder, my kernel still dies, but when I run everything line-by-line in the terminal after closing some applications, I no longer receive the segmentation fault. I now receive the error

cutestitf.c:34:10: fatal error: cutest.h: No such file or directory
 #include "cutest.h"
          ^~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1
Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
  File "/Users/hjmshi/anaconda/lib/python3.6/site-packages/pycutest/build_interface.py", line 312, in import_problem
    compile_and_install_interface(problemName, destination, sifParams, sifOptions, efirst, lfirst, nvfirst, quiet)
  File "/Users/hjmshi/anaconda/lib/python3.6/site-packages/pycutest/build_interface.py", line 271, in compile_and_install_interface
    raise RuntimeError("Failed to build the Python interface module")
RuntimeError: Failed to build the Python interface module

Do you know why there could be this discrepancy?

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jfowkes commented on August 18, 2024

Glad that fixed the linker warnings! It looks like GCC can’t find the CUTEst header file, I believe that normally cutest.h is installed by homebrew CUTEst into /usr/local/include/, so you could try symlinking it there where GCC should find it. I assume locate cutest.h finds that it is installed somewhere on your system?

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hjmshi commented on August 18, 2024

So I thought I had fixed the linker warnings, but they are appearing again after fixing the cutest.h issue.

Checking through everything again, gcc -v does give:

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/8.2.0/libexec/gcc/x86_64-apple-darwin17.7.0/8.2.0/lto-wrapper
Target: x86_64-apple-darwin17.7.0
Configured with: ../configure --build=x86_64-apple-darwin17.7.0 --prefix=/usr/local/Cellar/gcc/8.2.0 --libdir=/usr/local/Cellar/gcc/8.2.0/lib/gcc/8 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-8 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-checking=release --with-pkgversion='Homebrew GCC 8.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-nls --with-native-system-header-dir=/usr/include --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk
Thread model: posix
gcc version 8.2.0 (Homebrew GCC 8.2.0)

and PyCUTEst is looking at the path /usr/local/Cellar/gcc/8.2.0/lib/gcc/8/. So it does seem that these are consistent but the linker warnings still exist. I also tried reinstalling GCC. Could there be another reason for the linker warnings?

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jfowkes commented on August 18, 2024

So I take it you can run PyCUTEst now without the kernel dying (with linker warnings)?

I’ve done some testing on my Mac and I’m able to run PyCUTEst with either the system GCC or homebrew GCC (exactly the same versions as you’re using) no problem without any linker warnings.

So I think you’re right and there must be another reason for them appearing, and the only one I can think of is that somewhere your system is configured to compile code for MacOS 10.7 (Lion). Unfortunately I don’t know enough about all the different ways this can be configured (apart from the ones I mentioned previously) but I can see that both versions of GCC point to the MacOSX10.13.sdk and that may be configured to target MacOS 10.7 somehow.

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hjmshi commented on August 18, 2024

The kernel still dies and the linker warnings still appear, unfortunately. I will try to look into why my system may be compiling code for Mac OS 10.7. I will keep you posted if I am able to discover the root of this issue. Thanks again for your help!

EDIT: I was able to install PyCUTEst on my other Linux machine, and it works great!

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jfowkes commented on August 18, 2024

That's a shame, I would suggest using gdb (brew install gdb) to debug the kernel dying issue (which may be unrelated to the linker warnings):
http://droettboom.com/blog/2015/11/20/gdb-python-extensions/

Glad you got PyCUTEst working on your Linux machine!

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jfowkes commented on August 18, 2024

I think I have found where the settings are located, please check /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/SDKSettings.plist and make sure that MACOSX_DEPLOYMENT_TARGET is set to 10.13.

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hjmshi commented on August 18, 2024

Thanks Jari. Everything seems fine there. In particular, my SDKSettings.plist file looks like:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
        <key>CanonicalName</key>
        <string>macosx10.13</string>
        <key>CustomProperties</key>
        <dict>
                <key>KERNEL_EXTENSION_HEADER_SEARCH_PATHS</key>
                <string>$(KERNEL_FRAMEWORK)/PrivateHeaders $(KERNEL_FRAMEWORK_HEADERS)</string>
        </dict>
        <key>DefaultProperties</key>
        <dict>
                <key>MACOSX_DEPLOYMENT_TARGET</key>
                <string>10.13</string>
                <key>PLATFORM_NAME</key>
                <string>macosx</string>
                <key>DEFAULT_KEXT_INSTALL_PATH</key>
                <string>$(LIBRARY_KEXT_INSTALL_PATH)</string>
                <key>KASAN_DEFAULT_CFLAGS</key>
                <string>-DKASAN=1 -fsanitize=address -mllvm -asan-globals-live-support -mllvm -asan-force-dynamic-shadow</string>
        </dict>
        <key>DisplayName</key>
        <string>macOS 10.13</string>
        <key>MaximumDeploymentTarget</key>
        <string>10.13.99</string>
        <key>MinimalDisplayName</key>
        <string>10.13</string>
        <key>MinimumSupportedToolsVersion</key>
        <string>3.2</string>
        <key>SupportedBuildToolComponents</key>
        <array>
                <string>com.apple.compilers.gcc.headers.4_2</string>
        </array>
        <key>Version</key>
        <string>10.13</string>
        <key>IsBaseSDK</key>
        <string>YES</string>
</dict>
</plist>

There must be something else going on then...

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jfowkes commented on August 18, 2024

Yes that all looks fine to me (same as mine), the only difference between my homebrew GCC and yours is that mine doesn't have the --with-native-system-header-dir and --with-sysroot lines.

EDIT: According to the homebrew installer (https://github.com/Homebrew/homebrew-core/blob/master/Formula/gcc.rb) these lines are only added if it detects that you do not have the Command Line Tools installed, so I would try reinstalling them (see http://railsapps.github.io/xcode-command-line-tools.html).

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jfowkes commented on August 18, 2024

Just to let you know that we finally managed to get to the bottom of the linker warnings, they're caused by Anaconda setting a very old default MACOSX_DEPLOYMENT_TARGET, please see Issue #9.

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Encountering error when importing problem on Mac OS X 10.13 about pycutest HOT 16 CLOSED

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