Cythonizing fails because of unknown type name 'uint64_t'

Question

This may be a newbie problem. I can't cythonize a simple helloworld.pyx tutorial script while the exact same code works on linux:

print("hello world")

Here is the setup.py script:

from distutils.core import setup

from Cython.Build import cythonize

setup(ext_modules = cythonize('helloworld.pyx'))

But I get this after running python setup.py build_ext --inplace:

running build_ext
building 'helloworld' extension
creating build
creating build/temp.macosx-10.7-x86_64-3.6
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/haotian/anaconda3/include -arch x86_64 -I/Users/haotian/anaconda3/include -arch x86_64 -I/Users/haotian/anaconda3/include/python3.6m -c helloworld.c -o build/temp.macosx-10.7-x86_64-3.6/helloworld.o
In file included from helloworld.c:16:
In file included from /Users/haotian/anaconda3/include/python3.6m/Python.h:34:
In file included from /usr/include/stdlib.h:65:
In file included from /usr/include/sys/wait.h:110:
/usr/include/sys/resource.h:196:2: error: unknown type name 'uint8_t'
        uint8_t  ri_uuid[16];
        ^
/usr/include/sys/resource.h:197:2: error: unknown type name 'uint64_t'
        uint64_t ri_user_time;
        ^
/usr/include/sys/resource.h:198:2: error: unknown type name 'uint64_t'
        uint64_t ri_system_time;
        ^
/usr/include/sys/resource.h:199:2: error: unknown type name 'uint64_t'
        uint64_t ri_pkg_idle_wkups;
        ^
/usr/include/sys/resource.h:200:2: error: unknown type name 'uint64_t'
        uint64_t ri_interrupt_wkups;
        ^
/usr/include/sys/resource.h:201:2: error: unknown type name 'uint64_t'
        uint64_t ri_pageins;
        ^
/usr/include/sys/resource.h:202:2: error: unknown type name 'uint64_t'
        uint64_t ri_wired_size;
        ^
/usr/include/sys/resource.h:203:2: error: unknown type name 'uint64_t'
        uint64_t ri_resident_size;
        ^
/usr/include/sys/resource.h:204:2: error: unknown type name 'uint64_t'
        uint64_t ri_phys_footprint;
        ^
/usr/include/sys/resource.h:205:2: error: unknown type name 'uint64_t'
        uint64_t ri_proc_start_abstime;
        ^
/usr/include/sys/resource.h:206:2: error: unknown type name 'uint64_t'
        uint64_t ri_proc_exit_abstime;
        ^
/usr/include/sys/resource.h:210:2: error: unknown type name 'uint8_t'
        uint8_t  ri_uuid[16];
        ^
/usr/include/sys/resource.h:211:2: error: unknown type name 'uint64_t'
        uint64_t ri_user_time;
        ^
/usr/include/sys/resource.h:212:2: error: unknown type name 'uint64_t'
        uint64_t ri_system_time;
        ^
/usr/include/sys/resource.h:213:2: error: unknown type name 'uint64_t'
        uint64_t ri_pkg_idle_wkups;
        ^
/usr/include/sys/resource.h:214:2: error: unknown type name 'uint64_t'
        uint64_t ri_interrupt_wkups;
        ^
/usr/include/sys/resource.h:215:2: error: unknown type name 'uint64_t'
        uint64_t ri_pageins;
        ^
/usr/include/sys/resource.h:216:2: error: unknown type name 'uint64_t'
        uint64_t ri_wired_size;
        ^
/usr/include/sys/resource.h:217:2: error: unknown type name 'uint64_t'
        uint64_t ri_resident_size;
        ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
error: command 'gcc' failed with exit status 1

I'm on MacOS 10.13.1, python 3.6.3, Cython 0.27.3 and clang-900.0.38.

Apparently there is a problem with including stdint.h, how should I go about doing it in Cython?

EDIT: My gcc is in /usr/bin/gcc

gcc --version

shows:

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 9.0.0 (clang-900.0.38)
Target: x86_64-apple-darwin17.2.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Are you sure you are using clang and not gcc? Which version is your gcc, which is used if the log to be trusted? — ead, Dec 04 '17 at 14:39
helloworld.c might not contain `#include `. Alternatively, you are stuck in "crap mode", aka gnu90. Pass `-std=c99` or `-std=c11` to the gcc compiler. — Lundin, Dec 04 '17 at 14:47
It looks as if clang „pretends“ to be gcc and uses pretty old gcc-headers (4.2.1). You should either use clang directly (set CC environment variable to clang) or install a newer gcc version — ead, Dec 04 '17 at 17:33
setting the CC doesn't seems to work, and I tried manually run gcc-7: `/usr/local/bin/gcc-7 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/haotian/anaconda3/include -arch x86_64 -I/Users/haotian/anaconda3/include -arch x86_64 -I/Users/haotian/anaconda3/include/python3.6m -c helloworld.c -o build/temp.macosx-10.7-x86_64-3.6/helloworld.o` which also gives me same error — Haution L., Dec 04 '17 at 18:33

score 6 · Answer 1 · edited Apr 22 '18 at 14:11

6

I faced a similar situation after migrating to a new Mac. Just reinstalling brew did not solve the issues. I had to remove /usr/local/include to fix the issue.

(Comment from Cython Issue on Github)

edited Apr 22 '18 at 14:11

Stephen Rauch

47,830
31
106
135

answered Apr 22 '18 at 13:47

poWar

745
6
15

1

This was necessary for me to fix, as well. Thank you! – Bodhi Oct 14 '18 at 22:27
Instead of removing it, clean it out: https://stackoverflow.com/a/71449852/521662 – Seth Mar 12 '22 at 12:54

score 3 · Accepted Answer · answered Dec 08 '17 at 19:41

I have found a solution to my problem.

It seems like after installing High Sierra some header files in the /usr/local/include are messed up, and causing the brew installation to malfunction. Uninstall and reinstalling brew solved the problem.

rm -rf /usr/local/Cellar /usr/local/.git && brew cleanup
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install )"

Cythonizing fails because of unknown type name 'uint64_t'

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