build failure with Xcode 10 - libstdc++ not supported anymore

Code Sample, a copy-pastable example if possible

(pandas-dev) bilbo:pandas-rb robertbuckley$ python setup.py build_ext --inplace -j 4

running build_ext
building 'pandas._libs.window' extension
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/robertbuckley/anaconda3/envs/pandas-dev/include -arch x86_64 -I/Users/robertbuckley/anaconda3/envs/pandas-dev/include -arch x86_64 -Ipandas/_libs -I./pandas/_libs -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/Users/robertbuckley/anaconda3/envs/pandas-dev/lib/python3.6/site-packages/numpy/core/include -I/Users/robertbuckley/anaconda3/envs/pandas-dev/include/python3.6m -c pandas/_libs/window.cpp -o build/temp.macosx-10.7-x86_64-3.6/pandas/_libs/window.o -Wno-unused-function
warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
pandas/_libs/window.cpp:655:10: fatal error: 'ios' file not found
#include "ios"
         ^~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1

Problem description

I setup a dev environment on Mac OS 10.13 according to https://pandas.pydata.org/pandas-docs/stable/contributing.html#creating-a-development-environment and all was well

Upgraded to 10.14 (mojave) and Xcode 10, and now i get the above failure.

Xcode 10 release notes includes the following deprecation notice

Building with libstdc++ was deprecated with Xcode 8 and is not supported in Xcode 10 when targeting iOS. C++ projects must now migrate to libc++ and are recommended to set a deployment target of macOS 10.9 or later, or iOS 7 or later. Besides changing the C++ Standard Library build setting, developers should audit hard-coded linker flags and target dependencies to remove references to libstdc++ (including -lstdc++, -lstdc++.6.0.9, libstdc++.6.0.9.tbd, and libstdc++.6.0.9.dylib). Project dependencies such as static archives that were built against libstdc++ will also need to be rebuilt against libc++. (40885260)

Some workaround suggestions are at https://stackoverflow.com/questions/52425766/stdlibc-headers-not-found-error-on-xcode-10 and the answer its linked to.

I dont have access to Xcode 9 anymore, so i can’t try the workaround of copying the old libs from there

[robbuckley]

Hi, I got to the bottom of this issue, in the end, after a trawl through clang, distutils and python make/config files.

The compiler standard library defaults to either libstdc++ or libc++, depending on the targetted macOS version - libstdc++ for 10.8 and below, and libc++ for 10.9 and above. This is determined by the environment variable MACOSX_DEPLOYMENT_TARGET or the compiler option-mmacosx-version-min, defaulting to the system version otherwise.

When distuils builds extensions on macOS, it setsMACOSX_DEPLOYMENT_TARGET to the version that python was compiled with, even if the host system / Xcode is newer.

Recent macOS versions of python have a 64-bit only variant built for 10.9 (python.org), and a universal 64/32-bit variant built for 10.6 (python.org) or 10.7 (conda). I am running the conda universal variant, so distutils targets macOS 10.7, despite my system being 10.14, with Xcode 10 which doesn’t install libstdc++. Hence the failure I saw.

It may work for some users, for 1 of 2 reasons:

• libstdc++ is lying around somewhere from a previous Xcode 9 install
• when running a recent 64-bit only variant of python, which targets macOS 10.9 and hence libc++

I’ve pushed a revised change which sets the targeted macOS to 10.9, when running on a 10.9 or above system, with a python/distutils which targets pre-10.9. This should not break builds on pre-10.9 systems, unlike my previous approach. It fixes the issue on my system. CI is running now.

Please let me know if you’d like me to submit it as a PR (assuming CI passes)

[JustinZhengBC]

Not sure if it’s the same issue or if this is a good fix, but I also couldn’t build after updating to mojave (I got my error at a different point though). I fixed it by adding the argument extra_link_args=["-stdlib=libc++", "-mmacosx-version-min=10.9"] to the initialization of Extension object obj here.

https://github.com/pandas-dev/pandas/blob/d78bd7a65f87022bae5021d36c8656c0ea5a7b76/setup.py#L672-L680

Credit for idea here

Here’s my error log before performing the above step:

g++ -bundle -undefined dynamic_lookup -L/Users/admin/anaconda3/envs/pandas-dev/lib -arch x86_64 -L/Users/admin/anaconda3/envs/pandas-dev/lib -arch x86_64 -L/usr/local/opt/libarchive/lib -I/usr/local/opt/libarchive/include -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/pandas/_libs/window.o -o /Users/admin/Documents/Projects/pandas-jz/pandas/_libs/window.cpython-36m-darwin.so
clang: warning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]
ld: library not found for -lstdc++
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'g++' failed with exit status 1