Nixpkgs: building python3Packages.protobuf3_2 on OS X fails due to string include

Created on 12 Jun 2017 · 8Comments · Source: NixOS/nixpkgs

Issue description

Building the python 3 protobuf package fails for me on macOS.

$ nix-build '<nixpkgs>' -A python3Packages.protobuf3_2
...
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -I../src -I/nix/store/nkmdx27mxqq4mz9qvnbd8v754y290ndf-python3-3.6.1/include/python3.6m -c google/protobuf/pyext/descriptor.cc -o build/temp.macosx-10.6-x86_64-3.6/google/protobuf/pyext/descriptor.o -Wno-write-strings -Wno-invalid-offsetof -Wno-sign-compare -Wno-shorten-64-to-32 -std=c++11
clang-4.0: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument]
google/protobuf/pyext/descriptor.cc:35:10: fatal error: 'string' file not found
#include <string>
         ^~~~~~~~
1 error generated.
error: command 'clang' failed with exit status 1
builder for ‘/nix/store/2z36gcrnmi2bz1a3s3nppc8imp11ppgj-python3.6-protobuf-3.2.0.drv’ failed with exit code 1
error: build of ‘/nix/store/2z36gcrnmi2bz1a3s3nppc8imp11ppgj-python3.6-protobuf-3.2.0.drv’ failed

Digging in (by launching nix-shell -A python3Packages.protobuf3_2), the cause seems to be that python setup.py build_ext --cpp_implementation calls CC=clang instead of CXX=clang++. The clang call above fails, but the same call works after replacing clang by clang++. Similarly, CC=$CXX python setup.py build_ext --cpp_implementation works fine.

That in turn matters because of

if [[ "$isCpp" = 1 ]]; then
    if [[ "$cppInclude" = 1 ]]; then
        NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE ${NIX_CXXSTDLIB_COMPILE-}"
    fi
    NIX_CFLAGS_LINK="$NIX_CFLAGS_LINK $NIX_CXXSTDLIB_LINK"
fi

in the clang/clang++ wrappers, because the system include path NIX_CXXSTDLIB_COMPILE is missing in the clang case.

Technical details

System: mac OS 10.12.5
Nix version: nix-env (Nix) 1.11.8
Nixpkgs version: "17.09pre108299.ec9a23332f"
Sandboxing enabled: grep: /etc/nix/nix.conf: No such file or directory :)

When digging in, I used a checkout of nixpkgs with hash 63e9d1c51ec0ad41c3ef729851442f199ce06a25, but it seems to make no difference.

bug darwin python

Source

robx

Most helpful comment

Any reason we can't just change https://github.com/python/cpython/blob/master/Lib/distutils/unixccompiler.py#L58 to use c++? Seems like it would work on Linux just fine, and fix a bunch of other stuff.

copumpkin on 21 Jun 2017

👍2

All 8 comments

https://github.com/NixOS/nixpkgs/issues/16450 seems related.

robx on 12 Jun 2017

@knedlsepp uses Python on Darwin and might help here.

FRidh on 19 Jun 2017

I've had a look at the python setup tools: The relevant line is (rather: appears to be, I haven't tested this) https://github.com/python/cpython/blob/master/Lib/distutils/unixccompiler.py#L58:

    executables = {'preprocessor' : None,
                   'compiler'     : ["cc"],
                   'compiler_so'  : ["cc"],
                   'compiler_cxx' : ["cc"], // <- here
                   'linker_so'    : ["cc", "-shared"],
                   'linker_exe'   : ["cc"],
                   'archiver'     : ["ar", "-cr"],
                   'ranlib'       : None,
                  }

which causes C++ source files to be compile with $CC. Not sure whether this is the right or wrong thing to do...

I see two reasonable ways to fix this bug, in a more principled way than #26606:

fix python distutils to compile C++ files using $CXX
fix nixpkg clang-wrapper/bin/cc to treat cc like c++ with respect to $cppInclude and friends

If 1. is the right thing to do, it might still be nice to work around the bug in another way for now.

robx on 19 Jun 2017

I've also been bitten by this problem once:
https://github.com/NixOS/nixpkgs/issues/18729
The core problem is that setuptools pretty much ignores the difference between CC and CXX. This however is not a problem on a standard mac xcode installation, as both clang++ and clang link the C++ standard library there.
However our nix-clang does not link against the C++ standard library (and probably should not) and that's why you will encounter this problem every once in a while when dealing with darwin and c++ python extensions.
I'm not an expert on the darwin-stdenv, so I wouldn't know how to fix this in a way that does not require hacking our ways around that problem.
To hack around this problem you simply have to grep the pythonPackages for libcxx. There are a few packages that use a workaround that involves adding libcxx to the C-compile flags:
See e.g. here:
https://github.com/NixOS/nixpkgs/blob/6b999f3c42607342231b6fe119fcf0f934f40fd8/pkgs/development/python-modules/matplotlib/default.nix#L32

knedlsepp on 19 Jun 2017

The core problem is that setuptools pretty much ignores the difference between CC and CXX. This however is not a problem on a standard mac xcode installation, as both clang++ and clang link the C++ standard library there.
However our nix-clang does not link against the C++ standard library (and probably should not) and that's why you will encounter this problem every once in a while when dealing with darwin and c++ python extensions.

@LnL7 @copumpkin any clue how to solve this issue?

FRidh on 19 Jun 2017

The problem does not seem all-too widespread, but there are a few instances:

Search results for: "${libcxx}/include/c++/v1"