build fails with Anaconda environment

[tsjshg]

Hi there,

I got an error like this.

running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/kmeans1d
copying kmeans1d/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/kmeans1d
copying kmeans1d/core.py -> build/lib.macosx-10.7-x86_64-3.7/kmeans1d
copying kmeans1d/version.txt -> build/lib.macosx-10.7-x86_64-3.7/kmeans1d
running build_ext
building 'kmeans1d._core' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/kmeans1d
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/shingo/anaconda3/include -arch x86_64 -I/Users/shingo/anaconda3/include -arch x86_64 -I/Users/shingo/anaconda3/include/python3.7m -c kmeans1d/_core.cpp -o build/temp.macosx-10.7-x86_64-3.7/kmeans1d/_core.o -std=c++11
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]
kmeans1d/_core.cpp:3:10: fatal error: 'algorithm' file not found
#include <algorithm>
         ^~~~~~~~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1

The error occurs only with Anaconda python. I got no error when I use PSF made python command.

I found a similar error and its solutions. According to this, I modified setup.py as following.

extension = Extension('kmeans1d._core', ["kmeans1d/_core.cpp"], 
                        include_dirs=['/Library/Developer/CommandLineTools/usr/include/c++/v1'],
                       extra_link_args=["-stdlib=libc++"],
                       extra_compile_args=['-std=c++11'])

Then I successfully build the package with anaconda python.

I'm sending this just for your information.

[dstein64]

Thanks for reporting this.

I was able to reproduce the problem.

I guess that a general solution would be to distribute Python wheel files with the kmeans1d C++ code already compiled. This would have the added benefit that the library would then work even when a user doesn't have a compiler toolchain for building kmeans1d.

That would be a more substantial task, since I'd prefer to automate the process. In the meantime, I put in a fix in PR #3 that allows kmeans1d to compile on Anaconda on macOS. If the initial compilation fails, a second attempt is made using the -stdlib=libc++ argument for the compiler and linker.

[dstein64]

As of version 0.3.1, kmeans1d is packaged on PyPI with pre-built wheels, which should reduce the prevalence of similar installation problems.