Install issuses in MAC(Version:12.5.1, python version 3.6.5)

[zhuyewen]

Dear vtraag,

I also have this @problem(#19) in installation.

(mands4) yons@yonss-iMac ~ % pip install leidenalg
Collecting leidenalg
  Using cached leidenalg-0.8.10.tar.gz (3.8 MB)
Requirement already satisfied: igraph<0.10,>=0.9.0 in ./anaconda3/envs/mands4/lib/python3.6/site-packages (from leidenalg) (0.9.11)
...
...
...
  building 'leidenalg._c_leiden' extension
  creating build/temp.macosx-10.7-x86_64-3.6
  creating build/temp.macosx-10.7-x86_64-3.6/src
  creating build/temp.macosx-10.7-x86_64-3.6/src/leidenalg
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/yons/anaconda3/envs/mands4/include -arch x86_64 -I/Users/yons/anaconda3/envs/mands4/include -arch x86_64 -Iinclude -Ivendor/install/igraph/include/igraph -I/Users/yons/anaconda3/envs/mands4/include/python3.6m -c src/leidenalg/SignificanceVertexPartition.cpp -o build/temp.macosx-10.7-x86_64-3.6/src/leidenalg/SignificanceVertexPartition.o
  clang: warning: include path for libstdc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
  In file included from src/leidenalg/SignificanceVertexPartition.cpp:1:
  In file included from include/SignificanceVertexPartition.h:4:
  include/MutableVertexPartition.h:4:10: fatal error: 'string' file not found
  #include <string>
           ^~~~~~~~
  1 error generated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for leidenalg
  Running setup.py clean for leidenalg
Failed to build leidenalg
Installing collected packages: leidenalg
    Running setup.py install for leidenalg ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/yons/anaconda3/envs/mands4/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/wp/twc9753x10bgcqzdpjfxr9880000gn/T/pip-install-8fcjyrnm/leidenalg_2b8a3b83441744d3a99ac7dbbe4cf56c/setup.py'"'"'; __file__='"'"'/private/var/folders/wp/twc9753x10bgcqzdpjfxr9880000gn/T/pip-install-8fcjyrnm/leidenalg_2b8a3b83441744d3a99ac7dbbe4cf56c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/wp/twc9753x10bgcqzdpjfxr9880000gn/T/pip-record-82059m7c/install-record.txt --single-version-externally-managed --compile --install-headers /Users/yons/anaconda3/envs/mands4/include/python3.6m/leidenalg
         cwd: /private/var/folders/wp/twc9753x10bgcqzdpjfxr9880000gn/T/pip-install-8fcjyrnm/leidenalg_2b8a3b83441744d3a99ac7dbbe4cf56c/
    Complete output (37 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.7-x86_64-3.6
    creating build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/leidenalg/functions.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/leidenalg/Optimiser.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/leidenalg/VertexPartition.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/leidenalg/version.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/leidenalg/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    running build_ext
    running build_c_core
    Libraries: ['igraph', 'c++', 'xml2', 'z']
    Exclusions: []
    Found igraph as static library in vendor/install/igraph/lib/libigraph.a.
    Build type: dynamic extension with vendored igraph source
    Include path: vendor/install/igraph/include/igraph
    Library path: vendor/install/igraph/lib /usr/local/lib /usr/lib
    Runtime library path:
    Linked dynamic libraries: xml2 z
    Linked static libraries: vendor/install/igraph/lib/libigraph.a
    Extra compiler options:
    Extra linker options:
    building 'leidenalg._c_leiden' extension
    creating build/temp.macosx-10.7-x86_64-3.6
    creating build/temp.macosx-10.7-x86_64-3.6/src
    creating build/temp.macosx-10.7-x86_64-3.6/src/leidenalg
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/yons/anaconda3/envs/mands4/include -arch x86_64 -I/Users/yons/anaconda3/envs/mands4/include -arch x86_64 -Iinclude -Ivendor/install/igraph/include/igraph -I/Users/yons/anaconda3/envs/mands4/include/python3.6m -c src/leidenalg/SignificanceVertexPartition.cpp -o build/temp.macosx-10.7-x86_64-3.6/src/leidenalg/SignificanceVertexPartition.o
    clang: warning: include path for libstdc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
    In file included from src/leidenalg/SignificanceVertexPartition.cpp:1:
    In file included from include/SignificanceVertexPartition.h:4:
    include/MutableVertexPartition.h:4:10: fatal error: 'string' file not found
    #include <string>
             ^~~~~~~~
    1 error generated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/yons/anaconda3/envs/mands4/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/wp/twc9753x10bgcqzdpjfxr9880000gn/T/pip-install-8fcjyrnm/leidenalg_2b8a3b83441744d3a99ac7dbbe4cf56c/setup.py'"'"'; __file__='"'"'/private/var/folders/wp/twc9753x10bgcqzdpjfxr9880000gn/T/pip-install-8fcjyrnm/leidenalg_2b8a3b83441744d3a99ac7dbbe4cf56c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/wp/twc9753x10bgcqzdpjfxr9880000gn/T/pip-record-82059m7c/install-record.txt --single-version-externally-managed --compile --install-headers /Users/yons/anaconda3/envs/mands4/include/python3.6m/leidenalg Check the logs for full command output.

Then, I runconda install -c conda-forge leidenalg, and it comes out this

(mands4) yons@yonss-iMac ~ % conda install -c conda-forge leidenalg 
Solving environment: failed

InvalidVersionSpecError: Invalid version spec: =2.7

I also trie it in python2.7, failed also. I have no idea what is going on.

[zhuyewen]

The problem solved when I change the python version to 3.8.

[vtraag]

Hmm, strange, I do not know exactly what is going on. For some reason, it seems that the standard C++ library is not completely found correctly.

It seems you are using Anaconda, so it would be advisable anyway to install using conda. The error that you received

Solving environment: failed

InvalidVersionSpecError: Invalid version spec: =2.7

seems to indicate that your current environment is in an inconsistent state.

You can create a new environment that contains leidenalg (and all its necessary dependencies) using conda create -n leidenalg -c conda-forge leidenalg.