Install issuses in MAC(Version:12.5.1, python version 3.6.5)
zhuyewen opened this issue · 2 comments
zhuyewen commented
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 commented
The problem solved when I change the python version to 3.8.
vtraag commented
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.