Install issuses in MAC (macOS Mojave with version 10.14.4)

[eleozzr]

Collecting python-igraph>=0.7.1.0 (from leidenalg==0.7.0.post1+19.g0c2a937.dirty)
Building wheels for collected packages: leidenalg
  Building wheel for leidenalg (setup.py) ... error
  Complete output from command /Users/xiaoxiang/miniconda3/envs/py36/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/l9/xq949z0n50q3nywwb3rm3w2h0000gn/T/pip-req-build-8_p5nia0/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/l9/xq949z0n50q3nywwb3rm3w2h0000gn/T/pip-wheel-y7th2abw --python-tag cp36:
  running bdist_wheel
  running build
  running build_py
  UPDATING build/lib.macosx-10.7-x86_64-3.6/leidenalg/_version.py
  set build/lib.macosx-10.7-x86_64-3.6/leidenalg/_version.py to '0.7.0.post1+19.g0c2a937.dirty'
  running build_ext
  Build type: dynamic extension
  Include path: /usr/local/Cellar/igraph/0.7.1_6/include/igraph
  Library path: /usr/local/Cellar/igraph/0.7.1_6/lib
  Linked dynamic libraries: igraph
  Linked static libraries:
  Extra compiler options:
  Extra linker options:
  building 'leidenalg._c_leiden' extension
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/xiaoxiang/miniconda3/envs/py36/include -arch x86_64 -I/Users/xiaoxiang/miniconda3/envs/py36/include -arch x86_64 -Iinclude -I/usr/local/Cellar/igraph/0.7.1_6/include/igraph -I/Users/xiaoxiang/miniconda3/envs/py36/include/python3.6m -c src/SignificanceVertexPartition.cpp -o build/temp.macosx-10.7-x86_64-3.6/src/SignificanceVertexPartition.o -O3
  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]
  In file included from src/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 warning and 1 error generated.
  error: command 'gcc' failed with exit status 1

  ----------------------------------------
  Failed building wheel for leidenalg
  Running setup.py clean for leidenalg
Failed to build leidenalg
Installing collected packages: python-igraph, leidenalg
  Running setup.py install for leidenalg ... error
    Complete output from command /Users/xiaoxiang/miniconda3/envs/py36/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/l9/xq949z0n50q3nywwb3rm3w2h0000gn/T/pip-req-build-8_p5nia0/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/l9/xq949z0n50q3nywwb3rm3w2h0000gn/T/pip-record-65pc1iij/install-record.txt --single-version-externally-managed --compile:
    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/functions.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/Optimiser.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/VertexPartition.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/_version.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    copying src/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/leidenalg
    Fixing build/lib.macosx-10.7-x86_64-3.6/leidenalg/functions.py build/lib.macosx-10.7-x86_64-3.6/leidenalg/Optimiser.py build/lib.macosx-10.7-x86_64-3.6/leidenalg/VertexPartition.py build/lib.macosx-10.7-x86_64-3.6/leidenalg/_version.py build/lib.macosx-10.7-x86_64-3.6/leidenalg/__init__.py
    Skipping optional fixer: buffer
    Skipping optional fixer: idioms
    Skipping optional fixer: set_literal
    Skipping optional fixer: ws_comma
    Fixing build/lib.macosx-10.7-x86_64-3.6/leidenalg/functions.py build/lib.macosx-10.7-x86_64-3.6/leidenalg/Optimiser.py build/lib.macosx-10.7-x86_64-3.6/leidenalg/VertexPartition.py build/lib.macosx-10.7-x86_64-3.6/leidenalg/_version.py build/lib.macosx-10.7-x86_64-3.6/leidenalg/__init__.py
    Skipping optional fixer: buffer
    Skipping optional fixer: idioms
    Skipping optional fixer: set_literal
    Skipping optional fixer: ws_comma
    UPDATING build/lib.macosx-10.7-x86_64-3.6/leidenalg/_version.py
    set build/lib.macosx-10.7-x86_64-3.6/leidenalg/_version.py to '0.7.0.post1+19.g0c2a937.dirty'
    running build_ext
    Build type: dynamic extension
    Include path: /usr/local/Cellar/igraph/0.7.1_6/include/igraph
    Library path: /usr/local/Cellar/igraph/0.7.1_6/lib
    Linked dynamic libraries: igraph
    Linked static libraries:
    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
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/xiaoxiang/miniconda3/envs/py36/include -arch x86_64 -I/Users/xiaoxiang/miniconda3/envs/py36/include -arch x86_64 -Iinclude -I/usr/local/Cellar/igraph/0.7.1_6/include/igraph -I/Users/xiaoxiang/miniconda3/envs/py36/include/python3.6m -c src/SignificanceVertexPartition.cpp -o build/temp.macosx-10.7-x86_64-3.6/src/SignificanceVertexPartition.o -O3
    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]
    In file included from src/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 warning and 1 error generated.
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/Users/xiaoxiang/miniconda3/envs/py36/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/l9/xq949z0n50q3nywwb3rm3w2h0000gn/T/pip-req-build-8_p5nia0/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/l9/xq949z0n50q3nywwb3rm3w2h0000gn/T/pip-record-65pc1iij/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/l9/xq949z0n50q3nywwb3rm3w2h0000gn/T/pip-req-build-8_p5nia0/

I try all possible solutions in https://github.com/vtraag/leidenalg/issues/1, but it still not works.

For reference

(py36) xiaoxiang@ele:leidenalg$ gcc -v
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

and

(py36) xiaoxiang@ele:leidenalg$  brew info gcc

gcc: stable 9.2.0 (bottled), HEAD
GNU compiler collection
https://gcc.gnu.org/
/usr/local/Cellar/gcc/9.2.0 (1,462 files, 291.4MB) *
  Poured from bottle on 2019-09-08 at 19:13:53
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/gcc.rb
==> Dependencies
Required: gmp ✔, isl ✔, libmpc ✔, mpfr ✔
==> Options
--HEAD
    Install HEAD version
==> Analytics
install: 75,462 (30 days), 206,663 (90 days), 923,390 (365 days)
install_on_request: 34,043 (30 days), 93,420 (90 days), 438,057 (365 days)
build_error: 0 (30 days)

[vtraag]

Could you try installing using conda? Unfortunately I have no Mac, making it a bit more difficult to properly test that platform. It seems to build correctly for the Mac from the conda-forge channel. You should be able to install it simply using

conda install -c conda-forge leidenalg 

If that does not work, please report back the error.

[eleozzr]

Thank you. But when I run the code

conda install -c conda-forge leidenalg 

It throws the following errors

(py36) xiaoxiang@ele:~$ conda install -c conda-forge leidenalg 
Collecting package metadata (current_repodata.json): failed

NotWritableError: The current user does not have write permissions to a required path.
  path: /Users/xiaoxiang/miniconda3/pkgs/cache/b35683e8.json
  uid: 501
  gid: 20

If you feel that permissions on this path are set incorrectly, you can manually
change them by executing

  $ sudo chown 501:20 /Users/xiaoxiang/miniconda3/pkgs/cache/b35683e8.json

In general, it's not advisable to use 'sudo conda'.

Even I run conda with sudo

(py36) xiaoxiang@ele:~$ sudo conda install -c conda-forge leidenalg 
Password:
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/xiaoxiang/miniconda3

  added / updated specs:
    - leidenalg

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2019.9.11          |           py37_0         147 KB  conda-forge
    conda-4.7.12               |           py37_0         3.0 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.1 MB

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2019.8.28-0 --> conda-forge::ca-certificates-2019.9.11-hecc5488_0

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi                                         pkgs/main --> conda-forge
  conda                                           pkgs/main --> conda-forge
  openssl              pkgs/main::openssl-1.1.1d-h1de35cc_2 --> conda-forge::openssl-1.1.1c-h01d97ff_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
certifi-2019.9.11    | 147 KB    | ##################################################################################### | 100% 
conda-4.7.12         | 3.0 MB    | ##################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

It looks everything is ok. But when I run the example in https://github.com/vtraag/leidenalg, there is an error AttributeError: module 'leidenalg' has no attribute 'find_partition'. I don't know where I am wrong? Please see the details below.

(py36) xiaoxiang@ele:~$ python
Python 3.6.7 |Anaconda, Inc.| (default, Oct 23 2018, 14:01:38) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import leidenalg
>>> import igraph as ig
>>> G = ig.Graph.Erdos_Renyi(100, 0.1)
>>> part = leidenalg.find_partition(G, leidenalg.ModularityVertexPartition)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'leidenalg' has no attribute 'find_partition'

[vtraag]

That is rather strange. What is the value of leidenalg.__path__? Perhaps something is going wrong with the permissions. Typically, you should install Anaconda as a user (i.e. don't use sudo when installing Anaconda).

[vtraag]

Right now, new binary wheels are being build for the new release, including for macOS. This should fix this issue.