I want to install leidenalg package, but it failed both through pip and through Pycharm's package manager.
This is the error I get when installing with Pycharm package manager:
Using cached leidenalg-0.8.10.tar.gz (3.8 MB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: igraph<0.10,>=0.9.0 in /home/hm31/step_1/venv/lib64/python3.6/site-packages (from leidenalg) (0.9.11)
Requirement already satisfied: texttable>=1.6.2 in /home/hm31/step_1/venv/lib/python3.6/site-packages (from igraph<0.10,>=0.9.0->leidenalg) (1.7.0)
Building wheels for collected packages: leidenalg
Building wheel for leidenalg (setup.py): started
Building wheel for leidenalg (setup.py): finished with status 'error'
Running setup.py clean for leidenalg
Failed to build leidenalg
Installing collected packages: leidenalg
Running setup.py install for leidenalg: started
Running setup.py install for leidenalg: finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /home/hm31/step_1/venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-bj6ahghf/leidenalg_0b2f9bf76b0743108c873593854884a4/setup.py'"'"'; __file__='"'"'/tmp/pip-install-bj6ahghf/leidenalg_0b2f9bf76b0743108c873593854884a4/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'"'"'))' bdist_wheel -d /tmp/pip-wheel-jowsz042
cwd: /tmp/pip-install-bj6ahghf/leidenalg_0b2f9bf76b0743108c873593854884a4/
Complete output (28 lines):
/home/hm31/step_1/venv/lib/python3.6/site-packages/setuptools/installer.py:30: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
SetuptoolsDeprecationWarning,
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/Optimiser.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/VertexPartition.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/__init__.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/functions.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/version.py -> build/lib.linux-x86_64-3.6/leidenalg
running build_ext
running build_c_core
We are going to build the C core of igraph.
Source folder: vendor/source/igraph
Build folder: vendor/build/igraph
Install folder: vendor/install/igraph
Configuring build...
CMake Error at CMakeLists.txt:4 (cmake_minimum_required):
CMake 3.16 or higher is required. You are running version 2.8.12.2
-- Configuring incomplete, errors occurred!
Build failed for the C core of igraph.
----------------------------------------
ERROR: Failed building wheel for leidenalg
WARNING: Error parsing requirements for decorator: [Errno 2] No such file or directory: '/home/hm31/step_1/venv/lib/python3.6/site-packages/decorator-5.1.1.dist-info/METADATA'
ERROR: Command errored out with exit status 1:
command: /home/hm31/step_1/venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-bj6ahghf/leidenalg_0b2f9bf76b0743108c873593854884a4/setup.py'"'"'; __file__='"'"'/tmp/pip-install-bj6ahghf/leidenalg_0b2f9bf76b0743108c873593854884a4/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 /tmp/pip-record-8ze98gsh/install-record.txt --single-version-externally-managed --compile --install-headers /home/hm31/step_1/venv/include/site/python3.6/leidenalg
cwd: /tmp/pip-install-bj6ahghf/leidenalg_0b2f9bf76b0743108c873593854884a4/
Complete output (30 lines):
/home/hm31/step_1/venv/lib/python3.6/site-packages/setuptools/installer.py:30: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
SetuptoolsDeprecationWarning,
running install
/home/hm31/step_1/venv/lib/python3.6/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
setuptools.SetuptoolsDeprecationWarning,
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/Optimiser.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/VertexPartition.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/__init__.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/functions.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/version.py -> build/lib.linux-x86_64-3.6/leidenalg
running build_ext
running build_c_core
We are going to build the C core of igraph.
Source folder: vendor/source/igraph
Build folder: vendor/build/igraph
Install folder: vendor/install/igraph
Configuring build...
CMake Error at CMakeLists.txt:4 (cmake_minimum_required):
CMake 3.16 or higher is required. You are running version 2.8.12.2
-- Configuring incomplete, errors occurred!
Build failed for the C core of igraph.
----------------------------------------
ERROR: Command errored out with exit status 1: /home/hm31/step_1/venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-bj6ahghf/leidenalg_0b2f9bf76b0743108c873593854884a4/setup.py'"'"'; __file__='"'"'/tmp/pip-install-bj6ahghf/leidenalg_0b2f9bf76b0743108c873593854884a4/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 /tmp/pip-record-8ze98gsh/install-record.txt --single-version-externally-managed --compile --install-headers /home/hm31/step_1/venv/include/site/python3.6/leidenalg Check the logs for full command output.
I omitted the pip error due to space constraints. I am using Python 3.6.8. Additionally, I recall adding Leidenalg to a conda environment with some difficulties that I don't remember now. I'm currently using Venv.
Thanks.
P.S: Even after upgrading cmake, this is the error I get:
(venv) [hm31@chackoge-serv01 step_10_cluster]$ pip install leidenalg
Collecting leidenalg
Using cached leidenalg-0.8.10.tar.gz (3.8 MB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: igraph<0.10,>=0.9.0 in /home/hm31/step_1/venv/lib64/python3.6/site-packages (from leidenalg) (0.9.11)
Requirement already satisfied: texttable>=1.6.2 in /home/hm31/step_1/venv/lib/python3.6/site-packages (from igraph<0.10,>=0.9.0->leidenalg) (1.7.0)
Building wheels for collected packages: leidenalg
Building wheel for leidenalg (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/hm31/step_1/venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/setup.py'"'"'; __file__='"'"'/tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/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'"'"'))' bdist_wheel -d /tmp/pip-wheel-z3o7dnh2
cwd: /tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/
Complete output (1059 lines):
/home/hm31/step_1/venv/lib/python3.6/site-packages/setuptools/installer.py:30: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
SetuptoolsDeprecationWarning,
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/Optimiser.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/VertexPartition.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/__init__.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/functions.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/version.py -> build/lib.linux-x86_64-3.6/leidenalg
running build_ext
running build_c_core
We are going to build the C core of igraph.
Source folder: vendor/source/igraph
Build folder: vendor/build/igraph
Install folder: vendor/install/igraph
Configuring build...
-- Setting build type to 'Release' as none was specified.
-- Version number: 0.9.8
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS_NO_VARARGS_FLAG
-- Performing Test COMPILER_SUPPORTS_NO_VARARGS_FLAG - Success
-- Performing Test COMPILER_SUPPORTS_NO_UNKNOWN_WARNING_OPTION_FLAG
-- Performing Test COMPILER_SUPPORTS_NO_UNKNOWN_WARNING_OPTION_FLAG - Success
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found FLEX: /usr/bin/flex (found version "2.5.37")
-- Found BISON: /usr/bin/bison (found version "3.0.4")
-- Looking for expm1
-- Looking for expm1 - found
-- Looking for fmin
-- Looking for fmin - found
-- Looking for finite
-- Looking for finite - found
-- Looking for isfinite
-- Looking for isfinite - found
-- Looking for log2
-- Looking for log2 - found
-- Looking for log1p
-- Looking for log1p - found
-- Looking for rint
-- Looking for rint - found
-- Looking for rintf
-- Looking for rintf - found
-- Looking for round
-- Looking for round - found
-- Looking for stpcpy
-- Looking for stpcpy - found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strdup
-- Looking for strdup - found
-- Looking for _stricmp
-- Looking for _stricmp - not found
-- Looking for _LIBCPP_VERSION
-- Looking for _LIBCPP_VERSION - not found
-- Looking for __GLIBCXX__
-- Looking for __GLIBCXX__ - found
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Found Python3: /home/hm31/step_1/venv/bin/python3.6 (found version "3.6.8") found components: Interpreter
--
-- -----[ Build configuration ]----
-- Version: 0.9.8
-- CMake build type: Release
-- Library type: static
--
-- ----------[ Features ]----------
-- GLPK for optimization: yes
-- Reading GraphML files: yes
-- Thread-local storage: no
-- Link-time optimization: no
--
-- --------[ Dependencies ]--------
-- ARPACK: vendored
-- BISON: yes
-- BLAS: vendored
-- CXSparse: vendored
-- FLEX: yes
-- GLPK: vendored
-- GMP: vendored
-- LAPACK: vendored
-- LibXml2: yes
-- OpenMP: yes
-- PLFIT: vendored
--
-- -----------[ Testing ]----------
-- Diff tool: not found
-- Sanitizers: none
-- Code coverage: no
-- Verify 'finally' stack: no
--
-- --------[ Documentation ]-------
-- HTML: no
-- PDF: no
--
-- igraph configured successfully.
--
-- Configuring done (3.0s)
-- Generating done (0.2s)
-- Build files have been written to: /tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/vendor/build/igraph
Running build...
(Omitted due to space limits)
Installing build...
-- Installing: /tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/vendor/install/igraph/lib64/libigraph.a
-- Installing: /tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/vendor/install/igraph/include/igraph
-- Installing: /tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/vendor/install/igraph/include/igraph/igraph.h
h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/vendor/install/igraph/lib64/cmake/igraph/igraph-targets-release.cmake
Libraries: ['igraph', 'm', 'stdc++', 'xml2', 'z', 'gomp', 'pthread']
Exclusions: []
Found igraph as static library in vendor/install/igraph/lib64/libigraph.a.
Build type: dynamic extension with vendored igraph source
Include path: vendor/install/igraph/include/igraph
Library path: vendor/install/igraph/lib64 /usr/local/lib64 /usr/local/lib /usr/lib64 /usr/lib /lib64 /lib
Runtime library path:
Linked dynamic libraries: m xml2 z gomp pthread
Linked static libraries: vendor/install/igraph/lib64/libigraph.a
Extra compiler options:
Extra linker options:
building 'leidenalg._c_leiden' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/src
creating build/temp.linux-x86_64-3.6/src/leidenalg
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Iinclude -Ivendor/install/igraph/include/igraph -I/home/hm31/step_1/venv/include -I/usr/include/python3.6m -c src/leidenalg/CPMVertexPartition.cpp -o build/temp.linux-x86_64-3.6/src/leidenalg/CPMVertexPartition.o
In file included from include/MutableVertexPartition.h:5:0,
from include/ResolutionParameterVertexPartition.h:4,
from include/LinearResolutionParameterVertexPartition.h:4,
from include/CPMVertexPartition.h:4,
from src/leidenalg/CPMVertexPartition.cpp:1:
include/GraphHelper.h: In function ‘T sum(std::vector<T>)’:
include/GraphHelper.h:35:14: error: range-based ‘for’ loops are not allowed in C++98 mode
for (T x : vec)
^
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for leidenalg
Running setup.py clean for leidenalg
Failed to build leidenalg
WARNING: Error parsing requirements for decorator: [Errno 2] No such file or directory: '/home/hm31/step_1/venv/lib/python3.6/site-packages/decorator-5.1.1.dist-info/METADATA'
Installing collected packages: leidenalg
Running setup.py install for leidenalg ... error
ERROR: Command errored out with exit status 1:
command: /home/hm31/step_1/venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/setup.py'"'"'; __file__='"'"'/tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/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 /tmp/pip-record-9i4vehuu/install-record.txt --single-version-externally-managed --compile --install-headers /home/hm31/step_1/venv/include/site/python3.6/leidenalg
cwd: /tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/
Complete output (43 lines):
/home/hm31/step_1/venv/lib/python3.6/site-packages/setuptools/installer.py:30: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
SetuptoolsDeprecationWarning,
running install
/home/hm31/step_1/venv/lib/python3.6/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
setuptools.SetuptoolsDeprecationWarning,
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/Optimiser.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/VertexPartition.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/__init__.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/functions.py -> build/lib.linux-x86_64-3.6/leidenalg
copying src/leidenalg/version.py -> build/lib.linux-x86_64-3.6/leidenalg
running build_ext
running build_c_core
Libraries: ['igraph', 'm', 'stdc++', 'xml2', 'z', 'gomp', 'pthread']
Exclusions: []
Found igraph as static library in vendor/install/igraph/lib64/libigraph.a.
Build type: dynamic extension with vendored igraph source
Include path: vendor/install/igraph/include/igraph
Library path: vendor/install/igraph/lib64 /usr/local/lib64 /usr/local/lib /usr/lib64 /usr/lib /lib64 /lib
Runtime library path:
Linked dynamic libraries: m xml2 z gomp pthread
Linked static libraries: vendor/install/igraph/lib64/libigraph.a
Extra compiler options:
Extra linker options:
building 'leidenalg._c_leiden' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/src
creating build/temp.linux-x86_64-3.6/src/leidenalg
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Iinclude -Ivendor/install/igraph/include/igraph -I/home/hm31/step_1/venv/include -I/usr/include/python3.6m -c src/leidenalg/CPMVertexPartition.cpp -o build/temp.linux-x86_64-3.6/src/leidenalg/CPMVertexPartition.o
In file included from include/MutableVertexPartition.h:5:0,
from include/ResolutionParameterVertexPartition.h:4,
from include/LinearResolutionParameterVertexPartition.h:4,
from include/CPMVertexPartition.h:4,
from src/leidenalg/CPMVertexPartition.cpp:1:
include/GraphHelper.h: In function ‘T sum(std::vector<T>)’:
include/GraphHelper.h:35:14: error: range-based ‘for’ loops are not allowed in C++98 mode
for (T x : vec)
^
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/hm31/step_1/venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/setup.py'"'"'; __file__='"'"'/tmp/pip-install-h9r0okpt/leidenalg_f86369d826b04bc6bd372ccd68782138/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 /tmp/pip-record-9i4vehuu/install-record.txt --single-version-externally-managed --compile --install-headers /home/hm31/step_1/venv/include/site/python3.6/leidenalg Check the logs for full command output.```