Installation issue on Ubuntu 22.04

[ivan-marroquin]

Hi,

Many thanks for making available this great package!

I have Ubuntu 22.04 and I am using Python 3.9.0.

I tried the pip command installation without success. Then, I tried to compile it and got these error messages:

python3 setup.py install

Installing fa2 package (fastest forceatlas2 python implementation)

Cython is installed?
Yes

Starting to install!

running install
/home/ivan/python_3.9.0/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
/home/ivan/python_3.9.0/lib/python3.9/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running bdist_egg
running egg_info
creating fa2.egg-info
writing fa2.egg-info/PKG-INFO
writing dependency_links to fa2.egg-info/dependency_links.txt
writing requirements to fa2.egg-info/requires.txt
writing top-level names to fa2.egg-info/top_level.txt
writing manifest file 'fa2.egg-info/SOURCES.txt'
reading manifest file 'fa2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'fa2.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-cpython-39
creating build/lib.linux-x86_64-cpython-39/fa2
copying fa2/fa2util.py -> build/lib.linux-x86_64-cpython-39/fa2
copying fa2/forceatlas2.py -> build/lib.linux-x86_64-cpython-39/fa2
copying fa2/init.py -> build/lib.linux-x86_64-cpython-39/fa2
copying fa2/fa2util.c -> build/lib.linux-x86_64-cpython-39/fa2
copying fa2/fa2util.pxd -> build/lib.linux-x86_64-cpython-39/fa2
running build_ext
skipping 'fa2/fa2util.c' Cython extension (up-to-date)
building 'fa2.fa2util' extension
creating build/temp.linux-x86_64-cpython-39
creating build/temp.linux-x86_64-cpython-39/fa2
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/home/ivan/python_3.9.0/include/python3.9 -c fa2/fa2util.c -o build/temp.linux-x86_64-cpython-39/fa2/fa2util.o
fa2/fa2util.c: In function ‘__Pyx_ParseOptionalKeywords’:
fa2/fa2util.c:12107:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12107 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12107:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
12107 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan_phd/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12107:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12107 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan_phd/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12107:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12107 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan_phd/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12107:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
12107 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan_phd/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12107:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12107 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12123:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12123 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12123:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
12123 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12123:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12123 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12123:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12123 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan_phd/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12123:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
12123 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
| ^~~~~~~~~~~~~~~~~~~
fa2/fa2util.c:12123:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12123 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
| ^
In file included from /home/ivan/python_3.9.0/include/python3.9/unicodeobject.h:1026,
from /home/ivan/python_3.9.0/include/python3.9/Python.h:97,
from fa2/fa2util.c:4:
/home/ivan/python_3.9.0/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared build/temp.linux-x86_64-cpython-39/fa2/fa2util.o -o build/lib.linux-x86_64-cpython-39/fa2/fa2util.cpython-39-x86_64-linux-gnu.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/fa2
copying build/lib.linux-x86_64-cpython-39/fa2/fa2util.py -> build/bdist.linux-x86_64/egg/fa2
copying build/lib.linux-x86_64-cpython-39/fa2/fa2util.cpython-39-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg/fa2
copying build/lib.linux-x86_64-cpython-39/fa2/fa2util.pxd -> build/bdist.linux-x86_64/egg/fa2
copying build/lib.linux-x86_64-cpython-39/fa2/fa2util.c -> build/bdist.linux-x86_64/egg/fa2
copying build/lib.linux-x86_64-cpython-39/fa2/forceatlas2.py -> build/bdist.linux-x86_64/egg/fa2
copying build/lib.linux-x86_64-cpython-39/fa2/init.py -> build/bdist.linux-x86_64/egg/fa2
byte-compiling build/bdist.linux-x86_64/egg/fa2/fa2util.py to fa2util.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/fa2/forceatlas2.py to forceatlas2.cpython-39.pyc
byte-compiling build/bdist.linux-x86_64/egg/fa2/init.py to init.cpython-39.pyc
creating stub loader for fa2/fa2util.cpython-39-x86_64-linux-gnu.so
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying fa2.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying fa2.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying fa2.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying fa2.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying fa2.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/fa2-0.3.5-py3.9-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing fa2-0.3.5-py3.9-linux-x86_64.egg
Copying fa2-0.3.5-py3.9-linux-x86_64.egg to /home/ivan_phd/python_3.9.0/lib/python3.9/site-packages
Adding fa2 0.3.5 to easy-install.pth file

Installed /home/ivan/python_3.9.0/lib/python3.9/site-packages/fa2-0.3.5-py3.9-linux-x86_64.egg
Processing dependencies for fa2==0.3.5
Searching for tqdm==4.64.1
Best match: tqdm 4.64.1
Adding tqdm 4.64.1 to easy-install.pth file
Installing tqdm script to /home/ivan_phd/python_3.9.0/bin

Using /home/ivan/python_3.9.0/lib/python3.9/site-packages
Searching for scipy==1.9.1
Best match: scipy 1.9.1
Adding scipy 1.9.1 to easy-install.pth file

Using /home/ivan/python_3.9.0/lib/python3.9/site-packages
Searching for numpy==1.23.3
Best match: numpy 1.23.3
Adding numpy 1.23.3 to easy-install.pth file
Installing f2py script to /home/ivan_phd/python_3.9.0/bin
Installing f2py3 script to /home/ivan_phd/python_3.9.0/bin
Installing f2py3.9 script to /home/ivan_phd/python_3.9.0/bin

Using /home/ivan/python_3.9.0/lib/python3.9/site-packages
Finished processing dependencies for fa2==0.3.5

Any suggestions?

Best regards,

Ivan

[irahorecka]

Hey @ivan-marroquin, I was having the exact same issue as you. Check out the response by @ojdo in #34. This worked for me.

On a side note, make sure networkx version is < 3

[ivan-marroquin]

Thanks @irahorecka for letting me know about this solution. I will give it a try.

[ivan-marroquin]

Hi @irahorecka

I gave it a try, and got this error message:

fa2/fa2util.c:4:10: fatal error: Python.h: No such file or directory
4 | #include "Python.h"

I found this ticket in Stack Overflow:
https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory

The error message is still there. Did you encounter this issue?

Thanks,
Ivan

[irahorecka]

I did not! What Python version are you running? I'm running Python 3.10.6 on Ubuntu 22.04.2 LTS.

[ivan-marroquin]

I am using Python 3.9.0 and I compiled it from its code source. I guess that I need to compile a new version of Python