I have some problems creating an environment for my code.
The code requires a quite old Python version, but I am able to recreate the environment in my Ubuntu 22.04 LTS (Desktop). The problem arises when I try to install it on Ubuntu 20.04 (which is the OS of the machine in which I have to use it), because the installation fails. The environment is build from a file, the contents of which can be found in the following.
name: tractome
channels:
- https://repo.anaconda.com/pkgs/free
- conda-forge
- defaults
dependencies:
- cython=0.29.7
- pydicom=1.3.0
- dipy=0.14.0
- joblib=0.13.2
- matplotlib=1.5.1
- nibabel=2.4.0
- numpy=1.11
- pip=19.1
- pyglet=1.3.2
- pyqt=4.11.4
- pyside=1.2.4
- python=2.7.16
- qt=4.8.7
- pip:
- git+https://github.com/fos/fos.git
To create the environment I am using miniconda3, and it can install anything except for the pip dependencies. Any idea what’s going wrong?
EDIT:
The complete error displayed in the terminal is this:
Building wheels for collected packages: fos
Building wheel for fos (setup.py): started
Building wheel for fos (setup.py): finished with status 'error'
Running setup.py clean for fos
Failed to build fos
Installing collected packages: fos
Running setup.py install for fos: started
Running setup.py install for fos: finished with status 'error'
Pip subprocess error:
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Running command git clone -q https://github.com/fos/fos.git /tmp/pip-req-build-fKXgf6
ERROR: Complete output from command /home/connectbrain_admin/miniconda3/envs/tractome/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-req-build-fKXgf6/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 /tmp/pip-wheel-PtL9MQ --python-tag cp27:
ERROR: /home/connectbrain_admin/miniconda3/envs/tractome/lib/python2.7/site-packages/setuptools/dist.py:351: UserWarning: Normalizing '0.3.0.dev' to '0.3.0.dev0'
normalized_version,
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/fos
copying fos/coords.py -> build/lib.linux-x86_64-2.7/fos
copying fos/app.py -> build/lib.linux-x86_64-2.7/fos
copying fos/color.py -> build/lib.linux-x86_64-2.7/fos
copying fos/camera.py -> build/lib.linux-x86_64-2.7/fos
copying fos/__init__.py -> build/lib.linux-x86_64-2.7/fos
copying fos/world.py -> build/lib.linux-x86_64-2.7/fos
copying fos/modelmat.py -> build/lib.linux-x86_64-2.7/fos
copying fos/util.py -> build/lib.linux-x86_64-2.7/fos
copying fos/vsml.py -> build/lib.linux-x86_64-2.7/fos
copying fos/window.py -> build/lib.linux-x86_64-2.7/fos
copying fos/light.py -> build/lib.linux-x86_64-2.7/fos
copying fos/transform.py -> build/lib.linux-x86_64-2.7/fos
creating build/lib.linux-x86_64-2.7/fos/interact
copying fos/interact/__init__.py -> build/lib.linux-x86_64-2.7/fos/interact
creating build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/skeleton.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/axes.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/scatter.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/mesh.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/scalebar.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/network.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/__init__.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/microcircuit.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/chutext.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/line.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/slicer.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/text.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/base.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/primitives.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/tex3d.py -> build/lib.linux-x86_64-2.7/fos/actor
creating build/lib.linux-x86_64-2.7/fos/shader
copying fos/shader/lib.py -> build/lib.linux-x86_64-2.7/fos/shader
copying fos/shader/__init__.py -> build/lib.linux-x86_64-2.7/fos/shader
creating build/lib.linux-x86_64-2.7/fos/external
copying fos/external/__init__.py -> build/lib.linux-x86_64-2.7/fos/external
creating build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/ft_enums.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/ft_structs.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/__init__.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/ft_types.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/ft_errors.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
creating build/lib.linux-x86_64-2.7/fos/data
copying fos/data/__init__.py -> build/lib.linux-x86_64-2.7/fos/data
creating build/lib.linux-x86_64-2.7/fos/actor/dynamic
copying fos/actor/dynamic/skeleton.py -> build/lib.linux-x86_64-2.7/fos/actor/dynamic
copying fos/actor/dynamic/__init__.py -> build/lib.linux-x86_64-2.7/fos/actor/dynamic
running build_ext
cythoning fos/interact/collision.pyx to fos/interact/collision.c
/home/connectbrain_admin/miniconda3/envs/tractome/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-req-build-fKXgf6/fos/interact/collision.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
warning: fos/interact/collision.pyx:272:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:272:21: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:346:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:346:19: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:346:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:346:28: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:375:15: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:375:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:375:25: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:462:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:462:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:462:22: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:478:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:478:22: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:478:28: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:577:39: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:579:17: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:579:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:581:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:581:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:581:34: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:709:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:709:21: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:709:28: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:785:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:785:21: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:785:28: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:857:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:857:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:857:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:857:37: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:857:44: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:857:51: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: fos/interact/collision.pyx:859:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
building 'fos.interact.collision' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/fos
creating build/temp.linux-x86_64-2.7/fos/interact
gcc -pthread -B /home/connectbrain_admin/miniconda3/envs/tractome/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/connectbrain_admin/miniconda3/envs/tractome/lib/python2.7/site-packages/numpy/core/include -I/home/connectbrain_admin/miniconda3/envs/tractome/include/python2.7 -c fos/interact/collision.c -o build/temp.linux-x86_64-2.7/fos/interact/collision.o
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for fos
ERROR: Complete output from command /home/connectbrain_admin/miniconda3/envs/tractome/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-req-build-fKXgf6/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-PBazb4/install-record.txt --single-version-externally-managed --compile:
ERROR: /home/connectbrain_admin/miniconda3/envs/tractome/lib/python2.7/site-packages/setuptools/dist.py:351: UserWarning: Normalizing '0.3.0.dev' to '0.3.0.dev0'
normalized_version,
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/fos
copying fos/coords.py -> build/lib.linux-x86_64-2.7/fos
copying fos/app.py -> build/lib.linux-x86_64-2.7/fos
copying fos/color.py -> build/lib.linux-x86_64-2.7/fos
copying fos/camera.py -> build/lib.linux-x86_64-2.7/fos
copying fos/__init__.py -> build/lib.linux-x86_64-2.7/fos
copying fos/world.py -> build/lib.linux-x86_64-2.7/fos
copying fos/modelmat.py -> build/lib.linux-x86_64-2.7/fos
copying fos/util.py -> build/lib.linux-x86_64-2.7/fos
copying fos/vsml.py -> build/lib.linux-x86_64-2.7/fos
copying fos/window.py -> build/lib.linux-x86_64-2.7/fos
copying fos/light.py -> build/lib.linux-x86_64-2.7/fos
copying fos/transform.py -> build/lib.linux-x86_64-2.7/fos
creating build/lib.linux-x86_64-2.7/fos/interact
copying fos/interact/__init__.py -> build/lib.linux-x86_64-2.7/fos/interact
creating build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/skeleton.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/axes.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/scatter.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/mesh.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/scalebar.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/network.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/__init__.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/microcircuit.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/chutext.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/line.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/slicer.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/text.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/base.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/primitives.py -> build/lib.linux-x86_64-2.7/fos/actor
copying fos/actor/tex3d.py -> build/lib.linux-x86_64-2.7/fos/actor
creating build/lib.linux-x86_64-2.7/fos/shader
copying fos/shader/lib.py -> build/lib.linux-x86_64-2.7/fos/shader
copying fos/shader/__init__.py -> build/lib.linux-x86_64-2.7/fos/shader
creating build/lib.linux-x86_64-2.7/fos/external
copying fos/external/__init__.py -> build/lib.linux-x86_64-2.7/fos/external
creating build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/ft_enums.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/ft_structs.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/__init__.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/ft_types.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
copying fos/external/freetype/ft_errors.py -> build/lib.linux-x86_64-2.7/fos/external/freetype
creating build/lib.linux-x86_64-2.7/fos/data
copying fos/data/__init__.py -> build/lib.linux-x86_64-2.7/fos/data
creating build/lib.linux-x86_64-2.7/fos/actor/dynamic
copying fos/actor/dynamic/skeleton.py -> build/lib.linux-x86_64-2.7/fos/actor/dynamic
copying fos/actor/dynamic/__init__.py -> build/lib.linux-x86_64-2.7/fos/actor/dynamic
running build_ext
skipping 'fos/interact/collision.c' Cython extension (up-to-date)
building 'fos.interact.collision' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/fos
creating build/temp.linux-x86_64-2.7/fos/interact
gcc -pthread -B /home/connectbrain_admin/miniconda3/envs/tractome/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/connectbrain_admin/miniconda3/envs/tractome/lib/python2.7/site-packages/numpy/core/include -I/home/connectbrain_admin/miniconda3/envs/tractome/include/python2.7 -c fos/interact/collision.c -o build/temp.linux-x86_64-2.7/fos/interact/collision.o
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command "/home/connectbrain_admin/miniconda3/envs/tractome/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-req-build-fKXgf6/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-PBazb4/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-req-build-fKXgf6/
failed
CondaEnvException: Pip failed
>Solution :
The error says that you do not have gcc installed on your machine. You can check if you have it installed by running gcc --version which will output gcc version on console.
If it is not installed, you can run the following to install it on ubuntu:
sudo apt install build-essential