Trouble installing PyJulia
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- Python
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Description
```
Python 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import julia
>>> julia.install()
[ Info: Julia version info
Julia Version 1.5.0-rc1.0
Commit 24f033c951 (2020-06-26 20:13 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
"Fedora release 30 (Thirty)"
uname: Linux 5.3.7-200.fc30.x86_64 #1 SMP Fri Oct 18 20:13:59 UTC 2019 x86_64 x86_64
CPU: Intel(R) Xeon(R) Gold 6254 CPU @ 3.10GHz:
speed user nice sys idle irq
#1-18 3092 MHz 154700970 s 364803 s 58215826 s 2987251912 s 2277842 s
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_NUM_THREADS = 12
JULIA_PKG_SERVER = pkg.julialang.org
JULIA_PROJECT = /home/x/foo/code/private/julia/foo
HOME = /home/x
MANPATH = :/opt/puppetlabs/puppet/share/man
PATH = /home/x/.nimble/bin:/home/x/.npm-global/bin:/home/x/bin:/home/x/node-v12.14.1-linux-x64/bin:/home/x/.nimble/bin:/home/x/miniconda3/envs/foo
/bin:/home/x/miniconda3/condabin:/home/x/.npm-global/bin:/home/x/bin:/home/x/node-v12.14.1-linux-x64/bin:/home/x/.local/bin:/home/x/bin:/usr/local/bin
:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/x/bin:/home/x/bin
PYTHONPATH = /home/x/foo/code/private/python:/home/x/foo/code/shared/python:/home/x/foo/code/private/python:/home/x/foo/code/shared/python:
TERM = screen
[ Info: Julia executable: /data/home/x/julia-1.5.0-rc1/bin/julia
[ Info: Trying to import PyCall...
┌ Warning: PyCall is already installed. However, you may have trouble using
│ this Python executable because it is statically linked to libpython.
│
│ For more information, see:
│ https://pyjulia.readthedocs.io/en/latest/troubleshooting.html
│
│ Python executable:
│ /home/x/miniconda3/envs/foo/bin/python
│ Julia executable:
│ /data/home/x/julia-1.5.0-rc1/bin/julia
└ @ Main /data/home/x/miniconda3/envs/foo/lib/python3.7/site-packages/julia/install.jl:74
(foo) ➜ code python3 -m julia.sysimage sys.so
Activating new environment at `/tmp/tmp.pyjulia.sysimage.f6s6rkax/compiler_env/Project.toml`
[ Info: Installing PackageCompiler...
Updating registry at `~/.julia/registries/General`
Resolving package versions...
Updating `/tmp/tmp.pyjulia.sysimage.f6s6rkax/compiler_env/Project.toml`
[9b87118b] + PackageCompiler v1.2.1
Updating `/tmp/tmp.pyjulia.sysimage.f6s6rkax/compiler_env/Manifest.toml`
[9b87118b] + PackageCompiler v1.2.1
[2a0f44e3] + Base64
[ade2ca70] + Dates
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[56ddb016] + Logging
[d6f4376e] + Markdown
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
┌ Error: build.log for PackageCompiler [9b87118b-4619-50d2-8e1e-99f35a4d4d9d] not found
└ @ Main /data/home/x/miniconda3/envs/foo/lib/python3.7/site-packages/julia/install-packagecompiler.jl:18
[ Info: Loading PackageCompiler...
[ Info: PackageCompiler is successfully installed at /tmp/tmp.pyjulia.sysimage.f6s6rkax/compiler_env
Error processing line 1 of /data/home/x/miniconda3/envs/foo/lib/python3.7/site-packages/matplotlib-3.1.3-py3.7-nspkg.pth:
Fatal Python error: initsite: Failed to import the site module
Traceback (most recent call last):
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/site.py", line 168, in addpackage
exec(line)
File "", line 1, in
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/importlib/util.py", line 14, in
from contextlib import contextmanager
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/contextlib.py", line 5, in
from collections import deque
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/collections/__init__.py", line 24, in
import heapq as _heapq
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/heapq.py", line 587, in
from _heapq import *
SystemError: initialization of _heapq did not return an extension module
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/site.py", line 579, in
main()
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/site.py", line 566, in main
known_paths = addsitepackages(known_paths)
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/site.py", line 349, in addsitepackages
addsitedir(sitedir, known_paths)
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/site.py", line 207, in addsitedir
addpackage(sitedir, name, known_paths)
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/site.py", line 178, in addpackage
import traceback
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/traceback.py", line 3, in
import collections
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/collections/__init__.py", line 24, in
import heapq as _heapq
File "/data/home/x/miniconda3/envs/foo/lib/python3.7/heapq.py", line 587, in
from _heapq import *
SystemError: initialization of _heapq did not return an extension module
Command '['/home/x/miniconda3/envs/foo/bin/julia-py', '--julia', 'julia', '--color=yes', '/data/home/x/miniconda3/envs/foo/lib/python3.7/site-packages/julia/compile.jl', '/tmp/tmp.pyjulia.sysimage.f6s6rkax/compiler_env', '/data/home/x/miniconda3/envs/foo/lib/python3.7/site-packages/julia/precompile.jl', '/data/home/x/foo/code/sys.so']' returned non-zero exit status 1.
```
I'm trying to take the system image approach, but I'm getting the errors above. Any help please?
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