I have downloaded and installed the packages and files for MAJIQ, although, when I try running it, I get an error.
Looks
like the --voila-only option is not recognized (see attachment) and I
also get an error when I try to install the wheel (also: see
attachment),
maybe thats why the --voila-only option does not work?
How do I fix this?
(env) esther@esther-ThinkPad-S3-Yoga-14:~/.local/bin/majiq_academic$ python3.9 -m pip install git+
https://bitbucket.org/biociphers/majiq_academic#egg=majiq --install-option="--voila-only"
/home/esther/.local/lib/python3.9/site-packages/pip/_internal/commands/install.py:234: UserWarning: Disabling all use of wheels due to the use of --build-option / --global-option / --install-option.
cmdoptions.check_install_build_global(options)
Defaulting to user installation because normal site-packages is not writeable
Collecting majiq
Cloning
https://bitbucket.org/biociphers/majiq_academic to /tmp/pip-install-5uzqi60e/majiq_4a177fb14c3f4336bbb30c6baa92c888
Collecting Click==7.0
Using cached Click-7.0.tar.gz (286 kB)
Collecting Cython==0.29.14
Using cached Cython-0.29.14.tar.gz (2.1 MB)
Collecting Flask==1.0.2
Using cached Flask-1.0.2.tar.gz (644 kB)
Collecting Flask-Session==0.3.1
Using cached Flask-Session-0.3.1.tar.gz (27 kB)
Collecting Flask-WTF==0.14.2
Using cached Flask-WTF-0.14.2.tar.gz (254 kB)
Collecting gitdb2==2.0.6
Using cached gitdb2-2.0.6.tar.gz (393 kB)
Collecting GitPython==3.0.5
Using cached GitPython-3.0.5.tar.gz (433 kB)
Collecting gunicorn==19.9.0
Using cached gunicorn-19.9.0.tar.gz (415 kB)
Collecting h5py==2.10.0
Using cached h5py-2.10.0.tar.gz (301 kB)
Collecting itsdangerous==1.1.0
Using cached itsdangerous-1.1.0.tar.gz (53 kB)
Collecting Jinja2==2.11.1
Using cached Jinja2-2.11.1.tar.gz (258 kB)
Collecting MarkupSafe==1.1.1
Using cached MarkupSafe-1.1.1.tar.gz (19 kB)
Collecting numpy==1.18.1
Using cached numpy-1.18.1.zip (5.4 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Collecting psutil==5.6.7
Using cached psutil-5.6.7.tar.gz (448 kB)
Collecting scipy==1.4.1
Using cached scipy-1.4.1.tar.gz (24.6 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Collecting six==1.14.0
Using cached six-1.14.0.tar.gz (33 kB)
Collecting smmap2==2.0.5
Using cached smmap2-2.0.5.tar.gz (22 kB)
Collecting waitress==1.1.0
Using cached waitress-1.1.0.tar.gz (126 kB)
Collecting Werkzeug==0.16.0
Using cached Werkzeug-0.16.0.tar.gz (925 kB)
Collecting WTForms==2.2.1
Using cached WTForms-2.2.1.tar.gz (156 kB)
Skipping wheel build for majiq, due to binaries being disabled for it.
Skipping wheel build for Click, due to binaries being disabled for it.
Skipping wheel build for Cython, due to binaries being disabled for it.
Skipping wheel build for Flask, due to binaries being disabled for it.
Skipping wheel build for Flask-Session, due to binaries being disabled for it.
Skipping wheel build for Flask-WTF, due to binaries being disabled for it.
Skipping wheel build for gitdb2, due to binaries being disabled for it.
Skipping wheel build for GitPython, due to binaries being disabled for it.
Skipping wheel build for gunicorn, due to binaries being disabled for it.
Skipping wheel build for h5py, due to binaries being disabled for it.
Skipping wheel build for itsdangerous, due to binaries being disabled for it.
Skipping wheel build for Jinja2, due to binaries being disabled for it.
Skipping wheel build for MarkupSafe, due to binaries being disabled for it.
Skipping wheel build for psutil, due to binaries being disabled for it.
Skipping wheel build for six, due to binaries being disabled for it.
Skipping wheel build for smmap2, due to binaries being disabled for it.
Skipping wheel build for waitress, due to binaries being disabled for it.
Skipping wheel build for Werkzeug, due to binaries being disabled for it.
Skipping wheel build for WTForms, due to binaries being disabled for it.
Building wheels for collected packages: numpy, scipy
Building wheel for numpy (PEP 517) ... done
Created wheel for numpy: filename=numpy-1.18.1-cp39-cp39-linux_x86_64.whl size=11513446 sha256=b5d74d938697b3275922e9bcc9ed48da56baabf3a3e7ca84c29cb49b2878d727
Stored in directory: /home/esther/.cache/pip/wheels/d7/8f/69/b233132b552877f7f613530ca919c4f566aec2b4c88119979f
Building wheel for scipy (PEP 517) ... done
Created wheel for scipy: filename=scipy-1.4.1-cp39-cp39-linux_x86_64.whl size=46759643 sha256=934809aaa07f6e606061f932172ebd1bf17141923939e5623e65e4df54f38f6c
Stored in directory: /home/esther/.cache/pip/wheels/dd/70/40/456161126b69d62f62b883ad8a5c84b88de0c26575702f5217
Successfully built numpy scipy
Installing collected packages: MarkupSafe, Werkzeug, smmap2, Jinja2, itsdangerous, Click, WTForms, six, numpy, gitdb2, Flask, waitress, scipy, psutil, h5py, gunicorn, GitPython, Flask-WTF, Flask-Session, Cython, majiq
Running setup.py install for MarkupSafe ... error
ERROR: Command errored out with exit status 1:
command: /usr/local/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5uzqi60e/markupsafe_69a01687860c434abfda0df76c5d5f0e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5uzqi60e/markupsafe_69a01687860c434abfda0df76c5d5f0e/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-u28ci1gc/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/esther/.local/include/python3.9/MarkupSafe --voila-only
cwd: /tmp/pip-install-5uzqi60e/markupsafe_69a01687860c434abfda0df76c5d5f0e/
Complete output (6 lines):
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help
error: option --voila-only not recognized
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5uzqi60e/markupsafe_69a01687860c434abfda0df76c5d5f0e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5uzqi60e/markupsafe_69a01687860c434abfda0df76c5d5f0e/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-u28ci1gc/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/esther/.local/include/python3.9/MarkupSafe --voila-only Check the logs for full command output.
(env) esther@esther-ThinkPad-S3-Yoga-14:~/.local/bin/majiq_academic$ pip install wheel
Traceback (most recent call last):
File "/home/esther/.local/bin/majiq_academic/env/bin/pip", line 7, in <module>
from pip._internal.cli.main import main
File "/home/esther/.local/bin/majiq_academic/env/lib/python3.5/site-packages/pip/_internal/cli/main.py", line 60
sys.stderr.write(f"ERROR: {exc}")
^
SyntaxError: invalid syntax