Napari: Update of napari to 0.2.12 via pip failed with AssertionError
Bug
Update of napari via pip failed on Ubuntu 18.04 LTS.
Console Output
(imageanalysis) sebi06@sebastian-tuxedo:~$ pip install napari -U
Collecting napari
Downloading https://files.pythonhosted.org/packages/83/31/6becfb1e0c342ff6078c2284d2ac3f23cb38a100b666ec76a2ee2af703e1/napari-0.2.12.tar.gz (569kB)
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Requirement already satisfied, skipping upgrade: dask[array]>=2.1.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (2.9.1)
Requirement already satisfied, skipping upgrade: fsspec>=0.3.3 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (0.6.2)
Requirement already satisfied, skipping upgrade: imageio>=2.5.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (2.6.1)
Requirement already satisfied, skipping upgrade: ipykernel>=5.1.1 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (5.1.3)
Requirement already satisfied, skipping upgrade: numpy>=1.10.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (1.17.3)
Requirement already satisfied, skipping upgrade: qtpy>=1.7.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (1.9.0)
Requirement already satisfied, skipping upgrade: qtconsole>=4.5.1 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (4.6.0)
Requirement already satisfied, skipping upgrade: jupyter-client<6.0.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (5.3.4)
Requirement already satisfied, skipping upgrade: scipy>=1.2.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (1.4.1)
Requirement already satisfied, skipping upgrade: scikit-image>=0.15.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (0.16.2)
Requirement already satisfied, skipping upgrade: vispy>=0.6.4 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (0.6.4)
Requirement already satisfied, skipping upgrade: IPython>=7.7.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (7.11.1)
Requirement already satisfied, skipping upgrade: backcall>=0.1.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (0.1.0)
Requirement already satisfied, skipping upgrade: PyOpenGL>=3.1.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (3.1.5)
Requirement already satisfied, skipping upgrade: PySide2>=5.12.3 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (5.14.0)
Requirement already satisfied, skipping upgrade: wrapt>=1.11.1 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (1.11.2)
Requirement already satisfied, skipping upgrade: numpydoc>=0.9.2 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from napari) (0.9.2)
Collecting pluggy>=0.13.0
Using cached https://files.pythonhosted.org/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl
Requirement already satisfied, skipping upgrade: toolz>=0.7.3; extra == "array" in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from dask[array]>=2.1.0->napari) (0.10.0)
Requirement already satisfied, skipping upgrade: pillow in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from imageio>=2.5.0->napari) (7.0.0)
Requirement already satisfied, skipping upgrade: tornado>=4.2 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from ipykernel>=5.1.1->napari) (6.0.3)
Requirement already satisfied, skipping upgrade: traitlets>=4.1.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from ipykernel>=5.1.1->napari) (4.3.3)
Requirement already satisfied, skipping upgrade: ipython-genutils in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from qtconsole>=4.5.1->napari) (0.2.0)
Requirement already satisfied, skipping upgrade: jupyter-core in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from qtconsole>=4.5.1->napari) (4.6.1)
Requirement already satisfied, skipping upgrade: pygments in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from qtconsole>=4.5.1->napari) (2.5.2)
Requirement already satisfied, skipping upgrade: pyzmq>=13 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from jupyter-client<6.0.0->napari) (18.1.1)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.1 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from jupyter-client<6.0.0->napari) (2.8.1)
Requirement already satisfied, skipping upgrade: PyWavelets>=0.4.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from scikit-image>=0.15.0->napari) (1.1.1)
Requirement already satisfied, skipping upgrade: matplotlib!=3.0.0,>=2.0.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from scikit-image>=0.15.0->napari) (3.1.2)
Requirement already satisfied, skipping upgrade: networkx>=2.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from scikit-image>=0.15.0->napari) (2.4)
Requirement already satisfied, skipping upgrade: freetype-py in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from vispy>=0.6.4->napari) (2.1.0.post1)
Requirement already satisfied, skipping upgrade: setuptools>=18.5 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from IPython>=7.7.0->napari) (44.0.0.post20200102)
Requirement already satisfied, skipping upgrade: pexpect; sys_platform != "win32" in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from IPython>=7.7.0->napari) (4.7.0)
Requirement already satisfied, skipping upgrade: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from IPython>=7.7.0->napari) (3.0.2)
Requirement already satisfied, skipping upgrade: jedi>=0.10 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from IPython>=7.7.0->napari) (0.15.2)
Requirement already satisfied, skipping upgrade: pickleshare in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from IPython>=7.7.0->napari) (0.7.5)
Requirement already satisfied, skipping upgrade: decorator in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from IPython>=7.7.0->napari) (4.4.1)
Requirement already satisfied, skipping upgrade: shiboken2==5.14.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from PySide2>=5.12.3->napari) (5.14.0)
Requirement already satisfied, skipping upgrade: sphinx>=1.6.5 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from numpydoc>=0.9.2->napari) (2.3.1)
Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from numpydoc>=0.9.2->napari) (2.10.3)
Collecting importlib-metadata>=0.12; python_version < "3.8"
Downloading https://files.pythonhosted.org/packages/8b/03/a00d504808808912751e64ccf414be53c29cad620e3de2421135fcae3025/importlib_metadata-1.5.0-py2.py3-none-any.whl
Requirement already satisfied, skipping upgrade: six in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from traitlets>=4.1.0->ipykernel>=5.1.1->napari) (1.13.0)
Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image>=0.15.0->napari) (2.4.6)
Requirement already satisfied, skipping upgrade: cycler>=0.10 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image>=0.15.0->napari) (0.10.0)
Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image>=0.15.0->napari) (1.1.0)
Requirement already satisfied, skipping upgrade: ptyprocess>=0.5 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->IPython>=7.7.0->napari) (0.6.0)
Requirement already satisfied, skipping upgrade: wcwidth in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->IPython>=7.7.0->napari) (0.1.8)
Requirement already satisfied, skipping upgrade: parso>=0.5.2 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from jedi>=0.10->IPython>=7.7.0->napari) (0.5.2)
Requirement already satisfied, skipping upgrade: sphinxcontrib-jsmath in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.1)
Requirement already satisfied, skipping upgrade: packaging in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (20.0)
Requirement already satisfied, skipping upgrade: alabaster<0.8,>=0.7 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (0.7.12)
Requirement already satisfied, skipping upgrade: docutils>=0.12 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (0.15.2)
Requirement already satisfied, skipping upgrade: sphinxcontrib-applehelp in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.1)
Requirement already satisfied, skipping upgrade: requests>=2.5.0 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.22.0)
Requirement already satisfied, skipping upgrade: imagesize in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.2.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-devhelp in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.1)
Requirement already satisfied, skipping upgrade: sphinxcontrib-htmlhelp in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.2)
Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.0.0)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.8.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-serializinghtml in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.1.3)
Requirement already satisfied, skipping upgrade: sphinxcontrib-qthelp in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.2)
Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from Jinja2>=2.3->numpydoc>=0.9.2->napari) (1.1.1)
Collecting zipp>=0.5
Downloading https://files.pythonhosted.org/packages/b2/34/bfcb43cc0ba81f527bc4f40ef41ba2ff4080e047acb0586b56b3d017ace4/zipp-3.1.0-py3-none-any.whl
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2019.11.28)
Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.25.7)
Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=1.6.5->numpydoc>=0.9.2->napari) (3.0.4)
Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from requests>=2.5.0->sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.8)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in ./miniconda3/envs/imageanalysis/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2019.3)
Building wheels for collected packages: napari
Building wheel for napari (setup.py) ... done
Created wheel for napari: filename=napari-0.2.12-cp37-none-any.whl size=695596 sha256=ccb76d9b3ebc3af0fc0c24c3fb1d5e417a22e302f14c4b1486690c583f6e0c29
Stored in directory: /home/sebi06/.cache/pip/wheels/d3/c5/d5/a0fa9f9188ce2fbc81451e4785ecc1cfd7b515213b71114e18
Successfully built napari
Installing collected packages: zipp, importlib-metadata, pluggy, napari
Found existing installation: napari 0.2.9
Uninstalling napari-0.2.9:
Successfully uninstalled napari-0.2.9
Rolling back uninstall of napari
Moving to /home/sebi06/miniconda3/envs/imageanalysis/bin/napari
from /tmp/pip-uninstall-_sjwg9g7/napari
Moving to /home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/benchmarks/
from /home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/~enchmarks
Moving to /home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/napari-0.2.9.dist-info/
from /home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/~apari-0.2.9.dist-info
Moving to /home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/napari/
from /home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/~apari
ERROR: Exception:
Traceback (most recent call last):
File "/home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 153, in _main
status = self.run(options, args)
File "/home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 455, in run
use_user_site=options.use_user_site,
File "/home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/pip/_internal/req/__init__.py", line 62, in install_given_reqs
**kwargs
File "/home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 861, in install
use_user_site=use_user_site, pycompile=pycompile,
File "/home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 495, in move_wheel_files
warn_script_location=warn_script_location,
File "/home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/pip/_internal/wheel.py", line 461, in move_wheel_files
clobber(source, lib_dir, True)
File "/home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/pip/_internal/wheel.py", line 410, in clobber
', '.join(info_dir))
AssertionError: Multiple .dist-info directories: /home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/napari/plugins/_tests/fixtures/napari_working_plugin-0.1.0.dist-info, /home/sebi06/miniconda3/envs/imageanalysis/lib/python3.7/site-packages/napari-0.2.12.dist-info
sebi06
All 3 comments
This is likely the same error as in #1009 which can be fixed up updating your pip - 20.0.2 should work 19.2.3 should fail. We've fixed this in master so it shouldn't be an issue for our next release, but updating pip will probably be your fastest fix
sofroniewn
on 8 Mar 2020
❤1
pip 20.0.2 did the job for me.
sebi06
on 15 Mar 2020
👍1
Great! I will close as this is fixed in master and will be fixed on our next release.
sofroniewn
on 15 Mar 2020
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