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DeepLabCut / DeepLabCut

Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans
http://deeplabcut.org
GNU Lesser General Public License v3.0
4.54k stars 1.65k forks source link

CalledProcessError: Command '['convert', '--version']' returned non-zero exit status 1. for deeplabcut==2.2b8 #925

Closed monajalal closed 3 years ago

monajalal commented 3 years ago

Got the DLC-GPU.yaml from here: https://github.com/DeepLabCut/DeepLabCut/blob/master/conda-environments/DLC-GPU.yaml

(base) mona@mona:~/research$ conda env create --name dlc --file=DLC-GPU.yaml
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages
gettext-0.19.8.1     | 2.9 MB    | ################################################################################################################################################################ | 100% 
ipython-7.18.1       | 989 KB    | ################################################################################################################################################################ | 100% 
jupyter_console-6.2. | 26 KB     | ################################################################################################################################################################ | 100% 
qtconsole-4.7.7      | 96 KB     | ################################################################################################################################################################ | 100% 
prompt_toolkit-3.0.7 | 12 KB     | ################################################################################################################################################################ | 100% 
geos-3.8.0           | 961 KB    | ################################################################################################################################################################ | 100% 
pango-1.45.3         | 361 KB    | ################################################################################################################################################################ | 100% 
shapely-1.7.1        | 390 KB    | ################################################################################################################################################################ | 100% 
pyzmq-19.0.2         | 438 KB    | ################################################################################################################################################################ | 100% 
nb_conda_kernels-2.3 | 26 KB     | ################################################################################################################################################################ | 100% 
notebook-6.1.1       | 4.0 MB    | ################################################################################################################################################################ | 100% 
harfbuzz-2.4.0       | 850 KB    | ################################################################################################################################################################ | 100% 
jedi-0.17.2          | 912 KB    | ################################################################################################################################################################ | 100% 
gstreamer-1.14.0     | 3.1 MB    | ################################################################################################################################################################ | 100% 
argon2-cffi-20.1.0   | 46 KB     | ################################################################################################################################################################ | 100% 
pyrsistent-0.17.3    | 89 KB     | ################################################################################################################################################################ | 100% 
ipykernel-5.3.4      | 179 KB    | ################################################################################################################################################################ | 100% 
nb_conda-2.2.1       | 32 KB     | ################################################################################################################################################################ | 100% 
cffi-1.14.3          | 223 KB    | ################################################################################################################################################################ | 100% 
glib-2.65.0          | 2.9 MB    | ################################################################################################################################################################ | 100% 
fribidi-1.0.10       | 103 KB    | ################################################################################################################################################################ | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: \ Enabling nb_conda_kernels...
Status: enabled

/ Config option `kernel_spec_manager_class` not recognized by `EnableNBExtensionApp`.
Enabling notebook extension nb_conda/main...
      - Validating: OK
Enabling tree extension nb_conda/tree...
      - Validating: OK
Config option `kernel_spec_manager_class` not recognized by `EnableServerExtensionApp`.
Enabling: nb_conda
- Writing config: /home/mona/anaconda3/envs/dlc/etc/jupyter
    - Validating...
      nb_conda 2.2.1 OK

done
Installing pip dependencies: / Ran pip subprocess with arguments:
['/home/mona/anaconda3/envs/dlc/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/mona/research/condaenv.i4wb4gx_.requirements.txt']
Pip subprocess output:
Collecting deeplabcut
  Using cached deeplabcut-2.1.8.2-py3-none-any.whl (400 kB)
Requirement already satisfied, skipping upgrade: certifi in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (2020.6.20)
Collecting matplotlib==3.0.3
  Using cached matplotlib-3.0.3-cp37-cp37m-manylinux1_x86_64.whl (13.0 MB)
Collecting numpy==1.16.4
  Using cached numpy-1.16.4-cp37-cp37m-manylinux1_x86_64.whl (17.3 MB)
Collecting scikit-image
  Downloading scikit_image-0.17.2-cp37-cp37m-manylinux1_x86_64.whl (12.5 MB)
Collecting scikit-learn
  Downloading scikit_learn-0.23.2-cp37-cp37m-manylinux1_x86_64.whl (6.8 MB)
Requirement already satisfied, skipping upgrade: ipython-genutils in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (0.2.0)
Collecting ruamel.yaml~=0.15
  Using cached ruamel.yaml-0.16.12-py2.py3-none-any.whl (111 kB)
Collecting tqdm
  Using cached tqdm-4.49.0-py2.py3-none-any.whl (69 kB)
Requirement already satisfied, skipping upgrade: six in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (1.15.0)
Collecting tables
  Using cached tables-3.6.1-cp37-cp37m-manylinux1_x86_64.whl (4.3 MB)
Collecting tensorpack>=0.9.7.1
  Using cached tensorpack-0.10.1-py2.py3-none-any.whl (291 kB)
Collecting statsmodels
  Downloading statsmodels-0.12.0-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB)
Requirement already satisfied, skipping upgrade: ipython in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (7.18.1)
Requirement already satisfied, skipping upgrade: setuptools in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (49.6.0.post20200814)
Collecting pyyaml>=5.1
  Using cached PyYAML-5.3.1.tar.gz (269 kB)
Collecting intel-openmp
  Using cached intel_openmp-2020.0.133-py2.py3-none-manylinux1_x86_64.whl (919 kB)
Collecting opencv-python~=3.4
  Downloading opencv_python-3.4.11.43-cp37-cp37m-manylinux2014_x86_64.whl (49.1 MB)
Requirement already satisfied, skipping upgrade: python-dateutil in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (2.8.1)
Processing /home/mona/.cache/pip/wheels/db/37/b8/b3785332f8246f1306c2863553860ca65e1824fc4c8251c7f1/moviepy-1.0.1-py3-none-any.whl
Collecting patsy
  Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Processing /home/mona/.cache/pip/wheels/88/96/68/c2be18e7406804be2e593e1c37845f2dd20ac2ce1381ce40b0/easydict-1.9-py3-none-any.whl
Collecting pandas>=1.0.
  Using cached pandas-1.1.2-cp37-cp37m-manylinux1_x86_64.whl (10.5 MB)
Requirement already satisfied, skipping upgrade: wheel in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (0.35.1)
Collecting click
  Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Collecting imgaug
  Using cached imgaug-0.4.0-py2.py3-none-any.whl (948 kB)
Collecting chardet
  Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Requirement already satisfied, skipping upgrade: scipy in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (1.5.2)
Requirement already satisfied, skipping upgrade: h5py~=2.7 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (2.10.0)
Collecting requests
  Using cached requests-2.24.0-py2.py3-none-any.whl (61 kB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.2.0-cp37-cp37m-manylinux1_x86_64.whl (88 kB)
Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from matplotlib==3.0.3->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (2.4.7)
Collecting cycler>=0.10
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting pillow!=7.1.0,!=7.1.1,>=4.3.0
  Using cached Pillow-7.2.0-cp37-cp37m-manylinux1_x86_64.whl (2.2 MB)
Collecting imageio>=2.3.0
  Using cached imageio-2.9.0-py3-none-any.whl (3.3 MB)
Collecting tifffile>=2019.7.26
  Using cached tifffile-2020.9.22-py3-none-any.whl (153 kB)
Collecting networkx>=2.0
  Using cached networkx-2.5-py3-none-any.whl (1.6 MB)
Collecting PyWavelets>=1.1.1
  Downloading PyWavelets-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (4.4 MB)
Collecting threadpoolctl>=2.0.0
  Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Collecting joblib>=0.11
  Using cached joblib-0.16.0-py3-none-any.whl (300 kB)
Collecting ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.9"
  Using cached ruamel.yaml.clib-0.2.2-cp37-cp37m-manylinux1_x86_64.whl (547 kB)
Collecting numexpr>=2.6.2
  Using cached numexpr-2.7.1-cp37-cp37m-manylinux1_x86_64.whl (162 kB)
Collecting psutil>=5
  Using cached psutil-5.7.2.tar.gz (460 kB)
Collecting msgpack>=0.5.2
  Downloading msgpack-1.0.0-cp37-cp37m-manylinux1_x86_64.whl (275 kB)
Collecting msgpack-numpy>=0.4.4.2
  Using cached msgpack_numpy-0.4.7-py2.py3-none-any.whl (6.4 kB)
Collecting tabulate>=0.7.7
  Using cached tabulate-0.8.7-py3-none-any.whl (24 kB)
Requirement already satisfied, skipping upgrade: termcolor>=1.1 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (1.1.0)
Requirement already satisfied, skipping upgrade: pyzmq>=16 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (19.0.2)
Requirement already satisfied, skipping upgrade: traitlets>=4.2 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (4.3.3)
Requirement already satisfied, skipping upgrade: pygments in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (2.7.1)
Requirement already satisfied, skipping upgrade: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (3.0.7)
Requirement already satisfied, skipping upgrade: pexpect>4.3; sys_platform != "win32" in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (4.8.0)
Requirement already satisfied, skipping upgrade: decorator in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (4.4.2)
Requirement already satisfied, skipping upgrade: jedi>=0.10 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (0.17.2)
Requirement already satisfied, skipping upgrade: pickleshare in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (0.7.5)
Requirement already satisfied, skipping upgrade: backcall in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (0.2.0)
Processing /home/mona/.cache/pip/wheels/12/36/1f/dc61e6ac10781d63cf6fa045eb09fa613a667384e12cb6e6e0/proglog-0.1.9-py3-none-any.whl
Collecting imageio-ffmpeg>=0.2.0; python_version >= "3.4"
  Using cached imageio_ffmpeg-0.4.2-py3-none-manylinux2010_x86_64.whl (26.9 MB)
Collecting pytz>=2017.2
  Using cached pytz-2020.1-py2.py3-none-any.whl (510 kB)
Requirement already satisfied, skipping upgrade: Shapely in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from imgaug->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (1.7.1)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
  Using cached urllib3-1.25.10-py2.py3-none-any.whl (127 kB)
Collecting idna<3,>=2.5
  Using cached idna-2.10-py2.py3-none-any.whl (58 kB)
Requirement already satisfied, skipping upgrade: wcwidth in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (0.2.5)
Requirement already satisfied, skipping upgrade: ptyprocess>=0.5 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from pexpect>4.3; sys_platform != "win32"->ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (0.6.0)
Requirement already satisfied, skipping upgrade: parso<0.8.0,>=0.7.0 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from jedi>=0.10->ipython->deeplabcut->-r /home/mona/research/condaenv.i4wb4gx_.requirements.txt (line 1)) (0.7.0)
Building wheels for collected packages: pyyaml, psutil
  Building wheel for pyyaml (setup.py): started
  Building wheel for pyyaml (setup.py): finished with status 'done'
  Created wheel for pyyaml: filename=PyYAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44619 sha256=bb81132d4bd4786a05057991336e112ed3ff6dde5653560f264e447e3b2f0e9c
  Stored in directory: /home/mona/.cache/pip/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653
  Building wheel for psutil (setup.py): started
  Building wheel for psutil (setup.py): finished with status 'done'
  Created wheel for psutil: filename=psutil-5.7.2-cp37-cp37m-linux_x86_64.whl size=292666 sha256=2b7326dd5f5f648c6f167599c04470dc27949e7d56211052d7231aa9318db886
  Stored in directory: /home/mona/.cache/pip/wheels/2d/43/97/00701864a7bee6d9e1a52dd682537dcbf1d013d0e2e6f0c1f1
Successfully built pyyaml psutil
Installing collected packages: kiwisolver, cycler, numpy, matplotlib, pillow, imageio, tifffile, networkx, PyWavelets, scikit-image, threadpoolctl, joblib, scikit-learn, ruamel.yaml.clib, ruamel.yaml, tqdm, numexpr, tables, psutil, msgpack, msgpack-numpy, tabulate, tensorpack, pytz, pandas, patsy, statsmodels, pyyaml, intel-openmp, opencv-python, proglog, chardet, urllib3, idna, requests, imageio-ffmpeg, moviepy, easydict, click, imgaug, deeplabcut
  Attempting uninstall: numpy
    Found existing installation: numpy 1.19.1
    Uninstalling numpy-1.19.1:
      Successfully uninstalled numpy-1.19.1
Successfully installed PyWavelets-1.1.1 chardet-3.0.4 click-7.1.2 cycler-0.10.0 deeplabcut-2.1.8.2 easydict-1.9 idna-2.10 imageio-2.9.0 imageio-ffmpeg-0.4.2 imgaug-0.4.0 intel-openmp-2020.0.133 joblib-0.16.0 kiwisolver-1.2.0 matplotlib-3.0.3 moviepy-1.0.1 msgpack-1.0.0 msgpack-numpy-0.4.7 networkx-2.5 numexpr-2.7.1 numpy-1.16.4 opencv-python-3.4.11.43 pandas-1.1.2 patsy-0.5.1 pillow-7.2.0 proglog-0.1.9 psutil-5.7.2 pytz-2020.1 pyyaml-5.3.1 requests-2.24.0 ruamel.yaml-0.16.12 ruamel.yaml.clib-0.2.2 scikit-image-0.17.2 scikit-learn-0.23.2 statsmodels-0.12.0 tables-3.6.1 tabulate-0.8.7 tensorpack-0.10.1 threadpoolctl-2.1.0 tifffile-2020.9.22 tqdm-4.49.0 urllib3-1.25.10

done
#
# To activate this environment, use
#
#     $ conda activate dlc
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) mona@mona:~/research$ conda activate dlc
(dlc) mona@mona:~/research$ pip install deeplabcut==2.2b8
Collecting deeplabcut==2.2b8
  Using cached deeplabcut-2.2b8-py3-none-any.whl (663 kB)
Requirement already satisfied: tables in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (3.6.1)
Collecting opencv-python-headless
  Using cached opencv_python_headless-4.4.0.44-cp37-cp37m-manylinux2014_x86_64.whl (36.7 MB)
Requirement already satisfied: python-dateutil in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (2.8.1)
Requirement already satisfied: numpy==1.16.4 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (1.16.4)
Requirement already satisfied: moviepy<=1.0.1 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (1.0.1)
Requirement already satisfied: scikit-image in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (0.17.2)
Requirement already satisfied: pyyaml in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (5.3.1)
Requirement already satisfied: statsmodels>=0.11 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (0.12.0)
Requirement already satisfied: scipy>=1.4 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (1.5.2)
Collecting matplotlib==3.1.3
  Using cached matplotlib-3.1.3-cp37-cp37m-manylinux1_x86_64.whl (13.1 MB)
Processing /home/mona/.cache/pip/wheels/ce/e0/ee/a2b3c5caab3418c1ccd8c4de573d4cbe13315d7e8b0a55fbc2/filterpy-1.4.5-py3-none-any.whl
Collecting tensorpack==0.9.8
  Using cached tensorpack-0.9.8-py2.py3-none-any.whl (288 kB)
Requirement already satisfied: scikit-learn in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (0.23.2)
Requirement already satisfied: ruamel.yaml>=0.15.0 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (0.16.12)
Requirement already satisfied: certifi in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (2020.6.20)
Requirement already satisfied: pandas>=1.0.1 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (1.1.2)
Requirement already satisfied: chardet in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (3.0.4)
Requirement already satisfied: intel-openmp in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (2020.0.133)
Requirement already satisfied: patsy in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (0.5.1)
Requirement already satisfied: requests in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (2.24.0)
Requirement already satisfied: setuptools in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (49.6.0.post20200814)
Processing /home/mona/.cache/pip/wheels/fd/9b/71/f127d694e02eb40bcf18c7ae9613b88a6be4470f57a8528c5b/bayesian_optimization-1.2.0-py3-none-any.whl
Requirement already satisfied: ipython in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (7.18.1)
Requirement already satisfied: h5py in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (2.10.0)
Requirement already satisfied: six in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (1.15.0)
Requirement already satisfied: easydict in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (1.9)
Requirement already satisfied: ipython-genutils in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (0.2.0)
Requirement already satisfied: imgaug in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (0.4.0)
Requirement already satisfied: tqdm in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (4.49.0)
Requirement already satisfied: wheel in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (0.35.1)
Collecting cython
  Downloading Cython-0.29.21-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB)
     |████████████████████████████████| 2.0 MB 20 kB/s 
Collecting numba==0.51.1
  Using cached numba-0.51.1-cp37-cp37m-manylinux2014_x86_64.whl (3.1 MB)
Requirement already satisfied: click in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from deeplabcut==2.2b8) (7.1.2)
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Requirement already satisfied: proglog<=1.0.0 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from moviepy<=1.0.1->deeplabcut==2.2b8) (0.1.9)
Requirement already satisfied: decorator<5.0,>=4.0.2 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from moviepy<=1.0.1->deeplabcut==2.2b8) (4.4.2)
Requirement already satisfied: imageio<3.0,>=2.5; python_version >= "3.4" in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from moviepy<=1.0.1->deeplabcut==2.2b8) (2.9.0)
Requirement already satisfied: networkx>=2.0 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from scikit-image->deeplabcut==2.2b8) (2.5)
Requirement already satisfied: pillow!=7.1.0,!=7.1.1,>=4.3.0 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from scikit-image->deeplabcut==2.2b8) (7.2.0)
Requirement already satisfied: tifffile>=2019.7.26 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from scikit-image->deeplabcut==2.2b8) (2020.9.22)
Requirement already satisfied: PyWavelets>=1.1.1 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from scikit-image->deeplabcut==2.2b8) (1.1.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from matplotlib==3.1.3->deeplabcut==2.2b8) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from matplotlib==3.1.3->deeplabcut==2.2b8) (1.2.0)
Requirement already satisfied: cycler>=0.10 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from matplotlib==3.1.3->deeplabcut==2.2b8) (0.10.0)
Requirement already satisfied: termcolor>=1.1 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from tensorpack==0.9.8->deeplabcut==2.2b8) (1.1.0)
Requirement already satisfied: msgpack-numpy>=0.4.4.2 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from tensorpack==0.9.8->deeplabcut==2.2b8) (0.4.7)
Requirement already satisfied: pyzmq>=16 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from tensorpack==0.9.8->deeplabcut==2.2b8) (19.0.2)
Requirement already satisfied: psutil>=5 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from tensorpack==0.9.8->deeplabcut==2.2b8) (5.7.2)
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Requirement already satisfied: joblib>=0.11 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from scikit-learn->deeplabcut==2.2b8) (0.16.0)
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Requirement already satisfied: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.9" in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ruamel.yaml>=0.15.0->deeplabcut==2.2b8) (0.2.2)
Requirement already satisfied: pytz>=2017.2 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from pandas>=1.0.1->deeplabcut==2.2b8) (2020.1)
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Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut==2.2b8) (3.0.7)
Requirement already satisfied: pexpect>4.3; sys_platform != "win32" in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut==2.2b8) (4.8.0)
Requirement already satisfied: jedi>=0.10 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from ipython->deeplabcut==2.2b8) (0.17.2)
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Collecting llvmlite<0.35,>=0.34.0.dev0
  Using cached llvmlite-0.34.0-cp37-cp37m-manylinux2010_x86_64.whl (24.6 MB)
Requirement already satisfied: wcwidth in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->deeplabcut==2.2b8) (0.2.5)
Requirement already satisfied: ptyprocess>=0.5 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from pexpect>4.3; sys_platform != "win32"->ipython->deeplabcut==2.2b8) (0.6.0)
Requirement already satisfied: parso<0.8.0,>=0.7.0 in /home/mona/anaconda3/envs/dlc/lib/python3.7/site-packages (from jedi>=0.10->ipython->deeplabcut==2.2b8) (0.7.0)
Installing collected packages: opencv-python-headless, matplotlib, filterpy, tensorpack, bayesian-optimization, cython, llvmlite, numba, deeplabcut
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.0.3
    Uninstalling matplotlib-3.0.3:
      Successfully uninstalled matplotlib-3.0.3
  Attempting uninstall: tensorpack
    Found existing installation: tensorpack 0.10.1
    Uninstalling tensorpack-0.10.1:
      Successfully uninstalled tensorpack-0.10.1
  Attempting uninstall: deeplabcut
    Found existing installation: deeplabcut 2.1.8.2
    Uninstalling deeplabcut-2.1.8.2:
      Successfully uninstalled deeplabcut-2.1.8.2
Successfully installed bayesian-optimization-1.2.0 cython-0.29.21 deeplabcut-2.2b8 filterpy-1.4.5 llvmlite-0.34.0 matplotlib-3.1.3 numba-0.51.1 opencv-python-headless-4.4.0.44 tensorpack-0.9.8
(dlc) mona@mona:~/research$ ipython
Python 3.7.9 (default, Aug 31 2020, 12:42:55) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.18.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import deeplabcut as dlc
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
<ipython-input-1-7dc21562c90f> in <module>
----> 1 import deeplabcut as dlc

~/anaconda3/envs/dlc/lib/python3.7/site-packages/deeplabcut/__init__.py in <module>
     36 else:  # standard use [wxpython supported]
     37     mpl.use("WxAgg")
---> 38     from deeplabcut import generate_training_dataset
     39     from deeplabcut import refine_training_dataset
     40     from deeplabcut.generate_training_dataset import (

~/anaconda3/envs/dlc/lib/python3.7/site-packages/deeplabcut/generate_training_dataset/__init__.py in <module>
     16 else:
     17     from deeplabcut.generate_training_dataset.auxfun_drag_label import *
---> 18     from deeplabcut.generate_training_dataset.labeling_toolbox import *
     19     from deeplabcut.generate_training_dataset.multiple_individuals_labeling_toolbox import *
     20     from deeplabcut.generate_training_dataset.frame_extraction_toolbox import *

~/anaconda3/envs/dlc/lib/python3.7/site-packages/deeplabcut/generate_training_dataset/labeling_toolbox.py in <module>
     31 
     32 from deeplabcut.generate_training_dataset import auxfun_drag_label
---> 33 from deeplabcut.utils import auxiliaryfunctions
     34 
     35 # ###########################################################################

~/anaconda3/envs/dlc/lib/python3.7/site-packages/deeplabcut/utils/__init__.py in <module>
      4 from deeplabcut.utils.conversioncode import *
      5 from deeplabcut.utils.frameselectiontools import *
----> 6 from deeplabcut.utils.make_labeled_video import *
      7 from deeplabcut.utils.plotting import *
      8 from deeplabcut.utils.video_processor import *

~/anaconda3/envs/dlc/lib/python3.7/site-packages/deeplabcut/utils/make_labeled_video.py in <module>
     26 import matplotlib.pyplot as plt
     27 import numpy as np
---> 28 from matplotlib.animation import FFMpegWriter
     29 from matplotlib.collections import LineCollection
     30 from skimage.draw import circle, line_aa

~/anaconda3/envs/dlc/lib/python3.7/site-packages/matplotlib/animation.py in <module>
    735 # Combine ImageMagick options with pipe-based writing
    736 @writers.register('imagemagick')
--> 737 class ImageMagickWriter(ImageMagickBase, MovieWriter):
    738     '''Pipe-based animated gif.
    739 

~/anaconda3/envs/dlc/lib/python3.7/site-packages/matplotlib/animation.py in wrapper(writerClass)
    118         def wrapper(writerClass):
    119             self._registered[name] = writerClass
--> 120             if writerClass.isAvailable():
    121                 self.avail[name] = writerClass
    122             return writerClass

~/anaconda3/envs/dlc/lib/python3.7/site-packages/matplotlib/animation.py in isAvailable(cls)
    728     def isAvailable(cls):
    729         try:
--> 730             return super().isAvailable()
    731         except FileNotFoundError:  # May be raised by get_executable_info.
    732             return False

~/anaconda3/envs/dlc/lib/python3.7/site-packages/matplotlib/animation.py in isAvailable(cls)
    425         Check to see if a MovieWriter subclass is actually available.
    426         '''
--> 427         return shutil.which(cls.bin_path()) is not None
    428 
    429 

~/anaconda3/envs/dlc/lib/python3.7/site-packages/matplotlib/animation.py in bin_path(cls)
    722         binpath = super().bin_path()
    723         if binpath == 'convert':
--> 724             binpath = mpl._get_executable_info('magick').executable
    725         return binpath
    726 

~/anaconda3/envs/dlc/lib/python3.7/site-packages/matplotlib/__init__.py in _get_executable_info(name)
    383             raise FileNotFoundError(
    384                 "Failed to find an ImageMagick installation")
--> 385         return impl([path, "--version"], r"^Version: ImageMagick (\S*)")
    386     elif name == "pdftops":
    387         info = impl(["pdftops", "-v"], "^pdftops version (.*)",

~/anaconda3/envs/dlc/lib/python3.7/site-packages/matplotlib/__init__.py in impl(args, regex, min_ver, ignore_exit_code)
    328                 output = _cpe.output
    329             else:
--> 330                 raise _cpe
    331         match = re.search(regex, output)
    332         if match:

~/anaconda3/envs/dlc/lib/python3.7/site-packages/matplotlib/__init__.py in impl(args, regex, min_ver, ignore_exit_code)
    323             output = subprocess.check_output(
    324                 args, stderr=subprocess.STDOUT,
--> 325                 universal_newlines=True, errors="replace")
    326         except subprocess.CalledProcessError as _cpe:
    327             if ignore_exit_code:

~/anaconda3/envs/dlc/lib/python3.7/subprocess.py in check_output(timeout, *popenargs, **kwargs)
    409 
    410     return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
--> 411                **kwargs).stdout
    412 
    413 

~/anaconda3/envs/dlc/lib/python3.7/subprocess.py in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    510         if check and retcode:
    511             raise CalledProcessError(retcode, process.args,
--> 512                                      output=stdout, stderr=stderr)
    513     return CompletedProcess(process.args, retcode, stdout, stderr)
    514 

CalledProcessError: Command '['convert', '--version']' returned non-zero exit status 1.

In [2]: 

$ lsb_release -a 
LSB Version:    core-11.1.0ubuntu2-noarch:security-11.1.0ubuntu2-noarch
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.1 LTS
Release:    20.04
Codename:   focal
MMathisLab commented 3 years ago

Yep, as we say in the guide, this is for windows and macOS; for linux you need to install the correct wxPython version, thus make your own environment.

Given you have environments from 2019 for DLC, you can. use those and just run pip install deeplabcut==2.2b8within them! Hope that helps.

https://github.com/DeepLabCut/DeepLabCut/tree/master/conda-environments#creating-your-own-customized-conda-env-recommended-route-for-linux-ubuntu-centos-mint-etc

monajalal commented 3 years ago

Fix:

Since this was a new installation of Ubuntu, I didn't realize I didn't have ImageMagick installed. Installing ImageMagick solved the problem.

$ sudo apt install imagemagick
$ conda activate dlc
$ ipython
Python 3.7.9 (default, Aug 31 2020, 12:42:55) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.18.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import deeplabcut as dlc

In [2]: dlc.__version__
Out[2]: '2.2b8'
$ convert -version
Version: ImageMagick 6.9.10-23 Q16 x86_64 20190101 https://imagemagick.org
Copyright: © 1999-2019 ImageMagick Studio LLC
License: https://imagemagick.org/script/license.php
Features: Cipher DPC Modules OpenMP 
Delegates (built-in): bzlib djvu fftw fontconfig freetype jbig jng jpeg lcms lqr ltdl lzma openexr pangocairo png tiff webp wmf x xml zlib