Deeplabcut: Installation error when extracting DLC-CPU
Your Operating system and DeepLabCut version
MacOS Catalina10, Anaconda3 python 3.7, attempting first download of DLC so latest version 2.x
Please complete the following information about your system:
OS: [e.g. iOS, Windows 10, etc] Mac OS Catalina, Anaconda3
DeepLabCut Version [e.g. 22] (please check with import deeplabcut, deeplabcut.__version__) Cannot get to this step
Browser [e.g. chrome, safari] Chrome
Describe the problem
Getting the following error when attempting to run conda env create -f DLC-CPU.yam
*note I have tried this on a separate mac running this code on separate macbook with Mojave OS
Building wheels for collected packages: psutil
Building wheel for psutil (setup.py): started
Building wheel for psutil (setup.py): finished with status 'error'
Running setup.py clean for psutil
Failed to build psutil
Installing collected packages: joblib, numpy, scikit-learn, pytz, pandas, patsy, statsmodels, tqdm, proglog, urllib3, idna, chardet, requests, Pillow, imageio, imageio-ffmpeg, moviepy, cycler, kiwisolver, pyparsing, matplotlib, easydict, intel-openmp, pyyaml, numexpr, tables, ruamel.yaml.clib, ruamel.yaml, opencv-python, networkx, PyWavelets, scikit-image, imgaug, click, tabulate, msgpack, msgpack-numpy, psutil, tensorpack, deeplabcut
Attempting uninstall: numpy
Found existing installation: numpy 1.18.1
Uninstalling numpy-1.18.1:
Successfully uninstalled numpy-1.18.1
Running setup.py install for psutil: started
Running setup.py install for psutil: finished with status 'error'
Pip subprocess error:
ERROR: Command errored out with exit status 1:
command: /opt/anaconda3/envs/DLC-CPU/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"'; __file__='"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/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 /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-wheel-6k0ijunx
cwd: /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/
Complete output (43 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pswindows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_common.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psosx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psbsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psaix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pslinux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_compat.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psposix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pssunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
creating build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/runner.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_process.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_system.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_memory_leaks.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__main__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
running build_ext
building 'psutil._psutil_osx' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/psutil
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/envs/DLC-CPU/include -arch x86_64 -I/opt/anaconda3/envs/DLC-CPU/include -arch x86_64 -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=570 -DPSUTIL_OSX=1 -I/opt/anaconda3/envs/DLC-CPU/include/python3.7m -c psutil/_psutil_common.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_common.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for psutil
ERROR: moviepy 1.0.2 has requirement numpy>=1.17.3; python_version != "2.7", but you'll have numpy 1.16.4 which is incompatible.
ERROR: Command errored out with exit status 1:
command: /opt/anaconda3/envs/DLC-CPU/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"'; __file__='"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-record-tkrm042o/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/DLC-CPU/include/python3.7m/psutil
cwd: /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/
Complete output (43 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pswindows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_common.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psosx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psbsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psaix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pslinux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_compat.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psposix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pssunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
creating build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/runner.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_process.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_system.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_memory_leaks.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__main__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
running build_ext
building 'psutil._psutil_osx' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/psutil
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/envs/DLC-CPU/include -arch x86_64 -I/opt/anaconda3/envs/DLC-CPU/include -arch x86_64 -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=570 -DPSUTIL_OSX=1 -I/opt/anaconda3/envs/DLC-CPU/include/python3.7m -c psutil/_psutil_common.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_common.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/anaconda3/envs/DLC-CPU/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"'; __file__='"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-record-tkrm042o/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/DLC-CPU/include/python3.7m/psutil Check the logs for full command output.
CondaEnvException: Pip failed
How to Reproduce the problem
Steps to reproduce the behavior:
- download anaconda3 to the main disk (Macintosh HD)- folder is Macintosh-->opt-->anaconda3
- download DLC-CPU.yaml to desktop
- in terminal cd desktop
- run conda env create -f DLC-CPU.yaml
- downloads/extractions occur fine until the error above happens
Additional context
Have tried downloading anaconda to several different places, have also tried putting the DLC-CPU.yaml in the same location as the anaconda folder
Installation
samcentanni
All 16 comments
I'm not sure; doesn't seem related to the DLC code base ... I know there are some issues with anaconda and catalina (https://www.anaconda.com/how-to-restore-anaconda-after-macos-catalina-update/) so you might try searching along those lines.
I would be sure to remove this broken build though before trying again; i.e. in the anaconda app you can "put in trash" the environment, and or use these tips to remove the env:https://kapeli.com/cheat_sheets/Conda.docset/Contents/Resources/Documents/index
MMathisLab
on 10 Apr 2020
Yeah that's what I originally thought too but I went through that troubleshooting and no luck. I even tried the installation on a completely different macbook pro running OS High Sierra and got the same exact error. the DLC env is created in Anaconda, just appears to be functional.
samcentanni
on 10 Apr 2020
👍1
alright, i'll see whats up on my Macbook. in the meantime, can you share the whole transaction ?
MMathisLab
on 10 Apr 2020
just downloaded from deeplabcut.org the DLC-CPU file; renamed to DLC-CPUtesting.yaml and inside name: DLC-CPUtesting :
(base) mwmathis@Mackenzies-MacBook-Pro Downloads % conda env create -f DLC-CPUtesting.yaml
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.2
latest version: 4.8.3
Please update conda by running
$ conda update -n base -c defaults conda
Downloading and Extracting Packages
certifi-2020.4.5.1 | 155 KB | ################################################################################################################## | 100%
pyrsistent-0.16.0 | 91 KB | ################################################################################################################## | 100%
wcwidth-0.1.9 | 24 KB | ################################################################################################################## | 100%
jupyter_client-6.1.2 | 82 KB | ################################################################################################################## | 100%
setuptools-46.1.3 | 520 KB | ################################################################################################################## | 100%
jupyter_core-4.6.3 | 75 KB | ################################################################################################################## | 100%
openssl-1.1.1f | 2.2 MB | ################################################################################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: - b'Enabling nb_conda_kernels...\nStatus: enabled\n'
- b'Enabling notebook extension nb_conda/main...\n - Validating: \x1b[32mOK\x1b[0m\nEnabling tree extension nb_conda/tree...\n - Validating: \x1b[32mOK\x1b[0m\nEnabling: nb_conda\n- Writing config: /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/etc/jupyter\n - Validating...\n nb_conda 2.2.1 \x1b[32mOK\x1b[0m\n'
done
Ran pip subprocess with arguments:
['/Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt']
Pip subprocess output:
Collecting deeplabcut
Downloading deeplabcut-2.1.6.4-py3-none-any.whl (386 kB)
Collecting scikit-learn
Using cached scikit_learn-0.22.2.post1-cp37-cp37m-macosx_10_9_x86_64.whl (7.1 MB)
Requirement already satisfied, skipping upgrade: wheel in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.34.2)
Collecting requests
Using cached requests-2.23.0-py2.py3-none-any.whl (58 kB)
Requirement already satisfied, skipping upgrade: ipython in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (7.13.0)
Requirement already satisfied, skipping upgrade: six in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (1.14.0)
Collecting statsmodels
Using cached statsmodels-0.11.1-cp37-cp37m-macosx_10_13_x86_64.whl (8.4 MB)
Collecting chardet
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Requirement already satisfied, skipping upgrade: h5py~=2.7 in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (2.10.0)
Processing /Users/mwmathis/Library/Caches/pip/wheels/9a/88/ec/085d92753646b0eda1b7df49c7afe51a6ecc496556d3012e2e/easydict-1.9-cp37-none-any.whl
Collecting intel-openmp
Using cached intel_openmp-2019.0-py2.py3-none-macosx_10_12_intel.macosx_10_12_x86_64.whl (1.1 MB)
Requirement already satisfied, skipping upgrade: setuptools in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (46.1.3.post20200330)
Collecting tensorpack>=0.9.7.1
Using cached tensorpack-0.10-py2.py3-none-any.whl (290 kB)
Requirement already satisfied, skipping upgrade: ipython-genutils in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.2.0)
Requirement already satisfied, skipping upgrade: scipy in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (1.4.1)
Collecting ruamel.yaml~=0.15
Using cached ruamel.yaml-0.16.10-py2.py3-none-any.whl (111 kB)
Collecting numpy==1.16.4
Using cached numpy-1.16.4-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.9 MB)
Requirement already satisfied, skipping upgrade: certifi in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (2020.4.5.1)
Processing /Users/mwmathis/Library/Caches/pip/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653/PyYAML-5.3.1-cp37-cp37m-macosx_10_9_x86_64.whl
Processing /Users/mwmathis/Library/Caches/pip/wheels/f0/36/f2/32c37d2b7a4f04622ccec875f71ebf5f33f892cea410f26454/moviepy-1.0.2-py3-none-any.whl
Collecting imgaug
Using cached imgaug-0.4.0-py2.py3-none-any.whl (948 kB)
Collecting scikit-image
Using cached scikit_image-0.16.2-cp37-cp37m-macosx_10_6_intel.whl (30.3 MB)
Collecting matplotlib==3.0.3
Using cached matplotlib-3.0.3-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (14.3 MB)
Collecting opencv-python~=3.4
Downloading opencv_python-3.4.9.33-cp37-cp37m-macosx_10_9_x86_64.whl (48.7 MB)
Collecting patsy
Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Requirement already satisfied, skipping upgrade: python-dateutil in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (2.8.1)
Collecting tables
Using cached tables-3.6.1-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.3 MB)
Collecting tqdm
Downloading tqdm-4.45.0-py2.py3-none-any.whl (60 kB)
Collecting pandas
Using cached pandas-1.0.3-cp37-cp37m-macosx_10_9_x86_64.whl (10.0 MB)
Collecting click
Using cached click-7.1.1-py2.py3-none-any.whl (82 kB)
Collecting joblib>=0.11
Using cached joblib-0.14.1-py2.py3-none-any.whl (294 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
Using cached urllib3-1.25.8-py2.py3-none-any.whl (125 kB)
Collecting idna<3,>=2.5
Using cached idna-2.9-py2.py3-none-any.whl (58 kB)
Requirement already satisfied, skipping upgrade: pexpect; sys_platform != "win32" in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (4.8.0)
Requirement already satisfied, skipping upgrade: pygments in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (2.6.1)
Requirement already satisfied, skipping upgrade: jedi>=0.10 in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.16.0)
Requirement already satisfied, skipping upgrade: pickleshare in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.7.5)
Requirement already satisfied, skipping upgrade: backcall in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.1.0)
Requirement already satisfied, skipping upgrade: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (3.0.4)
Requirement already satisfied, skipping upgrade: decorator in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (4.4.2)
Requirement already satisfied, skipping upgrade: appnope; sys_platform == "darwin" in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.1.0)
Requirement already satisfied, skipping upgrade: traitlets>=4.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (4.3.3)
Requirement already satisfied, skipping upgrade: termcolor>=1.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (1.1.0)
Collecting msgpack>=0.5.2
Using cached msgpack-1.0.0-cp37-cp37m-macosx_10_13_x86_64.whl (78 kB)
Collecting tabulate>=0.7.7
Using cached tabulate-0.8.7-py3-none-any.whl (24 kB)
Collecting msgpack-numpy>=0.4.4.2
Using cached msgpack_numpy-0.4.4.3-py2.py3-none-any.whl (5.8 kB)
Requirement already satisfied, skipping upgrade: pyzmq>=16 in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (18.1.1)
Processing /Users/mwmathis/Library/Caches/pip/wheels/b6/e7/50/aee9cc966163d74430f13f208171dee22f11efa4a4a826661c/psutil-5.7.0-cp37-cp37m-macosx_10_9_x86_64.whl
Collecting ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.9"
Using cached ruamel.yaml.clib-0.2.0-cp37-cp37m-macosx_10_9_x86_64.whl (147 kB)
Collecting imageio-ffmpeg>=0.2.0; python_version >= "3.4"
Using cached imageio_ffmpeg-0.4.1-py3-none-macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (20.7 MB)
Processing /Users/mwmathis/Library/Caches/pip/wheels/65/56/60/1d0306a8d90b188af393c1812ddb502a8821b70917f82dcc00/proglog-0.1.9-cp37-none-any.whl
Collecting imageio<3.0,>=2.5; python_version >= "3.4"
Using cached imageio-2.8.0-py3-none-any.whl (3.3 MB)
Requirement already satisfied, skipping upgrade: Shapely in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from imgaug->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (1.6.4.post2)
Collecting Pillow
Downloading Pillow-7.1.1-cp37-cp37m-macosx_10_10_x86_64.whl (2.2 MB)
Collecting PyWavelets>=0.4.0
Using cached PyWavelets-1.1.1-cp37-cp37m-macosx_10_9_x86_64.whl (4.3 MB)
Collecting networkx>=2.0
Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting cycler>=0.10
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.2.0-cp37-cp37m-macosx_10_9_x86_64.whl (60 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting numexpr>=2.6.2
Using cached numexpr-2.7.1-cp37-cp37m-macosx_10_6_intel.whl (186 kB)
Collecting pytz>=2017.2
Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Requirement already satisfied, skipping upgrade: ptyprocess>=0.5 in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.6.0)
Requirement already satisfied, skipping upgrade: parso>=0.5.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from jedi>=0.10->ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.6.2)
Requirement already satisfied, skipping upgrade: wcwidth in /Users/mwmathis/opt/anaconda3/envs/DLC-CPUtesting/lib/python3.7/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->deeplabcut->-r /Users/mwmathis/Downloads/condaenv.oigb215f.requirements.txt (line 1)) (0.1.9)
Installing collected packages: numpy, joblib, scikit-learn, chardet, urllib3, idna, requests, patsy, pytz, pandas, statsmodels, easydict, intel-openmp, msgpack, tabulate, msgpack-numpy, tqdm, psutil, tensorpack, ruamel.yaml.clib, ruamel.yaml, pyyaml, imageio-ffmpeg, proglog, Pillow, imageio, moviepy, PyWavelets, cycler, kiwisolver, pyparsing, matplotlib, networkx, scikit-image, opencv-python, imgaug, numexpr, tables, click, deeplabcut
Attempting uninstall: numpy
Found existing installation: numpy 1.18.1
Uninstalling numpy-1.18.1:
Successfully uninstalled numpy-1.18.1
Successfully installed Pillow-7.1.1 PyWavelets-1.1.1 chardet-3.0.4 click-7.1.1 cycler-0.10.0 deeplabcut-2.1.6.4 easydict-1.9 idna-2.9 imageio-2.8.0 imageio-ffmpeg-0.4.1 imgaug-0.4.0 intel-openmp-2019.0 joblib-0.14.1 kiwisolver-1.2.0 matplotlib-3.0.3 moviepy-1.0.2 msgpack-1.0.0 msgpack-numpy-0.4.4.3 networkx-2.4 numexpr-2.7.1 numpy-1.16.4 opencv-python-3.4.9.33 pandas-1.0.3 patsy-0.5.1 proglog-0.1.9 psutil-5.7.0 pyparsing-2.4.7 pytz-2019.3 pyyaml-5.3.1 requests-2.23.0 ruamel.yaml-0.16.10 ruamel.yaml.clib-0.2.0 scikit-image-0.16.2 scikit-learn-0.22.2.post1 statsmodels-0.11.1 tables-3.6.1 tabulate-0.8.7 tensorpack-0.10 tqdm-4.45.0 urllib3-1.25.8
#
# To activate this environment, use
#
# $ conda activate DLC-CPUtesting
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) mwmathis@Mackenzies-MacBook-Pro Downloads %
Thanks for the help. I appreciate it.
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(base) MacBook-Pro:desktop samcentanni129$
(base) MacBook-Pro:desktop samcentanni129$ conda env create -f DLC-CPU.yaml
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.2
latest version: 4.8.3
Please update conda by running
$ conda update -n base -c defaults conda
Downloading and Extracting Packages
jupyter_core-4.6.3 | 75 KB | ##################################### | 100%
gast-0.3.3 | 14 KB | ##################################### | 100%
python-3.7.7 | 19.8 MB | ##################################### | 100%
decorator-4.4.2 | 14 KB | ##################################### | 100%
tensorboard-1.13.1 | 3.1 MB | ##################################### | 100%
tensorflow-base-1.13 | 65.7 MB | ##################################### | 100%
backports.lzma-0.0.1 | 50 KB | ##################################### | 100%
shapely-1.6.4 | 292 KB | ##################################### | 100%
absl-py-0.9.0 | 164 KB | ##################################### | 100%
readline-8.0 | 326 KB | ##################################### | 100%
ipython-7.13.0 | 990 KB | ##################################### | 100%
astor-0.8.0 | 46 KB | ##################################### | 100%
qtconsole-4.7.2 | 94 KB | ##################################### | 100%
termcolor-1.1.0 | 8 KB | ##################################### | 100%
nb_conda-2.2.1 | 32 KB | ##################################### | 100%
openssl-1.1.1f | 2.2 MB | ##################################### | 100%
tensorflow-estimator | 181 KB | ##################################### | 100%
prompt_toolkit-3.0.4 | 11 KB | ##################################### | 100%
certifi-2020.4.5.1 | 155 KB | ##################################### | 100%
wcwidth-0.1.9 | 24 KB | ##################################### | 100%
wxpython-4.0.4 | 12.3 MB | ##################################### | 100%
libprotobuf-3.11.4 | 2.6 MB | ##################################### | 100%
grpcio-1.16.1 | 840 KB | ##################################### | 100%
keras-applications-1 | 33 KB | ##################################### | 100%
jupyter_client-6.1.2 | 82 KB | ##################################### | 100%
tornado-6.0.4 | 597 KB | ##################################### | 100%
pyrsistent-0.16.0 | 91 KB | ##################################### | 100%
pygments-2.6.1 | 654 KB | ##################################### | 100%
setuptools-46.1.3 | 520 KB | ##################################### | 100%
protobuf-3.11.4 | 628 KB | ##################################### | 100%
markdown-3.1.1 | 117 KB | ##################################### | 100%
_tflow_select-2.3.0 | 3 KB | ##################################### | 100%
keras-preprocessing- | 36 KB | ##################################### | 100%
prompt-toolkit-3.0.4 | 244 KB | ##################################### | 100%
parso-0.6.2 | 70 KB | ##################################### | 100%
nb_conda_kernels-2.2 | 38 KB | ##################################### | 100%
c-ares-1.15.0 | 73 KB | ##################################### | 100%
jedi-0.16.0 | 779 KB | ##################################### | 100%
tensorflow-1.13.1 | 5 KB | ##################################### | 100%
geos-3.8.0 | 813 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: / b'Enabling nb_conda_kernels...\nStatus: enabled\n'
| b'Enabling notebook extension nb_conda/main...\n - Validating: \x1b[32mOK\x1b[0m\nEnabling tree extension nb_conda/tree...\n - Validating: \x1b[32mOK\x1b[0m\nEnabling: nb_conda\n- Writing config: /opt/anaconda3/envs/DLC-CPU/etc/jupyter\n - Validating...\n nb_conda 2.2.1 \x1b[32mOK\x1b[0m\n'
done
Ran pip subprocess with arguments:
['/opt/anaconda3/envs/DLC-CPU/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt']
Pip subprocess output:
Collecting deeplabcut
Using cached deeplabcut-2.1.6.4-py3-none-any.whl (386 kB)
Requirement already satisfied, skipping upgrade: setuptools in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (46.1.3.post20200330)
Collecting scikit-learn
Using cached scikit_learn-0.22.2.post1-cp37-cp37m-macosx_10_9_x86_64.whl (7.1 MB)
Collecting statsmodels
Using cached statsmodels-0.11.1-cp37-cp37m-macosx_10_13_x86_64.whl (8.4 MB)
Processing /Users/samcentanni 1/Library/Caches/pip/wheels/f0/36/f2/32c37d2b7a4f04622ccec875f71ebf5f33f892cea410f26454/moviepy-1.0.2-py3-none-any.whl
Requirement already satisfied, skipping upgrade: h5py~=2.7 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (2.10.0)
Collecting numpy==1.16.4
Using cached numpy-1.16.4-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.9 MB)
Collecting matplotlib==3.0.3
Using cached matplotlib-3.0.3-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (14.3 MB)
Collecting pandas
Using cached pandas-1.0.3-cp37-cp37m-macosx_10_9_x86_64.whl (10.0 MB)
Processing /Users/samcentanni 1/Library/Caches/pip/wheels/88/96/68/c2be18e7406804be2e593e1c37845f2dd20ac2ce1381ce40b0/easydict-1.9-py3-none-any.whl
Requirement already satisfied, skipping upgrade: six in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (1.14.0)
Collecting patsy
Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Requirement already satisfied, skipping upgrade: python-dateutil in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (2.8.1)
Collecting intel-openmp
Using cached intel_openmp-2019.0-py2.py3-none-macosx_10_12_intel.macosx_10_12_x86_64.whl (1.1 MB)
Processing /Users/samcentanni 1/Library/Caches/pip/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653/PyYAML-5.3.1-cp37-cp37m-macosx_10_9_x86_64.whl
Collecting tables
Using cached tables-3.6.1-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.3 MB)
Collecting ruamel.yaml~=0.15
Using cached ruamel.yaml-0.16.10-py2.py3-none-any.whl (111 kB)
Collecting requests
Using cached requests-2.23.0-py2.py3-none-any.whl (58 kB)
Requirement already satisfied, skipping upgrade: certifi in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (2020.4.5.1)
Collecting tqdm
Using cached tqdm-4.45.0-py2.py3-none-any.whl (60 kB)
Collecting opencv-python~=3.4
Using cached opencv_python-3.4.9.33-cp37-cp37m-macosx_10_9_x86_64.whl (48.7 MB)
Collecting chardet
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting imgaug
Using cached imgaug-0.4.0-py2.py3-none-any.whl (948 kB)
Collecting click
Using cached click-7.1.1-py2.py3-none-any.whl (82 kB)
Requirement already satisfied, skipping upgrade: ipython-genutils in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.2.0)
Collecting tensorpack>=0.9.7.1
Using cached tensorpack-0.10-py2.py3-none-any.whl (290 kB)
Collecting scikit-image
Using cached scikit_image-0.16.2-cp37-cp37m-macosx_10_6_intel.whl (30.3 MB)
Requirement already satisfied, skipping upgrade: scipy in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (1.4.1)
Requirement already satisfied, skipping upgrade: ipython in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (7.13.0)
Requirement already satisfied, skipping upgrade: wheel in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.34.2)
Collecting joblib>=0.11
Using cached joblib-0.14.1-py2.py3-none-any.whl (294 kB)
Processing /Users/samcentanni 1/Library/Caches/pip/wheels/12/36/1f/dc61e6ac10781d63cf6fa045eb09fa613a667384e12cb6e6e0/proglog-0.1.9-py3-none-any.whl
Requirement already satisfied, skipping upgrade: decorator<5.0,>=4.0.2 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from moviepy->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (4.4.2)
Collecting imageio<3.0,>=2.5; python_version >= "3.4"
Using cached imageio-2.8.0-py3-none-any.whl (3.3 MB)
Collecting imageio-ffmpeg>=0.2.0; python_version >= "3.4"
Using cached imageio_ffmpeg-0.4.1-py3-none-macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (20.7 MB)
Collecting cycler>=0.10
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting kiwisolver>=1.0.1
Using cached kiwisolver-1.2.0-cp37-cp37m-macosx_10_9_x86_64.whl (60 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting pytz>=2017.2
Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Collecting numexpr>=2.6.2
Using cached numexpr-2.7.1-cp37-cp37m-macosx_10_6_intel.whl (186 kB)
Collecting ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.9"
Using cached ruamel.yaml.clib-0.2.0-cp37-cp37m-macosx_10_9_x86_64.whl (147 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
Using cached urllib3-1.25.8-py2.py3-none-any.whl (125 kB)
Collecting idna<3,>=2.5
Using cached idna-2.9-py2.py3-none-any.whl (58 kB)
Collecting Pillow
Using cached Pillow-7.1.1-cp37-cp37m-macosx_10_10_x86_64.whl (2.2 MB)
Requirement already satisfied, skipping upgrade: Shapely in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from imgaug->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (1.6.4.post2)
Requirement already satisfied, skipping upgrade: termcolor>=1.1 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (1.1.0)
Collecting tabulate>=0.7.7
Using cached tabulate-0.8.7-py3-none-any.whl (24 kB)
Collecting msgpack-numpy>=0.4.4.2
Using cached msgpack_numpy-0.4.4.3-py2.py3-none-any.whl (5.8 kB)
Collecting psutil>=5
Using cached psutil-5.7.0.tar.gz (449 kB)
Requirement already satisfied, skipping upgrade: pyzmq>=16 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (18.1.1)
Collecting msgpack>=0.5.2
Using cached msgpack-1.0.0-cp37-cp37m-macosx_10_13_x86_64.whl (78 kB)
Collecting networkx>=2.0
Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting PyWavelets>=0.4.0
Using cached PyWavelets-1.1.1-cp37-cp37m-macosx_10_9_x86_64.whl (4.3 MB)
Requirement already satisfied, skipping upgrade: jedi>=0.10 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.16.0)
Requirement already satisfied, skipping upgrade: pexpect; sys_platform != "win32" in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (4.8.0)
Requirement already satisfied, skipping upgrade: traitlets>=4.2 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (4.3.3)
Requirement already satisfied, skipping upgrade: pickleshare in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.7.5)
Requirement already satisfied, skipping upgrade: appnope; sys_platform == "darwin" in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.1.0)
Requirement already satisfied, skipping upgrade: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (3.0.4)
Requirement already satisfied, skipping upgrade: backcall in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.1.0)
Requirement already satisfied, skipping upgrade: pygments in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (2.6.1)
Requirement already satisfied, skipping upgrade: parso>=0.5.2 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from jedi>=0.10->ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.6.2)
Requirement already satisfied, skipping upgrade: ptyprocess>=0.5 in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.6.0)
Requirement already satisfied, skipping upgrade: wcwidth in /opt/anaconda3/envs/DLC-CPU/lib/python3.7/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->deeplabcut->-r /Users/samcentanni 1/Desktop/condaenv.6801dfqj.requirements.txt (line 1)) (0.1.9)
Building wheels for collected packages: psutil
Building wheel for psutil (setup.py): started
Building wheel for psutil (setup.py): finished with status 'error'
Running setup.py clean for psutil
Failed to build psutil
Installing collected packages: joblib, numpy, scikit-learn, pytz, pandas, patsy, statsmodels, tqdm, proglog, urllib3, idna, chardet, requests, Pillow, imageio, imageio-ffmpeg, moviepy, cycler, kiwisolver, pyparsing, matplotlib, easydict, intel-openmp, pyyaml, numexpr, tables, ruamel.yaml.clib, ruamel.yaml, opencv-python, networkx, PyWavelets, scikit-image, imgaug, click, tabulate, msgpack, msgpack-numpy, psutil, tensorpack, deeplabcut
Attempting uninstall: numpy
Found existing installation: numpy 1.18.1
Uninstalling numpy-1.18.1:
Successfully uninstalled numpy-1.18.1
Running setup.py install for psutil: started
Running setup.py install for psutil: finished with status 'error'
Pip subprocess error:
ERROR: Command errored out with exit status 1:
command: /opt/anaconda3/envs/DLC-CPU/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"'; __file__='"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/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 /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-wheel-6k0ijunx
cwd: /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/
Complete output (43 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pswindows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_common.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psosx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psbsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psaix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pslinux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_compat.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psposix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pssunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
creating build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/runner.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_process.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_system.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_memory_leaks.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__main__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
running build_ext
building 'psutil._psutil_osx' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/psutil
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/envs/DLC-CPU/include -arch x86_64 -I/opt/anaconda3/envs/DLC-CPU/include -arch x86_64 -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=570 -DPSUTIL_OSX=1 -I/opt/anaconda3/envs/DLC-CPU/include/python3.7m -c psutil/_psutil_common.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_common.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for psutil
ERROR: moviepy 1.0.2 has requirement numpy>=1.17.3; python_version != "2.7", but you'll have numpy 1.16.4 which is incompatible.
ERROR: Command errored out with exit status 1:
command: /opt/anaconda3/envs/DLC-CPU/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"'; __file__='"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-record-tkrm042o/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/DLC-CPU/include/python3.7m/psutil
cwd: /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/
Complete output (43 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pswindows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_common.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psosx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psbsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psaix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pslinux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_compat.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_psposix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
copying psutil/_pssunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil
creating build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/runner.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_process.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_system.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_memory_leaks.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
copying psutil/tests/__main__.py -> build/lib.macosx-10.9-x86_64-3.7/psutil/tests
running build_ext
building 'psutil._psutil_osx' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/psutil
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch
creating build/temp.macosx-10.9-x86_64-3.7/psutil/arch/osx
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/envs/DLC-CPU/include -arch x86_64 -I/opt/anaconda3/envs/DLC-CPU/include -arch x86_64 -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=570 -DPSUTIL_OSX=1 -I/opt/anaconda3/envs/DLC-CPU/include/python3.7m -c psutil/_psutil_common.c -o build/temp.macosx-10.9-x86_64-3.7/psutil/_psutil_common.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/anaconda3/envs/DLC-CPU/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"'; __file__='"'"'/private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-install-rbpmkeoi/psutil/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/28/frw8jxcn0979kbf84vdhh7_h0000gp/T/pip-record-tkrm042o/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/DLC-CPU/include/python3.7m/psutil Check the logs for full command output.
CondaEnvException: Pip failed
can you update "pip" in your (base) env? pip install pip --upgrade
MMathisLab
on 10 Apr 2020
did that didnt change anything. one line that appears different is this line in mine vs this line in yours
(mine)
Collecting deeplabcut
Using cached deeplabcut-2.1.6.4-py3-none-any.whl (386 kB)
(yours)
Collecting deeplabcut
Downloading deeplabcut-2.1.6.4-py3-none-any.whl (386 kB)
samcentanni
on 10 Apr 2020
^ yes, mine is caches because I have deeplabcut installed already on my computer. Env are not like dockers, i.e. the are not totally isolated from the computer; so I have dlc installed in other envs
MMathisLab
on 10 Apr 2020
@samcentanni check out this: https://github.com/conda/conda/issues/8347 TLDR: don't use homebrew, be sure you use something else:
MMathisLab
on 11 Apr 2020
I'll close as this is being assisted/ it seems a conda situation not related to DLC yaml file (as the default build file is functional: https://github.com/AlexEMG/DeepLabCut/issues/650#issuecomment-612128814)
But, let me know when you solve it for your system.
MMathisLab
on 11 Apr 2020
Thanks again for your help @MMathisLab. Unfortunately I wasn't using homebrew so this didnt change anything. Tried a few different terminals and the same errors. I'll keep digging but if you come across others with this issue please do let me know.
samcentanni
on 15 Apr 2020
👍1
It鈥檚 a bit of a long shot, but it it doesn鈥檛 ruin other env you have, could you try to reinstall anaconda?
MMathisLab
on 15 Apr 2020
Yeah I've tried this a few times. One issue I am having with downloading anaconda is my homefolder has a space in it (samcentanni 1) so it wont let me download it directly to this directory and I obviously can only access my home directory through terminal. I have been downloading anaconda and moving it to the home folder and that seems to move over there fine, but maybe its not fully moving it to this directory? Like you said probably getting beyond a DLC issue but still frustrating trying to figure this out.
samcentanni
on 15 Apr 2020
Hmm... the moving worries me; can you try to just install it in opt/ and see how it goes?
MMathisLab
on 15 Apr 2020
Hey @MMathisLab I figured it out. It appears I needed to install the command line toolkit Xcode. (In terminal: xcode-select --install). Once I did this everything ran fine. Thanks again for your help and hopefully this will help anyone else having this issue in the future.
samcentanni
on 15 Apr 2020
🎉1
Okay! Great to know - I thought this was installed by default on every MacOS, but good to know it鈥檚 not!
MMathisLab
on 15 Apr 2020
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