search

kushalkolar / MESmerize

Platform for Calcium Imaging analysis. DEPRECATED.
GNU General Public License v3.0
59 stars 14 forks source link

Installation fails on Mac Mojave #14

Closed rem7101 closed 4 years ago

rem7101 commented 4 years ago

Problem

Hello - I am trying to install Mesmerize on a Mac system version 10.14.6, but I am receiving error messages when I reach the launch steps (http://www.mesmerizelab.org/user_guides/installation.html). Reading the gitter messages, it seems like this may be similar to what smsadegh was reporting. I previously had Caiman running successfully, but uninstalled everything prior to starting the Mesmerize install. Full code pasted below of the install process in terminal.

Error message/Exception in spyder console. Any screenshots

Last login: Sat May 16 11:47:55 on ttys000
(base) macbook-pro-4:~ user1$ conda create --name mesmerize python=3.6
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /anaconda3/envs/mesmerize

  added / updated specs:
    - python=3.6

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/osx-64::certifi-2020.4.5.1-py36_0
  libcxx             pkgs/main/osx-64::libcxx-10.0.0-1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.3-h0a44026_1
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0
  pip                pkgs/main/osx-64::pip-20.0.2-py36_3
  python             pkgs/main/osx-64::python-3.6.10-hf48f09d_2
  readline           pkgs/main/osx-64::readline-8.0-h1de35cc_0
  setuptools         pkgs/main/osx-64::setuptools-46.0.0-py36_0
  sqlite             pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  wheel              pkgs/main/osx-64::wheel-0.34.2-py36_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate mesmerize
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) macbook-pro-4:~ user1$ conda activate mesmerize
(mesmerize) macbook-pro-4:~ user1$ conda install cython numpy pandas
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /anaconda3/envs/mesmerize

  added / updated specs:
    - cython
    - numpy
    - pandas

The following NEW packages will be INSTALLED:

  blas               pkgs/main/osx-64::blas-1.0-mkl
  cython             pkgs/main/osx-64::cython-0.29.17-py36h0a44026_0
  intel-openmp       pkgs/main/osx-64::intel-openmp-2019.4-233
  libgfortran        pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
  mkl                pkgs/main/osx-64::mkl-2019.4-233
  mkl-service        pkgs/main/osx-64::mkl-service-2.3.0-py36hfbe908c_0
  mkl_fft            pkgs/main/osx-64::mkl_fft-1.0.15-py36h5e564d8_0
  mkl_random         pkgs/main/osx-64::mkl_random-1.1.0-py36ha771720_0
  numpy              pkgs/main/osx-64::numpy-1.18.1-py36h7241aed_0
  numpy-base         pkgs/main/osx-64::numpy-base-1.18.1-py36h6575580_1
  pandas             pkgs/main/osx-64::pandas-1.0.3-py36h6c726b0_0
  python-dateutil    pkgs/main/noarch::python-dateutil-2.8.1-py_0
  pytz               pkgs/main/noarch::pytz-2020.1-py_0
  six                pkgs/main/osx-64::six-1.14.0-py36_0

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(mesmerize) macbook-pro-4:~ user1$ git clond https://github.com/kushalkolar/MESmerize.git
git: 'clond' is not a git command. See 'git --help'.

The most similar command is
    clone
(mesmerize) macbook-pro-4:~ user1$ git clone https://github.com/kushalkolar/MESmerize.git
Cloning into 'MESmerize'...
remote: Enumerating objects: 881, done.
remote: Counting objects: 100% (881/881), done.
remote: Compressing objects: 100% (645/645), done.
remote: Total 11621 (delta 503), reused 513 (delta 211), pack-reused 10740
Receiving objects: 100% (11621/11621), 299.72 MiB | 12.83 MiB/s, done.
Resolving deltas: 100% (7651/7651), done.
Checking out files: 100% (1198/1198), done.
warning: the following paths have collided (e.g. case-sensitive paths
on a case-insensitive filesystem) and only one from the same
colliding group is in the working tree:

  'mesmerize/plotting/colormaps/Spectral.png'
  'mesmerize/plotting/colormaps/spectral.png'
  'mesmerize/plotting/widgets/colormaps/Spectral.png'
  'mesmerize/plotting/widgets/colormaps/spectral.png'
(mesmerize) macbook-pro-4:~ user1$ cd MESmerize
(mesmerize) macbook-pro-4:MESmerize user1$ git checkout snap
M   mesmerize/plotting/colormaps/Spectral.png
M   mesmerize/plotting/widgets/colormaps/Spectral.png
Branch 'snap' set up to track remote branch 'snap' from 'origin'.
Switched to a new branch 'snap'
(mesmerize) macbook-pro-4:MESmerize user1$ pip install -r requirements.txt
Collecting cycler==0.10.0
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting dask==1.1.1
  Using cached dask-1.1.1-py2.py3-none-any.whl (701 kB)
Processing /Users/user1/Library/Caches/pip/wheels/c4/f0/e2/8e4ecc9e1b12a428a7657ba683576d3e79d0a75982f63e8fd2/future-0.17.1-py3-none-any.whl
Collecting h5py==2.9.0
  Using cached h5py-2.9.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (6.3 MB)
Collecting hickle==3.4.3
  Using cached hickle-3.4.3-py3-none-any.whl (40 kB)
Collecting ipython==7.3.0
  Using cached ipython-7.3.0-py3-none-any.whl (768 kB)
Collecting ipyparallel==6.2.3
  Using cached ipyparallel-6.2.3-py2.py3-none-any.whl (197 kB)
Collecting MarkupSafe==1.1.1
  Using cached MarkupSafe-1.1.1-cp36-cp36m-macosx_10_6_intel.whl (18 kB)
Collecting matplotlib==2.1.2
  Using cached matplotlib-2.1.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.2 MB)
Collecting opencv-contrib-python==3.4.1.15
  Using cached opencv_contrib_python-3.4.1.15-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (47.4 MB)
Collecting opencv-python==3.4.1.15
  Using cached opencv_python-3.4.1.15-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (41.9 MB)
Collecting pandas==0.25.3
  Using cached pandas-0.25.3-cp36-cp36m-macosx_10_9_x86_64.whl (10.4 MB)
Collecting Pillow==5.4.1
  Using cached Pillow-5.4.1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.7 MB)
Processing /Users/user1/Library/Caches/pip/wheels/55/d9/6e/753ea9b05c8842e1f8d3d745713226395aaa7090b27a4e6293/psutil-5.5.1-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting PyQt5==5.9.2
  Using cached PyQt5-5.9.2-5.9.3-cp35.cp36.cp37-abi3-macosx_10_6_intel.whl (81.7 MB)
Collecting QtPy==1.6.0
  Using cached QtPy-1.6.0-py2.py3-none-any.whl (43 kB)
Collecting scikit-image==0.14.2
  Using cached scikit_image-0.14.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (28.9 MB)
Collecting scikit-learn==0.20.3
  Using cached scikit_learn-0.20.3-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (8.0 MB)
Collecting scipy==1.3.0
  Using cached scipy-1.3.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (27.7 MB)
Collecting seaborn==0.9.0
  Using cached seaborn-0.9.0-py3-none-any.whl (208 kB)
Processing /Users/user1/Library/Caches/pip/wheels/23/9d/42/5ec745cbbb17517000a53cecc49d6a865450d1f5cb16dc8a9c/sklearn-0.0-py2.py3-none-any.whl
Collecting spyder==3.3.3
  Using cached spyder-3.3.3-py3-none-any.whl (2.8 MB)
Collecting tifffile==0.15.1
  Using cached tifffile-0.15.1-cp36-cp36m-macosx_10_7_x86_64.whl (116 kB)
Collecting tqdm==4.37.0
  Using cached tqdm-4.37.0-py2.py3-none-any.whl (53 kB)
Processing /Users/user1/Library/Caches/pip/wheels/f4/16/80/410b5e600f73d21e3cc507ecc5bb970998db55084e3d38fdf4/PeakUtils-1.3.2-py3-none-any.whl
Collecting tables==3.5.2
  Using cached tables-3.5.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.4 MB)
Collecting joblib==0.13.2
  Using cached joblib-0.13.2-py2.py3-none-any.whl (278 kB)
Collecting graphviz==0.13
  Using cached graphviz-0.13-py2.py3-none-any.whl (17 kB)
Collecting numba==0.42.1
  Using cached numba-0.42.1-cp36-cp36m-macosx_10_9_x86_64.whl (1.6 MB)
Processing /Users/user1/Library/Caches/pip/wheels/66/97/1a/1df12a9b145ec52cfc551ab4ae669c8eb6ed5e18aefc751ec7/Bottleneck-1.2.1-cp36-cp36m-macosx_10_9_x86_64.whl
Requirement already satisfied: six in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from cycler==0.10.0->-r requirements.txt (line 1)) (1.14.0)
Requirement already satisfied: numpy>=1.7 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from h5py==2.9.0->-r requirements.txt (line 4)) (1.18.1)
Collecting pickleshare
  Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting appnope; sys_platform == "darwin"
  Using cached appnope-0.1.0-py2.py3-none-any.whl (4.0 kB)
Collecting jedi>=0.10
  Using cached jedi-0.17.0-py2.py3-none-any.whl (1.1 MB)
Requirement already satisfied: setuptools>=18.5 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipython==7.3.0->-r requirements.txt (line 6)) (46.0.0.post20200309)
Collecting traitlets>=4.2
  Using cached traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
Processing /Users/user1/Library/Caches/pip/wheels/b4/cb/f1/d142b3bb45d488612cf3943d8a1db090eb95e6687045ba61d1/backcall-0.1.0-py3-none-any.whl
Collecting prompt-toolkit<2.1.0,>=2.0.0
  Using cached prompt_toolkit-2.0.10-py3-none-any.whl (340 kB)
Collecting pygments
  Using cached Pygments-2.6.1-py3-none-any.whl (914 kB)
Collecting decorator
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting pexpect; sys_platform != "win32"
  Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Processing /Users/user1/Library/Caches/pip/wheels/37/a7/db/2d592e44029ef817f3ef63ea991db34191cebaef087a96f505/tornado-6.0.4-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting ipython-genutils
  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting ipykernel>=4.4
  Using cached ipykernel-5.2.1-py3-none-any.whl (118 kB)
Requirement already satisfied: python-dateutil>=2.1 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipyparallel==6.2.3->-r requirements.txt (line 7)) (2.8.1)
Collecting jupyter-client
  Using cached jupyter_client-6.1.3-py3-none-any.whl (106 kB)
Collecting pyzmq>=13
  Using cached pyzmq-19.0.1-cp36-cp36m-macosx_10_9_intel.whl (1.4 MB)
Requirement already satisfied: pytz in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from matplotlib==2.1.2->-r requirements.txt (line 9)) (2020.1)
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 sip<4.20,>=4.19.4
  Using cached sip-4.19.8-cp36-cp36m-macosx_10_6_intel.whl (51 kB)
Collecting PyWavelets>=0.4.0
  Using cached PyWavelets-1.1.1-cp36-cp36m-macosx_10_9_x86_64.whl (4.3 MB)
Collecting networkx>=1.8
  Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting cloudpickle>=0.2.1
  Using cached cloudpickle-1.4.1-py3-none-any.whl (26 kB)
Collecting qtconsole>=4.2.0
  Using cached qtconsole-4.7.4-py2.py3-none-any.whl (118 kB)
Collecting qtawesome>=0.4.1
  Using cached QtAwesome-0.7.2-py2.py3-none-any.whl (832 kB)
Collecting nbconvert
  Using cached nbconvert-5.6.1-py2.py3-none-any.whl (455 kB)
Collecting pyflakes
  Using cached pyflakes-2.2.0-py2.py3-none-any.whl (66 kB)
Collecting sphinx
  Using cached Sphinx-3.0.3-py3-none-any.whl (2.8 MB)
Collecting pycodestyle
  Using cached pycodestyle-2.6.0-py2.py3-none-any.whl (41 kB)
Processing /Users/user1/Library/Caches/pip/wheels/7a/97/5e/6885d024ee585fe437a65cc815cbdb10b810ceaa65242ccbea/numpydoc-0.9.2-py3-none-any.whl
Processing /Users/user1/Library/Caches/pip/wheels/f1/90/67/ebd231ce083da4fd4ca67684aa2f0b0e45b135d321335f8598/rope-0.17.0-py3-none-any.whl
Collecting keyring; sys_platform != "linux2"
  Using cached keyring-21.2.1-py3-none-any.whl (31 kB)
Collecting pylint
  Using cached pylint-2.5.2-py3-none-any.whl (324 kB)
Collecting spyder-kernels<1.0,>=0.4.2
  Using cached spyder_kernels-0.5.2-py2.py3-none-any.whl (42 kB)
Collecting chardet>=2.0.0
  Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting mock>=2.0
  Using cached mock-4.0.2-py3-none-any.whl (28 kB)
Collecting numexpr>=2.6.2
  Using cached numexpr-2.7.1-cp36-cp36m-macosx_10_6_intel.whl (185 kB)
Collecting llvmlite>=0.27.0dev0
  Using cached llvmlite-0.32.1-cp36-cp36m-macosx_10_9_x86_64.whl (15.9 MB)
Collecting parso>=0.7.0
  Using cached parso-0.7.0-py2.py3-none-any.whl (100 kB)
Collecting wcwidth
  Using cached wcwidth-0.1.9-py2.py3-none-any.whl (19 kB)
Collecting ptyprocess>=0.5
  Using cached ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB)
Collecting jupyter-core>=4.6.0
  Using cached jupyter_core-4.6.3-py2.py3-none-any.whl (83 kB)
Collecting entrypoints>=0.2.2
  Using cached entrypoints-0.3-py2.py3-none-any.whl (11 kB)
Collecting mistune<2,>=0.8.1
  Using cached mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Collecting nbformat>=4.4
  Using cached nbformat-5.0.6-py3-none-any.whl (170 kB)
Collecting testpath
  Using cached testpath-0.4.4-py2.py3-none-any.whl (163 kB)
Collecting defusedxml
  Using cached defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
Collecting bleach
  Using cached bleach-3.1.5-py2.py3-none-any.whl (151 kB)
Processing /Users/user1/Library/Caches/pip/wheels/46/c4/40/718c6fd14c2129ccaee10e0cf03ef6c4d01d98cad5dbbfda38/pandocfilters-1.4.2-py3-none-any.whl
Collecting jinja2>=2.4
  Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting sphinxcontrib-applehelp
  Using cached sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
Collecting sphinxcontrib-jsmath
  Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting babel>=1.3
  Using cached Babel-2.8.0-py2.py3-none-any.whl (8.6 MB)
Collecting packaging
  Using cached packaging-20.3-py2.py3-none-any.whl (37 kB)
Collecting sphinxcontrib-qthelp
  Using cached sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Collecting requests>=2.5.0
  Using cached requests-2.23.0-py2.py3-none-any.whl (58 kB)
Collecting alabaster<0.8,>=0.7
  Using cached alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Collecting docutils>=0.12
  Using cached docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting imagesize
  Using cached imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB)
Collecting sphinxcontrib-serializinghtml
  Using cached sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB)
Collecting sphinxcontrib-devhelp
  Using cached sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting sphinxcontrib-htmlhelp
  Using cached sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB)
Collecting snowballstemmer>=1.1
  Using cached snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB)
Collecting importlib-metadata; python_version < "3.8"
  Using cached importlib_metadata-1.6.0-py2.py3-none-any.whl (30 kB)
Collecting mccabe<0.7,>=0.6
  Using cached mccabe-0.6.1-py2.py3-none-any.whl (8.6 kB)
Collecting toml>=0.7.1
  Using cached toml-0.10.1-py2.py3-none-any.whl (19 kB)
Collecting isort<5,>=4.2.5
  Using cached isort-4.3.21-py2.py3-none-any.whl (42 kB)
Collecting astroid<=2.5,>=2.4.0
  Using cached astroid-2.4.1-py3-none-any.whl (214 kB)
Collecting wurlitzer; platform_system != "Windows"
  Using cached wurlitzer-2.0.0-py2.py3-none-any.whl (6.0 kB)
Collecting jsonschema!=2.5.0,>=2.4
  Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting webencodings
  Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
  Using cached urllib3-1.25.9-py2.py3-none-any.whl (126 kB)
Collecting idna<3,>=2.5
  Using cached idna-2.9-py2.py3-none-any.whl (58 kB)
Requirement already satisfied: certifi>=2017.4.17 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from requests>=2.5.0->sphinx->spyder==3.3.3->-r requirements.txt (line 22)) (2020.4.5.1)
Collecting zipp>=0.5
  Using cached zipp-3.1.0-py3-none-any.whl (4.9 kB)
Processing /Users/user1/Library/Caches/pip/wheels/32/42/7f/23cae9ff6ef66798d00dc5d659088e57dbba01566f6c60db63/wrapt-1.12.1-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting typed-ast<1.5,>=1.4.0; implementation_name == "cpython" and python_version < "3.8"
  Using cached typed_ast-1.4.1-cp36-cp36m-macosx_10_9_x86_64.whl (223 kB)
Processing /Users/user1/Library/Caches/pip/wheels/74/16/66/f3b601fb6040a9bbc1652bf154faa76f51a84e2f6f850cb7bd/lazy_object_proxy-1.4.3-cp36-cp36m-macosx_10_9_x86_64.whl
Processing /Users/user1/Library/Caches/pip/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464/pyrsistent-0.16.0-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting attrs>=17.4.0
  Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Installing collected packages: cycler, dask, future, h5py, hickle, pickleshare, appnope, parso, jedi, ipython-genutils, decorator, traitlets, backcall, wcwidth, prompt-toolkit, pygments, ptyprocess, pexpect, ipython, tornado, jupyter-core, pyzmq, jupyter-client, ipykernel, ipyparallel, MarkupSafe, pyparsing, matplotlib, opencv-contrib-python, opencv-python, pandas, Pillow, psutil, sip, PyQt5, QtPy, scipy, PyWavelets, networkx, cloudpickle, scikit-image, scikit-learn, seaborn, sklearn, qtconsole, qtawesome, entrypoints, mistune, pyrsistent, zipp, importlib-metadata, attrs, jsonschema, nbformat, testpath, defusedxml, webencodings, packaging, bleach, pandocfilters, jinja2, nbconvert, pyflakes, sphinxcontrib-applehelp, sphinxcontrib-jsmath, babel, sphinxcontrib-qthelp, urllib3, idna, chardet, requests, alabaster, docutils, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, snowballstemmer, sphinx, pycodestyle, numpydoc, rope, keyring, mccabe, toml, isort, wrapt, typed-ast, lazy-object-proxy, astroid, pylint, wurlitzer, spyder-kernels, spyder, tifffile, tqdm, PeakUtils, mock, numexpr, tables, joblib, graphviz, llvmlite, numba, bottleneck
  Attempting uninstall: pandas
    Found existing installation: pandas 1.0.3
    Uninstalling pandas-1.0.3:
      Successfully uninstalled pandas-1.0.3
Successfully installed MarkupSafe-1.1.1 PeakUtils-1.3.2 Pillow-5.4.1 PyQt5-5.9.2 PyWavelets-1.1.1 QtPy-1.6.0 alabaster-0.7.12 appnope-0.1.0 astroid-2.4.1 attrs-19.3.0 babel-2.8.0 backcall-0.1.0 bleach-3.1.5 bottleneck-1.2.1 chardet-3.0.4 cloudpickle-1.4.1 cycler-0.10.0 dask-1.1.1 decorator-4.4.2 defusedxml-0.6.0 docutils-0.16 entrypoints-0.3 future-0.17.1 graphviz-0.13 h5py-2.9.0 hickle-3.4.3 idna-2.9 imagesize-1.2.0 importlib-metadata-1.6.0 ipykernel-5.2.1 ipyparallel-6.2.3 ipython-7.3.0 ipython-genutils-0.2.0 isort-4.3.21 jedi-0.17.0 jinja2-2.11.2 joblib-0.13.2 jsonschema-3.2.0 jupyter-client-6.1.3 jupyter-core-4.6.3 keyring-21.2.1 lazy-object-proxy-1.4.3 llvmlite-0.32.1 matplotlib-2.1.2 mccabe-0.6.1 mistune-0.8.4 mock-4.0.2 nbconvert-5.6.1 nbformat-5.0.6 networkx-2.4 numba-0.42.1 numexpr-2.7.1 numpydoc-0.9.2 opencv-contrib-python-3.4.1.15 opencv-python-3.4.1.15 packaging-20.3 pandas-0.25.3 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prompt-toolkit-2.0.10 psutil-5.5.1 ptyprocess-0.6.0 pycodestyle-2.6.0 pyflakes-2.2.0 pygments-2.6.1 pylint-2.5.2 pyparsing-2.4.7 pyrsistent-0.16.0 pyzmq-19.0.1 qtawesome-0.7.2 qtconsole-4.7.4 requests-2.23.0 rope-0.17.0 scikit-image-0.14.2 scikit-learn-0.20.3 scipy-1.3.0 seaborn-0.9.0 sip-4.19.8 sklearn-0.0 snowballstemmer-2.0.0 sphinx-3.0.3 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 spyder-3.3.3 spyder-kernels-0.5.2 tables-3.5.2 testpath-0.4.4 tifffile-0.15.1 toml-0.10.1 tornado-6.0.4 tqdm-4.37.0 traitlets-4.3.3 typed-ast-1.4.1 urllib3-1.25.9 wcwidth-0.1.9 webencodings-0.5.1 wrapt-1.12.1 wurlitzer-2.0.0 zipp-3.1.0
(mesmerize) macbook-pro-4:MESmerize user1$ CFLAGS='-stdlib=libc++' python setup.py build_ext -i
running build_ext
cythoning tslearn/cygak.pyx to tslearn/cygak.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cygak.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/cysax.pyx to tslearn/cysax.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cysax.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/cycc.pyx to tslearn/cycc.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cycc.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/soft_dtw_fast.pyx to tslearn/soft_dtw_fast.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/soft_dtw_fast.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
skipping 'caiman/source_extraction/cnmf/oasis.cpp' Cython extension (up-to-date)
building 'tslearn.cygak' extension
creating build
creating build/temp.macosx-10.9-x86_64-3.6
creating build/temp.macosx-10.9-x86_64-3.6/tslearn
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/cygak.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/cygak.o
In file included from tslearn/cygak.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/cygak.o -o /Users/user1/MESmerize/tslearn/cygak.cpython-36m-darwin.so
building 'tslearn.cysax' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/cysax.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/cysax.o
In file included from tslearn/cysax.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/cysax.o -o /Users/user1/MESmerize/tslearn/cysax.cpython-36m-darwin.so
building 'tslearn.cycc' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/cycc.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/cycc.o
In file included from tslearn/cycc.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/cycc.o -o /Users/user1/MESmerize/tslearn/cycc.cpython-36m-darwin.so
building 'tslearn.soft_dtw_fast' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/soft_dtw_fast.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/soft_dtw_fast.o
In file included from tslearn/soft_dtw_fast.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/soft_dtw_fast.o -o /Users/user1/MESmerize/tslearn/soft_dtw_fast.cpython-36m-darwin.so
building 'caiman.source_extraction.cnmf.oasis' extension
creating build/temp.macosx-10.9-x86_64-3.6/caiman
creating build/temp.macosx-10.9-x86_64-3.6/caiman/source_extraction
creating build/temp.macosx-10.9-x86_64-3.6/caiman/source_extraction/cnmf
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c caiman/source_extraction/cnmf/oasis.cpp -o build/temp.macosx-10.9-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o
In file included from caiman/source_extraction/cnmf/oasis.cpp:627:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define
      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
g++ -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o -o /Users/user1/MESmerize/caiman/source_extraction/cnmf/oasis.cpython-36m-darwin.so
(mesmerize) macbook-pro-4:MESmerize user1$ export PYTHONPATH=</Users/user1/MESmerize>
-bash: syntax error near unexpected token `newline'
(mesmerize) macbook-pro-4:MESmerize user1$ 

(mesmerize) macbook-pro-4:MESmerize user1$ export PYTHONPATH=</Users/user1/MESmerize>
-bash: syntax error near unexpected token `newline'
(mesmerize) macbook-pro-4:MESmerize user1$ echo "backend: qt5" >> ~/.matplotlib/matplotlibrc
(mesmerize) macbook-pro-4:MESmerize user1$ export PYTHONPATH=</Users/user1/MESmerize>
-bash: syntax error near unexpected token `newline'
(mesmerize) macbook-pro-4:MESmerize user1$ python </Users/user1/MESmerize>/mesmerize
-bash: /mesmerize: Permission denied
(mesmerize) macbook-pro-4:MESmerize user1$

Steps to reproduce the problem

Operating System

Mac system version 10.14.6

Commit ID

kushalkolar commented 4 years ago

Thanks for posting the issue. This just seems like a simple misunderstanding of the instructions. Whenever you see paths listed like this <some_path>/other_path, the < > are just used to indicated that this is a placeholder, you do not enter them.

For example, if the path to the MESmerize dir on my system is at /Users/name/MESmerize, you just do export PYTHONPATH=/Users/name/MESmerize, NOT export PYTHONPATH=</Users/name/MESmerize>

rem7101 commented 4 years ago

Thanks for the quick and helpful response - this fixed the issue and it launches successfully now.