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clean miniconda install of spyder with python 3.7.2 on MacOS does not create necessary link #10599

Open jrminter opened 5 years ago

jrminter commented 5 years ago

I just did a clean install of miniconda 64 bit on macosx 10.14.03 (Mojave) installing python 3.7.2. I installed to my user directory. I installed spyder (3.3.2).

Expected Behavior

Starting the GUI.

Instead, it failed with the message:

/Users/jrminter/miniconda3/bin/pythonw: line 3: /Users/jrminter/miniconda3/python.app/Contents/MacOS/python: No such file or directory

Indicating that a symbolic link was not created. I fixed the issue by creating a symbolic link

ln -s /Users/jrminter/miniconda3/bin/python /Users/jrminter/miniconda3/python.app/Contents/MacOS/python

Steps to Reproduce

Clean install. Verify paths. Try to start

Anaconda or Miniconda version:

latest miniconda MacOSX 64 installer

Operating System:

macosx 10.14.03 (Mojave)

conda info
     active environment : None
       user config file : /Users/jrminter/.condarc
 populated config files : /Users/jrminter/.condarc
          conda version : 4.6.3
    conda-build version : not installed
         python version : 3.7.2.final.0
       base environment : /Users/jrminter/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/jrminter/miniconda3/pkgs
                          /Users/jrminter/.conda/pkgs
       envs directories : /Users/jrminter/miniconda3/envs
                          /Users/jrminter/.conda/envs
               platform : osx-64
             user-agent : conda/4.6.3 requests/2.21.0 CPython/3.7.2 Darwin/18.2.0 OSX/10.14.3
                UID:GID : 501:20
             netrc file : None
           offline mode : False
conda list --show-channel-urls
# packages in environment at /Users/jrminter/miniconda3:
#
# Name                    Version                   Build  Channel
alabaster                 0.7.12                     py_0    conda-forge
appnope                   0.1.0                 py37_1000    conda-forge
asn1crypto                0.24.0                py37_1003    conda-forge
astroid                   2.1.0                 py37_1000    conda-forge
attrs                     18.2.0                     py_0    conda-forge
babel                     2.6.0                      py_1    conda-forge
backcall                  0.1.0                      py_0    conda-forge
blas                      1.0                         mkl    anaconda
bleach                    3.1.0                      py_0    conda-forge
bzip2                     1.0.6             h1de35cc_1002    conda-forge
ca-certificates           2019.1.23                     0    anaconda
certifi                   2018.11.29               py37_0    anaconda
cffi                      1.11.5          py37h342bebf_1001    conda-forge
chardet                   3.0.4                 py37_1003    conda-forge
cloudpickle               0.7.0                      py_0    conda-forge
conda                     4.6.3                    py37_0    conda-forge
conda-env                 2.6.0                         1    conda-forge
cryptography              2.4.2            py37ha12b0ac_0    anaconda
cycler                    0.10.0                     py_1    conda-forge
cython                    0.29.4           py37h0a44026_0    conda-forge
cytoolz                   0.9.0.1          py37h470a237_1    conda-forge
dask-core                 1.1.1                      py_0    conda-forge
dbus                      1.13.0            h776b7f1_1000    conda-forge
decorator                 4.3.2                      py_0    conda-forge
docutils                  0.14                  py37_1001    conda-forge
entrypoints               0.3                   py37_1000    conda-forge
expat                     2.2.5             h0a44026_1002    conda-forge
fastcache                 1.0.2           py37h1de35cc_1001    conda-forge
freetype                  2.9.1             h597ad8a_1005    conda-forge
gettext                   0.19.8.1          hcca000d_1001    conda-forge
glib                      2.58.2            h2836805_1001    conda-forge
gmp                       6.1.2             h0a44026_1000    conda-forge
gmpy2                     2.0.8           py37h3aece09_1002    conda-forge
icu                       58.2              h0a44026_1000    conda-forge
idna                      2.8                   py37_1000    conda-forge
imageio                   2.4.1                 py37_1000    conda-forge
imagesize                 1.1.0                      py_0    conda-forge
intel-openmp              2019.1                      144    defaults
ipykernel                 5.1.0           py37h24bf2e0_1002    conda-forge
ipython                   7.2.0           py37h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
isort                     4.3.4                 py37_1000    conda-forge
iversions                 0.0.10                   pypi_0    pypi
jedi                      0.13.2                py37_1000    conda-forge
jinja2                    2.10                       py_1    conda-forge
jpeg                      9c                h1de35cc_1001    conda-forge
jsonschema                3.0.0a3               py37_1000    conda-forge
jupyter                   1.0.0                      py_1    conda-forge
jupyter_client            5.2.4                      py_1    conda-forge
jupyter_console           6.0.0                      py_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
keyring                   17.1.1                py37_1000    conda-forge
kiwisolver                1.0.1           py37h04f5b5a_1002    conda-forge
lazy-object-proxy         1.3.1           py37h1de35cc_1000    conda-forge
libcxx                    7.0.0                h2d50403_2    conda-forge
libcxxabi                 4.0.1                hebd6815_0    conda-forge
libedit                   3.1.20170329      hcfe32e1_1001    conda-forge
libffi                    3.2.1             h0a44026_1005    conda-forge
libgfortran               3.0.1                h93005f0_2    defaults
libiconv                  1.15              h1de35cc_1004    conda-forge
libpng                    1.6.36            ha441bb4_1000    conda-forge
libsodium                 1.0.16            h1de35cc_1001    conda-forge
libtiff                   4.0.10            h79f4b77_1001    conda-forge
llvm-meta                 7.0.0                         0    conda-forge
lz4                       2.1.6            py37h1de35cc_0    defaults
lz4-c                     1.8.3             h0a44026_1001    conda-forge
mahotas                   1.4.5           py37h1702cab_1000    conda-forge
markupsafe                1.1.0           py37h1de35cc_1000    conda-forge
matplotlib                3.0.2                 py37_1002    conda-forge
matplotlib-base           3.0.2           py37hf043ca5_1002    conda-forge
matplotlib-scalebar       0.5.1                    pypi_0    pypi
mccabe                    0.6.1                      py_1    conda-forge
mistune                   0.8.4           py37h1de35cc_1000    conda-forge
mkl                       2019.1                      144    defaults
mkl_fft                   1.0.10           py37h1de35cc_1    conda-forge
mkl_random                1.0.2            py37h1702cab_2    conda-forge
mpc                       1.1.0             h3aece09_1006    conda-forge
mpfr                      4.0.1             h0a95893_1000    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
networkx                  2.2                        py_1    conda-forge
notebook                  5.7.4                 py37_1000    conda-forge
numpy                     1.15.4           py37hacdab7b_0    defaults
numpy-base                1.15.4           py37h6575580_0    defaults
numpydoc                  0.8.0                      py_1    conda-forge
olefile                   0.46                       py_0    conda-forge
openssl                   1.1.1                h1de35cc_0    anaconda
packaging                 19.0                       py_0    conda-forge
pandas                    0.24.1           py37h0a44026_0    conda-forge
pandoc                    2.6                           1    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.3.3                      py_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.41              h0a44026_1003    conda-forge
pexpect                   4.6.0                 py37_1000    conda-forge
pickleshare               0.7.5                 py37_1000    conda-forge
pillow                    5.4.1           py37hbddbef0_1000    conda-forge
pip                       19.0.1                   py37_0    conda-forge
prometheus_client         0.5.0                      py_0    conda-forge
prompt_toolkit            2.0.8                      py_0    conda-forge
psutil                    5.5.0            py37h1de35cc_0    conda-forge
ptyprocess                0.6.0                 py37_1000    conda-forge
pycodestyle               2.5.0                      py_0    conda-forge
pycosat                   0.6.3           py37h1de35cc_1001    conda-forge
pycparser                 2.19                       py_0    conda-forge
pyflakes                  2.1.0                      py_0    conda-forge
pygments                  2.3.1                      py_0    conda-forge
pylint                    2.2.2                 py37_1000    conda-forge
pyopenssl                 19.0.0                   py37_0    conda-forge
pyparsing                 2.3.1                      py_0    conda-forge
pyqt                      5.6.0           py37hc26a216_1008    conda-forge
pyrsistent                0.14.9          py37h1de35cc_1000    conda-forge
pysocks                   1.6.8                 py37_1002    conda-forge
python                    3.7.2                haf84260_0    anaconda
python-dateutil           2.8.0                      py_0    conda-forge
python.app                1.2             py37h1de35cc_1200    conda-forge
pytz                      2018.9                     py_0    conda-forge
pywavelets                1.0.1           py37h917ab60_1000    conda-forge
pyzmq                     17.1.2          py37h111632d_1001    conda-forge
qt                        5.6.2             h822fa55_1013    conda-forge
qtawesome                 0.5.6              pyh8a2030e_0    conda-forge
qtconsole                 4.4.3                      py_0    conda-forge
qtpy                      1.6.0              pyh8a2030e_0    conda-forge
readline                  7.0               hcfe32e1_1001    conda-forge
requests                  2.21.0                py37_1000    conda-forge
rope                      0.10.7                     py_1    conda-forge
ruamel_yaml               0.15.71         py37h1de35cc_1000    conda-forge
scikit-image              0.14.2           py37h0a44026_1    conda-forge
scipy                     1.2.0            py37h1410ff5_0    defaults
seaborn                   0.9.0                      py_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                40.8.0                   py37_0    conda-forge
sip                       4.18.1          py37h0a44026_1000    conda-forge
six                       1.12.0                py37_1000    conda-forge
snowballstemmer           1.2.1                      py_1    conda-forge
sphinx                    1.8.4                    py37_0    conda-forge
sphinxcontrib             1.0                      py37_1    defaults
sphinxcontrib-websupport  1.1.0                      py_1    conda-forge
spyder                    3.3.2                    py37_0    anaconda
spyder-kernels            0.4.1                    py37_0    conda-forge
sqlite                    3.26.0            h1765d9f_1000    conda-forge
statsmodels               0.9.0           py37h917ab60_1000    conda-forge
sympy                     1.3                   py37_1000    conda-forge
terminado                 0.8.1                 py37_1001    conda-forge
testpath                  0.4.2                 py37_1000    conda-forge
tk                        8.6.9             ha441bb4_1000    conda-forge
toolz                     0.9.0                      py_1    conda-forge
tornado                   5.1.1           py37h1de35cc_1000    conda-forge
traitlets                 4.3.2                 py37_1000    conda-forge
urllib3                   1.24.1                py37_1000    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.32.3                   py37_0    conda-forge
widgetsnbextension        3.4.2                 py37_1000    conda-forge
wrapt                     1.11.1           py37h1de35cc_0    conda-forge
wurlitzer                 1.0.2                 py37_1000    conda-forge
xlwt                      1.3.0                      py_1    conda-forge
xz                        5.2.4             h1de35cc_1001    conda-forge
yaml                      0.1.7             h1de35cc_1001    conda-forge
zeromq                    4.2.5             h0a44026_1006    conda-forge
zlib                      1.2.11            h1de35cc_1004    conda-forge
zstd                      1.3.8             hfaf8727_1001    conda-forge
sitadrost commented 4 years ago

I just ran into the exact same issue (MacOS 10.15.5). I fixed it by changing the path in pythonw to miniconda3/python.app/pythonapp/Contents/MacOS/python. Still, I wanted to mention it here, as I would have expected this to work automatically.