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Anaconda Navigator: Environment Creation Fails #11273

Open mark-zajac opened 5 years ago

mark-zajac commented 5 years ago

Actual Behavior

Creating a new environment fails (see "Steps to Reproduce" for a blow-by-blow description).

Expected Behavior

I expected the creation of a new environment.

Steps to Reproduce

I installed Anaconda Navigator for macOS 10.13.6 according to instructions at this site: https://bit.ly/2kd9JXU

After installation I performed "conda update --all" and "conda update anaconda-navigator" at the command line.

I launched Anaconda Navigator. I clicked the "Environments" tab from the sidebar. I clicked the "[+] create" button.

In the "Create new environment" pop-up window I selected python 3.7 and entered "widgets" as a name. I clicked the "create" button.

A blue "progress bar" appeared at the bottom of the screen, a "cancel" button appeared. After some time, the progress bar disappeared.

No environment is created.

Anaconda or Miniconda version:

Anaconda3-2019.07-MacOSX-x86_64.pkg

Operating System:

macOS 10.13.6

conda info
``` active environment : base active env location : /Users/mzajac/anaconda3 shell level : 1 user config file : /Users/mzajac/.condarc populated config files : /Users/mzajac/.condarc conda version : 4.7.11 conda-build version : 3.18.9 python version : 3.7.4.final.0 virtual packages : base environment : /Users/mzajac/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /Users/mzajac/anaconda3/pkgs /Users/mzajac/.conda/pkgs envs directories : /Users/mzajac/anaconda3/envs /Users/mzajac/.conda/envs platform : osx-64 user-agent : conda/4.7.11 requests/2.22.0 CPython/3.7.4 Darwin/17.7.0 OSX/10.13.6 UID:GID : 501:20 netrc file : None offline mode : False ```
conda list --show-channel-urls
``` # packages in environment at /Users/mzajac/anaconda3: # # Name Version Build Channel _anaconda_depends 2019.03 py37_0 defaults _ipyw_jlab_nb_ext_conf 0.1.0 py37_0 defaults alabaster 0.7.12 py37_0 defaults anaconda custom py37_1 defaults anaconda-client 1.7.2 py37_0 defaults anaconda-navigator 1.9.7 py37_0 defaults anaconda-project 0.8.3 py_0 defaults appnope 0.1.0 py37_0 defaults appscript 1.1.0 py37h1de35cc_0 defaults asn1crypto 0.24.0 py37_0 defaults astroid 2.2.5 py37_0 defaults astropy 3.2.1 py37h1de35cc_0 defaults atomicwrites 1.3.0 py37_1 defaults attrs 19.1.0 py37_1 defaults babel 2.7.0 py_0 defaults backcall 0.1.0 py37_0 defaults backports 1.0 py_2 defaults backports.functools_lru_cache 1.5 py_2 defaults backports.os 0.1.1 py37_0 defaults backports.shutil_get_terminal_size 1.0.0 py37_2 defaults backports.tempfile 1.0 py_1 defaults backports.weakref 1.0.post1 py_1 defaults beautifulsoup4 4.8.0 py37_0 defaults bitarray 1.0.1 py37h1de35cc_0 defaults bkcharts 0.2 py37_0 defaults blas 1.0 mkl defaults bleach 3.1.0 py37_0 defaults blosc 1.16.3 hd9629dc_0 defaults bokeh 1.3.4 py37_0 defaults boto 2.49.0 py37_0 defaults bottleneck 1.2.1 py37h1d22016_1 defaults bzip2 1.0.8 h1de35cc_0 defaults ca-certificates 2019.5.15 1 defaults certifi 2019.6.16 py37_1 defaults cffi 1.12.3 py37hb5b8e2f_0 defaults chardet 3.0.4 py37_1003 defaults click 7.0 py37_0 defaults cloudpickle 1.2.1 py_0 defaults clyent 1.2.2 py37_1 defaults colorama 0.4.1 py37_0 defaults conda 4.7.11 py37_0 defaults conda-build 3.18.9 py37_3 defaults conda-env 2.6.0 1 defaults conda-package-handling 1.3.11 py37_0 defaults conda-verify 3.4.2 py_1 defaults contextlib2 0.5.5 py37_0 defaults cryptography 2.7 py37ha12b0ac_0 defaults curl 7.65.3 ha441bb4_0 defaults cycler 0.10.0 py37_0 defaults cython 0.29.13 py37h0a44026_0 defaults cytoolz 0.10.0 py37h1de35cc_0 defaults dask 2.3.0 py_0 defaults dask-core 2.3.0 py_0 defaults dbus 1.13.6 h90a0687_0 defaults decorator 4.4.0 py37_1 defaults defusedxml 0.6.0 py_0 defaults distributed 2.3.2 py_1 defaults docutils 0.15.2 py37_0 defaults entrypoints 0.3 py37_0 defaults et_xmlfile 1.0.1 py37_0 defaults expat 2.2.6 h0a44026_0 defaults fastcache 1.1.0 py37h1de35cc_0 defaults filelock 3.0.12 py_0 defaults flask 1.1.1 py_0 defaults freetype 2.9.1 hb4e5f40_0 defaults fsspec 0.4.0 py_0 defaults future 0.17.1 py37_0 defaults get_terminal_size 1.0.0 h7520d66_0 defaults gettext 0.19.8.1 h15daf44_3 defaults gevent 1.4.0 py37h1de35cc_0 defaults glib 2.56.2 hd9629dc_0 defaults glob2 0.7 py_0 defaults gmp 6.1.2 hb37e062_1 defaults gmpy2 2.0.8 py37h6ef4df4_2 defaults greenlet 0.4.15 py37h1de35cc_0 defaults h5py 2.9.0 py37h3134771_0 defaults hdf5 1.10.4 hfa1e0ec_0 defaults heapdict 1.0.0 py37_2 defaults html5lib 1.0.1 py37_0 defaults icu 58.2 h4b95b61_1 defaults idna 2.8 py37_0 defaults imageio 2.5.0 py37_0 defaults imagesize 1.1.0 py37_0 defaults importlib_metadata 0.19 py37_0 defaults intel-openmp 2019.4 233 defaults ipykernel 5.1.2 py37h39e3cac_0 defaults ipython 7.8.0 py37h39e3cac_0 defaults ipython_genutils 0.2.0 py37_0 defaults ipywidgets 7.5.1 py_0 defaults isort 4.3.21 py37_0 defaults itsdangerous 1.1.0 py37_0 defaults jbig 2.1 h4d881f8_0 defaults jdcal 1.4.1 py_0 defaults jedi 0.15.1 py37_0 defaults jinja2 2.10.1 py37_0 defaults joblib 0.13.2 py37_0 defaults jpeg 9b he5867d9_2 defaults json5 0.8.5 py_0 defaults jsonschema 3.0.2 py37_0 defaults jupyter 1.0.0 py37_7 defaults jupyter_client 5.3.1 py_0 defaults jupyter_console 6.0.0 py37_0 defaults jupyter_core 4.5.0 py_0 defaults jupyterlab 1.0.2 py37hf63ae98_0 defaults jupyterlab_server 1.0.0 py_1 defaults keyring 18.0.0 py37_0 defaults kiwisolver 1.1.0 py37h0a44026_0 defaults krb5 1.16.1 hddcf347_7 defaults lazy-object-proxy 1.4.2 py37h1de35cc_0 defaults libarchive 3.3.3 h786848e_5 defaults libcurl 7.65.3 h051b688_0 defaults libcxx 4.0.1 hcfea43d_1 defaults libcxxabi 4.0.1 hcfea43d_1 defaults libedit 3.1.20181209 hb402a30_0 defaults libffi 3.2.1 h475c297_4 defaults libgfortran 3.0.1 h93005f0_2 defaults libiconv 1.15 hdd342a3_7 defaults liblief 0.9.0 h2a1bed3_2 defaults libpng 1.6.37 ha441bb4_0 defaults libsodium 1.0.16 h3efe00b_0 defaults libssh2 1.8.2 ha12b0ac_0 defaults libtiff 4.0.10 hcb84e12_2 defaults libxml2 2.9.9 hf6e021a_1 defaults libxslt 1.1.33 h33a18ac_0 defaults llvm-openmp 4.0.1 hcfea43d_1 defaults llvmlite 0.29.0 py37h98b8051_0 defaults locket 0.2.0 py37_1 defaults lxml 4.4.1 py37hef8c89e_0 defaults lz4-c 1.8.1.2 h1de35cc_0 defaults lzo 2.10 h362108e_2 defaults markupsafe 1.1.1 py37h1de35cc_0 defaults matplotlib 3.1.1 py37h54f8f79_0 defaults mccabe 0.6.1 py37_1 defaults mistune 0.8.4 py37h1de35cc_0 defaults mkl 2019.4 233 defaults mkl-service 2.3.0 py37hfbe908c_0 defaults mkl_fft 1.0.14 py37h5e564d8_0 defaults mkl_random 1.0.2 py37h27c97d8_0 defaults mock 3.0.5 py37_0 defaults more-itertools 7.2.0 py37_0 defaults mpc 1.1.0 h6ef4df4_1 defaults mpfr 4.0.1 h3018a27_3 defaults mpmath 1.1.0 py37_0 defaults msgpack-python 0.6.1 py37h04f5b5a_1 defaults multipledispatch 0.6.0 py37_0 defaults navigator-updater 0.2.1 py37_0 defaults nbconvert 5.5.0 py_0 defaults nbformat 4.4.0 py37_0 defaults ncurses 6.1 h0a44026_1 defaults networkx 2.3 py_0 defaults nltk 3.4.5 py37_0 defaults nose 1.3.7 py37_2 defaults notebook 6.0.1 py37_0 defaults numba 0.45.1 py37h6440ff4_0 defaults numexpr 2.7.0 py37h7413580_0 defaults numpy 1.16.4 py37hacdab7b_0 defaults numpy-base 1.16.4 py37h6575580_0 defaults numpydoc 0.9.1 py_0 defaults olefile 0.46 py37_0 defaults openpyxl 2.6.2 py_0 defaults openssl 1.1.1d h1de35cc_0 defaults packaging 19.1 py37_0 defaults pandas 0.25.1 py37h0a44026_0 defaults pandoc 2.2.3.2 0 defaults pandocfilters 1.4.2 py37_1 defaults parso 0.5.1 py_0 defaults partd 1.0.0 py_0 defaults path.py 12.0.1 py_0 defaults pathlib2 2.3.4 py37_0 defaults patsy 0.5.1 py37_0 defaults pcre 8.43 h0a44026_0 defaults pep8 1.7.1 py37_0 defaults pexpect 4.7.0 py37_0 defaults pickleshare 0.7.5 py37_0 defaults pillow 6.1.0 py37hb68e598_0 defaults pip 19.2.2 py37_0 defaults pkginfo 1.5.0.1 py37_0 defaults pluggy 0.12.0 py_0 defaults ply 3.11 py37_0 defaults prometheus_client 0.7.1 py_0 defaults prompt_toolkit 2.0.9 py37_0 defaults psutil 5.6.3 py37h1de35cc_0 defaults ptyprocess 0.6.0 py37_0 defaults py 1.8.0 py37_0 defaults py-lief 0.9.0 py37h1413db1_2 defaults pycodestyle 2.5.0 py37_0 defaults pycosat 0.6.3 py37h1de35cc_0 defaults pycparser 2.19 py37_0 defaults pycrypto 2.6.1 py37h1de35cc_9 defaults pycurl 7.43.0.3 py37ha12b0ac_0 defaults pyflakes 2.1.1 py37_0 defaults pygments 2.4.2 py_0 defaults pylint 2.3.1 py37_0 defaults pyodbc 4.0.27 py37h0a44026_0 defaults pyopenssl 19.0.0 py37_0 defaults pyparsing 2.4.2 py_0 defaults pyqt 5.9.2 py37h655552a_2 defaults pyrsistent 0.14.11 py37h1de35cc_0 defaults pysocks 1.7.0 py37_0 defaults pytables 3.5.2 py37h5bccee9_1 defaults pytest 5.0.1 py37_0 defaults pytest-arraydiff 0.3 py37h39e3cac_0 defaults pytest-astropy 0.5.0 py37_0 defaults pytest-doctestplus 0.3.0 py37_0 defaults pytest-openfiles 0.3.2 py37_0 defaults pytest-remotedata 0.3.2 py37_0 defaults python 3.7.4 h359304d_1 defaults python-dateutil 2.8.0 py37_0 defaults python-libarchive-c 2.8 py37_13 defaults python.app 2 py37_9 defaults pytz 2019.2 py_0 defaults pywavelets 1.0.3 py37h1d22016_1 defaults pyyaml 5.1.2 py37h1de35cc_0 defaults pyzmq 18.1.0 py37h0a44026_0 defaults qt 5.9.7 h468cd18_1 defaults qtawesome 0.5.7 py37_1 defaults qtconsole 4.5.5 py_0 defaults qtpy 1.9.0 py_0 defaults readline 7.0 h1de35cc_5 defaults requests 2.22.0 py37_0 defaults ripgrep 0.10.0 hc07d326_0 defaults rope 0.14.0 py_0 defaults ruamel_yaml 0.15.46 py37h1de35cc_0 defaults scikit-image 0.15.0 py37h0a44026_0 defaults scikit-learn 0.21.2 py37h27c97d8_0 defaults scipy 1.3.1 py37h1410ff5_0 defaults seaborn 0.9.0 py37_0 defaults send2trash 1.5.0 py37_0 defaults setuptools 41.0.1 py37_0 defaults simplegeneric 0.8.1 py37_2 defaults singledispatch 3.4.0.3 py37_0 defaults sip 4.19.8 py37h0a44026_0 defaults six 1.12.0 py37_0 defaults snappy 1.1.7 he62c110_3 defaults snowballstemmer 1.9.0 py_0 defaults sortedcollections 1.1.2 py37_0 defaults sortedcontainers 2.1.0 py37_0 defaults soupsieve 1.9.2 py37_0 defaults sphinx 2.1.2 py_0 defaults sphinxcontrib 1.0 py37_1 defaults sphinxcontrib-applehelp 1.0.1 py_0 defaults sphinxcontrib-devhelp 1.0.1 py_0 defaults sphinxcontrib-htmlhelp 1.0.2 py_0 defaults sphinxcontrib-jsmath 1.0.1 py_0 defaults sphinxcontrib-qthelp 1.0.2 py_0 defaults sphinxcontrib-serializinghtml 1.1.3 py_0 defaults sphinxcontrib-websupport 1.1.2 py_0 defaults spyder 3.3.6 py37_0 defaults spyder-kernels 0.5.1 py37_0 defaults sqlalchemy 1.3.7 py37h1de35cc_0 defaults sqlite 3.29.0 ha441bb4_0 defaults statsmodels 0.10.1 py37h1d22016_0 defaults sympy 1.4 py37_0 defaults tbb 2019.4 h04f5b5a_0 defaults tblib 1.4.0 py_0 defaults terminado 0.8.2 py37_0 defaults testpath 0.4.2 py37_0 defaults tk 8.6.8 ha441bb4_0 defaults toolz 0.10.0 py_0 defaults tornado 6.0.3 py37h1de35cc_0 defaults tqdm 4.32.1 py_0 defaults traitlets 4.3.2 py37_0 defaults unicodecsv 0.14.1 py37_0 defaults unixodbc 2.3.7 h1de35cc_0 defaults urllib3 1.24.2 py37_0 defaults wcwidth 0.1.7 py37_0 defaults webencodings 0.5.1 py37_1 defaults werkzeug 0.15.5 py_0 defaults wheel 0.33.4 py37_0 defaults widgetsnbextension 3.5.1 py37_0 defaults wrapt 1.11.2 py37h1de35cc_0 defaults wurlitzer 1.0.3 py37_0 defaults xlrd 1.2.0 py37_0 defaults xlsxwriter 1.1.8 py_0 defaults xlwings 0.15.8 py37_0 defaults xlwt 1.3.0 py37_0 defaults xz 5.2.4 h1de35cc_4 defaults yaml 0.1.7 hc338f04_2 defaults zeromq 4.3.1 h0a44026_3 defaults zict 1.0.0 py_0 defaults zipp 0.5.2 py_0 defaults zlib 1.2.11 h1de35cc_3 defaults zstd 1.3.7 h5bba6e5_0 defaults ```
zevisert commented 5 years ago

Pitching in here since I think some failures I saw in my CI builds might be caused by the same issue, and may be linked to https://github.com/ContinuumIO/anaconda-issues/issues/11274

conda update --name base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - conda

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2019.5.15  |                1         126 KB
    certifi-2019.6.16          |           py37_1         152 KB
    chardet-3.0.4              |        py37_1003         174 KB
    conda-4.7.11               |           py37_0         2.8 MB
    openssl-1.1.1d             |       h7b6447c_0         3.7 MB
    pip-19.2.2                 |           py37_0         1.6 MB
    python-libarchive-c-2.8    |          py37_13          24 KB
    ------------------------------------------------------------
                                           Total:         8.7 MB

The following packages will be UPDATED:
  ca-certificates                               2019.5.15-0 --> 2019.5.15-1
  certifi                                  2019.6.16-py37_0 --> 2019.6.16-py37_1
  chardet                                      3.0.4-py37_1 --> 3.0.4-py37_1003
  conda                                       4.7.10-py37_0 --> 4.7.11-py37_0
  openssl                                 1.1.1c-h7b6447c_1 --> 1.1.1d-h7b6447c_0
  pip                                         19.1.1-py37_0 --> 19.2.2-py37_0
  python-libarchive~                            2.8-py37_11 --> 2.8-py37_13

Downloading and Extracting Packages

conda-4.7.11         | 2.8 MB    | ########## | 100% 
ca-certificates-2019 | 126 KB    | ########## | 100% 
chardet-3.0.4        | 174 KB    | ########## | 100% 
pip-19.2.2           | 1.6 MB    | ########## | 100% 
openssl-1.1.1d       | 3.7 MB    | ########## | 100% 
python-libarchive-c- | 24 KB     | ########## | 100% 
certifi-2019.6.16    | 152 KB    | ########## | 100% 

[Errno 13] Permission denied: '/.cph_tmpi6i_tr3k'
[Errno 13] Permission denied: '/.cph_tmphhtnldzd'
[Errno 13] Permission denied: '/.cph_tmpei90jspd'
[Errno 13] Permission denied: '/.cph_tmpgg28h1xz'
[Errno 13] Permission denied: '/.cph_tmp1yoigmyq'
[Errno 13] Permission denied: '/.cph_tmpbhrmp6fz'

I diffed my build logs and this only started occurring when conda decided it was time to update it's base environment; caused by conda 4.7.11's release.

Pinning openssl in /opt/conda/conda-meta/pinned to 1.1.1c fixed these permission denied issues

mark-zajac commented 5 years ago

I had an old mac running OS X 10.10.5 and I am having the same issue there. I can't create new environments from within Anaconda Navigator. How can I even view a log file, in hopes of debugging for myself?

mingwandroid commented 5 years ago

I had an old mac running OS X 10.10.5

Sorry @mark-zajac, we do not support macOS < 10.12 for Anaconda Navigator (or anything that uses Qt, this is an upstream decision, forced upon them by one of their upstreams (Chromium)). Our documentation does not reflect this fact. Pinging @rrigdon so it doesn't drop off of our radar.

Thank you for the bug report.

mark-zajac commented 5 years ago

we do not support macOS < 10.12 for Anaconda Navigator

Just to be clear, I am having the exact same problem on macOS 10.13.6 also. I only tried 10.10.5 in hopes that an older version was more stable.

mark-zajac commented 5 years ago

I found a second report of my problem on Google Groups: "MacBook macOS Mojave can not install or upgrade applications"

The example above is for Mojave, the latest version of macOS. So, the problem is not just people with older versions of the OS.

Here is another report from Reddit: "Anaconda Navigator can't create new environment"

mingwandroid commented 5 years ago

I only tried 10.10.5 in hopes that an older version was more stable.

This stems from my confusion when you answered my question to rjknight over at https://github.com/ContinuumIO/anaconda-issues/issues/11274#issuecomment-533823063

I would expect such an error from trying to run things on macOS 10.10.5, but no matter. I can guarantee you that will be a bust from a Qt/native-graphical perspective (you should still be able to run everything else though, jupyter notebooks included).

When I am next in macOS I will try to reproduce this problem and get back to you.

mark-zajac commented 4 years ago

I found another report of my problem on Google Groups: "[Anaconda Community] Re: MacBook macOS Mojave can not install or upgrade applications"

mark-zajac commented 4 years ago

Duplicate of #11240

mark-zajac commented 4 years ago

I found another report of the same Anaconda Navigator issue.

When might there be some action on this report?

FRLCH commented 4 years ago

I had the same issue. Running Anaconda as administrator did the trick.