navigator app launcher doesn't launch app in correct env

[jasontwinters]

Maybe I'm misunderstanding something fundamental about Anaconda but...

Actual Behavior

Using Anaconda Navigator...

1. I creating a new environment, called 'Test'
2. I hit the Spyder 4.0.1 "Install" button in Test env to install Spyder 4.0.1
3. Now I hit the Spyder launch button, it brings up Spyder 3.3.6
4. Also, any packages I've installed in th Test env are not found.

However, if I use the Environments tab and green triangle to open a terminal on my 'Test' env and type 'spyder', it brings up Spyder 4.0.1 and the installed packages are found.

Expected Behavior

If I select a particular env in the "Applications on" drop-down and launch Spyder 4.0.1, I expect Spyder 4.0.1. I also expect any packages I've installed in that env be be available.

Steps to Reproduce

Using Anaconda Navigator

1. Create a new env
2. Install Spyder 4.0.1 with the "Install" button
3. Launch Spyder 4.0.1 with the "Launch" button
4. Spyder 3.3.6 is loaded (not what I was expecting)
5. Go to Environments, and use triangle to open a terminal
6. Typing spyder launches Spyder 4.0.1 (what I expected)

Anaconda or Miniconda version: 1.9.12

Operating System: Linux

conda info

``` active environment : base active env location : /home/jason/anaconda3 shell level : 1 user config file : /home/jason/.condarc populated config files : /home/jason/.condarc conda version : 4.8.2 conda-build version : 3.18.9 python version : 3.7.4.final.0 virtual packages : __cuda=10.2 __glibc=2.27 base environment : /home/jason/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/jason/anaconda3/pkgs /home/jason/.conda/pkgs envs directories : /home/jason/anaconda3/envs /home/jason/.conda/envs platform : linux-64 user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.4 Linux/5.3.0-40-generic linuxmint/19.3 glibc/2.27 UID:GID : 1000:1000 netrc file : None offline mode : False ```

conda list --show-channel-urls

``` # packages in environment at /home/jason/anaconda3: # # Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py37_0 defaults _libgcc_mutex 0.1 main defaults alabaster 0.7.12 py37_0 defaults anaconda 2019.10 py37_0 defaults anaconda-client 1.7.2 py37_0 defaults anaconda-navigator 1.9.12 py37_1 defaults anaconda-project 0.8.3 py_0 defaults asn1crypto 1.0.1 py37_0 defaults astroid 2.3.1 py37_0 defaults astropy 3.2.2 py37h7b6447c_0 defaults atomicwrites 1.3.0 py37_1 defaults attrs 19.2.0 py_0 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 py37h7b6447c_0 defaults bkcharts 0.2 py37_0 defaults blas 1.0 mkl defaults bleach 3.1.0 py37_0 defaults blosc 1.16.3 hd408876_0 defaults bokeh 1.3.4 py37_0 defaults boto 2.49.0 py37_0 defaults bottleneck 1.2.1 py37h035aef0_1 defaults bzip2 1.0.8 h7b6447c_0 defaults ca-certificates 2019.8.28 0 defaults cairo 1.14.12 h8948797_3 defaults certifi 2019.9.11 py37_0 defaults cffi 1.12.3 py37h2e261b9_0 defaults chardet 3.0.4 py37_1003 defaults click 7.0 py37_0 defaults cloudpickle 1.2.2 py_0 defaults clyent 1.2.2 py37_1 defaults colorama 0.4.1 py37_0 defaults conda 4.8.2 py37_0 defaults conda-build 3.18.9 py37_3 defaults conda-env 2.6.0 1 defaults conda-package-handling 1.6.0 py37h7b6447c_0 defaults conda-verify 3.4.2 py_1 defaults contextlib2 0.6.0 py_0 defaults cryptography 2.7 py37h1ba5d50_0 defaults curl 7.65.3 hbc83047_0 defaults cycler 0.10.0 py37_0 defaults cython 0.29.13 py37he6710b0_0 defaults cytoolz 0.10.0 py37h7b6447c_0 defaults dask 2.5.2 py_0 defaults dask-core 2.5.2 py_0 defaults dbus 1.13.6 h746ee38_0 defaults decorator 4.4.0 py37_1 defaults defusedxml 0.6.0 py_0 defaults distributed 2.5.2 py_0 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 he6710b0_0 defaults fastcache 1.1.0 py37h7b6447c_0 defaults filelock 3.0.12 py_0 defaults flask 1.1.1 py_0 defaults fontconfig 2.13.0 h9420a91_0 defaults freetype 2.9.1 h8a8886c_1 defaults fribidi 1.0.5 h7b6447c_0 defaults fsspec 0.5.2 py_0 defaults future 0.17.1 py37_0 defaults get_terminal_size 1.0.0 haa9412d_0 defaults gevent 1.4.0 py37h7b6447c_0 defaults glib 2.56.2 hd408876_0 defaults glob2 0.7 py_0 defaults gmp 6.1.2 h6c8ec71_1 defaults gmpy2 2.0.8 py37h10f8cd9_2 defaults graphite2 1.3.13 h23475e2_0 defaults greenlet 0.4.15 py37h7b6447c_0 defaults gst-plugins-base 1.14.0 hbbd80ab_1 defaults gstreamer 1.14.0 hb453b48_1 defaults h5py 2.9.0 py37h7918eee_0 defaults harfbuzz 1.8.8 hffaf4a1_0 defaults hdf5 1.10.4 hb1b8bf9_0 defaults heapdict 1.0.1 py_0 defaults html5lib 1.0.1 py37_0 defaults icu 58.2 h9c2bf20_1 defaults idna 2.8 py37_0 defaults imageio 2.6.0 py37_0 defaults imagesize 1.1.0 py37_0 defaults importlib_metadata 0.23 py37_0 defaults intel-openmp 2019.4 243 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 hdba287a_0 defaults jdcal 1.4.1 py_0 defaults jedi 0.15.1 py37_0 defaults jeepney 0.4.1 py_0 defaults jinja2 2.10.3 py_0 defaults joblib 0.13.2 py37_0 defaults jpeg 9b h024ee3a_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 5.3.3 py37_1 defaults jupyter_console 6.0.0 py37_0 defaults jupyter_core 4.5.0 py_0 defaults jupyterlab 1.1.4 pyhf63ae98_0 defaults jupyterlab_server 1.0.6 py_0 defaults keyring 18.0.0 py37_0 defaults kiwisolver 1.1.0 py37he6710b0_0 defaults krb5 1.16.1 h173b8e3_7 defaults lazy-object-proxy 1.4.2 py37h7b6447c_0 defaults libarchive 3.3.3 h5d8350f_5 defaults libcurl 7.65.3 h20c2e04_0 defaults libedit 3.1.20181209 hc058e9b_0 defaults libffi 3.2.1 hd88cf55_4 defaults libgcc-ng 9.1.0 hdf63c60_0 defaults libgfortran-ng 7.3.0 hdf63c60_0 defaults liblief 0.9.0 h7725739_2 defaults libpng 1.6.37 hbc83047_0 defaults libsodium 1.0.16 h1bed415_0 defaults libssh2 1.8.2 h1ba5d50_0 defaults libstdcxx-ng 9.1.0 hdf63c60_0 defaults libtiff 4.0.10 h2733197_2 defaults libtool 2.4.6 h7b6447c_5 defaults libuuid 1.0.3 h1bed415_2 defaults libxcb 1.13 h1bed415_1 defaults libxml2 2.9.9 hea5a465_1 defaults libxslt 1.1.33 h7d1a2b0_0 defaults llvmlite 0.29.0 py37hd408876_0 defaults locket 0.2.0 py37_1 defaults lxml 4.4.1 py37hefd8a0e_0 defaults lz4-c 1.8.1.2 h14c3975_0 defaults lzo 2.10 h49e0be7_2 defaults markupsafe 1.1.1 py37h7b6447c_0 defaults matplotlib 3.1.1 py37h5429711_0 defaults mccabe 0.6.1 py37_1 defaults mistune 0.8.4 py37h7b6447c_0 defaults mkl 2019.4 243 defaults mkl-service 2.3.0 py37he904b0f_0 defaults mkl_fft 1.0.14 py37ha843d7b_0 defaults mkl_random 1.1.0 py37hd6b4f25_0 defaults mock 3.0.5 py37_0 defaults more-itertools 7.2.0 py37_0 defaults mpc 1.1.0 h10f8cd9_1 defaults mpfr 4.0.1 hdf1c602_3 defaults mpmath 1.1.0 py37_0 defaults msgpack-python 0.6.1 py37hfd86e86_1 defaults multipledispatch 0.6.0 py37_0 defaults navigator-updater 0.2.1 py37_0 defaults nbconvert 5.6.0 py37_1 defaults nbformat 4.4.0 py37_0 defaults ncurses 6.1 he6710b0_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 py37h962f231_0 defaults numexpr 2.7.0 py37h9e4a6bb_0 defaults numpy 1.17.2 py37haad9e8e_0 defaults numpy-base 1.17.2 py37hde5b4d6_0 defaults numpydoc 0.9.1 py_0 defaults olefile 0.46 py37_0 defaults openpyxl 3.0.0 py_0 defaults openssl 1.1.1d h7b6447c_2 defaults packaging 19.2 py_0 defaults pandas 0.25.1 py37he6710b0_0 defaults pandoc 2.2.3.2 0 defaults pandocfilters 1.4.2 py37_1 defaults pango 1.42.4 h049681c_0 defaults parso 0.5.1 py_0 defaults partd 1.0.0 py_0 defaults patchelf 0.9 he6710b0_3 defaults path.py 12.0.1 py_0 defaults pathlib2 2.3.5 py37_0 defaults patsy 0.5.1 py37_0 defaults pcre 8.43 he6710b0_0 defaults pep8 1.7.1 py37_0 defaults pexpect 4.7.0 py37_0 defaults pickleshare 0.7.5 py37_0 defaults pillow 6.2.0 py37h34e0f95_0 defaults pip 19.2.3 py37_0 defaults pixman 0.38.0 h7b6447c_0 defaults pkginfo 1.5.0.1 py37_0 defaults pluggy 0.13.0 py37_0 defaults ply 3.11 py37_0 defaults prometheus_client 0.7.1 py_0 defaults prompt_toolkit 2.0.10 py_0 defaults psutil 5.6.3 py37h7b6447c_0 defaults ptyprocess 0.6.0 py37_0 defaults py 1.8.0 py37_0 defaults py-lief 0.9.0 py37h7725739_2 defaults pycodestyle 2.5.0 py37_0 defaults pycosat 0.6.3 py37h14c3975_0 defaults pycparser 2.19 py37_0 defaults pycrypto 2.6.1 py37h14c3975_9 defaults pycurl 7.43.0.3 py37h1ba5d50_0 defaults pyflakes 2.1.1 py37_0 defaults pygments 2.4.2 py_0 defaults pylint 2.4.2 py37_0 defaults pyodbc 4.0.27 py37he6710b0_0 defaults pyopenssl 19.0.0 py37_0 defaults pyparsing 2.4.2 py_0 defaults pyqt 5.9.2 py37h05f1152_2 defaults pyrsistent 0.15.4 py37h7b6447c_0 defaults pysocks 1.7.1 py37_0 defaults pytables 3.5.2 py37h71ec239_1 defaults pytest 5.2.1 py37_0 defaults pytest-arraydiff 0.3 py37h39e3cac_0 defaults pytest-astropy 0.5.0 py37_0 defaults pytest-doctestplus 0.4.0 py_0 defaults pytest-openfiles 0.4.0 py_0 defaults pytest-remotedata 0.3.2 py37_0 defaults python 3.7.4 h265db76_1 defaults python-dateutil 2.8.0 py37_0 defaults python-libarchive-c 2.8 py37_13 defaults pytz 2019.3 py_0 defaults pywavelets 1.0.3 py37hdd07704_1 defaults pyyaml 5.1.2 py37h7b6447c_0 defaults pyzmq 18.1.0 py37he6710b0_0 defaults qt 5.9.7 h5867ecd_1 defaults qtawesome 0.6.0 py_0 defaults qtconsole 4.5.5 py_0 defaults qtpy 1.9.0 py_0 defaults readline 7.0 h7b6447c_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 py37h14c3975_0 defaults scikit-image 0.15.0 py37he6710b0_0 defaults scikit-learn 0.21.3 py37hd81dba3_0 defaults scipy 1.3.1 py37h7c811a0_0 defaults seaborn 0.9.0 py37_0 defaults secretstorage 3.1.1 py37_0 defaults send2trash 1.5.0 py37_0 defaults setuptools 41.4.0 py37_0 defaults simplegeneric 0.8.1 py37_2 defaults singledispatch 3.4.0.3 py37_0 defaults sip 4.19.8 py37hf484d3e_0 defaults six 1.12.0 py37_0 defaults snappy 1.1.7 hbae5bb6_3 defaults snowballstemmer 2.0.0 py_0 defaults sortedcollections 1.1.2 py37_0 defaults sortedcontainers 2.1.0 py37_0 defaults soupsieve 1.9.3 py37_0 defaults sphinx 2.2.0 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 0.5.2 py37_0 defaults sqlalchemy 1.3.9 py37h7b6447c_0 defaults sqlite 3.30.0 h7b6447c_0 defaults statsmodels 0.10.1 py37hdd07704_0 defaults sympy 1.4 py37_0 defaults tbb 2019.4 hfd86e86_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 hbc83047_0 defaults toolz 0.10.0 py_0 defaults tornado 6.0.3 py37h7b6447c_0 defaults tqdm 4.36.1 py_0 defaults traitlets 4.3.3 py37_0 defaults unicodecsv 0.14.1 py37_0 defaults unixodbc 2.3.7 h14c3975_0 defaults urllib3 1.24.2 py37_0 defaults wcwidth 0.1.7 py37_0 defaults webencodings 0.5.1 py37_1 defaults werkzeug 0.16.0 py_0 defaults wheel 0.33.6 py37_0 defaults widgetsnbextension 3.5.1 py37_0 defaults wrapt 1.11.2 py37h7b6447c_0 defaults wurlitzer 1.0.3 py37_0 defaults xlrd 1.2.0 py37_0 defaults xlsxwriter 1.2.1 py_0 defaults xlwt 1.3.0 py37_0 defaults xmltodict 0.12.0 py_0 defaults xz 5.2.4 h14c3975_4 defaults yaml 0.1.7 had09818_2 defaults zeromq 4.3.1 he6710b0_3 defaults zict 1.0.0 py_0 defaults zipp 0.6.0 py_0 defaults zlib 1.2.11 h7b6447c_3 defaults zstd 1.3.7 h0b5b093_0 defaults ```

[jasontwinters]

Just so I understand, how is Anaconda supposed to work? Is my expected behavior valid, or do I not understand Anaconda works?

[forrestwaters]

@jasontwinters your expected behavior is valid. It looks like this is a bug in Anaconda Navigator 1.9.12 on Linux which will require a new release of Navigator to fix it. In the meantime, the workaround you described of activating the environment via terminal and launching there should work.

[mereshow]

Just so I understand, how is Anaconda supposed to work? Is my expected behavior valid, or do I not understand Anaconda works?

It is a bug, I reported it as an issue in Spyder but they closed it because it is related to anaconda-navigator. It is solved if anaconda navigator is downgraded to 1.9.7: conda install anaconda-navigator=1.9.7

[mereshow]

I forgot to mention that Spyder works correctly with anaconda-navigator 1.9.12 if it is launched from a terminal, i.e.:

conda activate my_environment
spyder&

[jasontwinters]

Thanks for taking a look and confirming

[gucciard]

What is strange is that, if one activates an environment in Navigator, and from there launches Spyder, the version actually launched is the one in the base environment, not the one belonging to the environment selected. Actually Navigator does not switch to the correct environment path (also, the packages are not found). On the other hand, if one activates an environment and from there launches a terminal (click on green triangle and select open terminal), then Navigator brings to the correct environment. So, if from that terminal window we launch Spyder, everything works correctly. Hope they will fix the bug quickly

[csoja]

This was a bug in Navigator 1.9.12. It should be fixed in Anaconda Navigator 1.10.0 that was released today. Please update to the latest from the Anaconda Prompt or a terminal: conda update anaconda-navigator