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Anaconda issue tracking
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Anaconda Errors #12521

Open mpuccetti opened 3 years ago

mpuccetti commented 3 years ago

Actual Behavior

  1. After the anaconda installation, the "spyder" command doesn't work.
``` **/Applications/anaconda3/bin/pythonw: line 3: /Applications/anaconda3/python.app/Contents/MacOS/python: No such file or directory** ```
  1. When i try to launch the "anaconda-navigator" command it doesn't work.
``` **Traceback (most recent call last): File "/Applications/anaconda3/lib/python3.8/site-packages/anaconda_navigator/widgets/main_window.py", line 536, in setup self.post_setup(conda_data=conda_data) File "/Applications/anaconda3/lib/python3.8/site-packages/anaconda_navigator/widgets/main_window.py", line 583, in post_setup self.tab_home.setup(conda_data) File "/Applications/anaconda3/lib/python3.8/site-packages/anaconda_navigator/widgets/tabs/home.py", line 165, in setup self.set_applications(applications, packages) File "/Applications/anaconda3/lib/python3.8/site-packages/anaconda_navigator/widgets/tabs/home.py", line 200, in set_applications apps = self.api.process_apps(applications, prefix=self.current_prefix) File "/Applications/anaconda3/lib/python3.8/site-packages/anaconda_navigator/api/anaconda_api.py", line 624, in process_apps linked_apps = self.conda_linked_apps_info(prefix) File "/Applications/anaconda3/lib/python3.8/site-packages/anaconda_navigator/api/conda_api.py", line 648, in linked_apps_info with open(fpath) as f: PermissionError: [Errno 13] Permission denied: '/Applications/anaconda3/pkgs/_anaconda_depends-2020.07-py38_0/info/index.json'** ```

Expected Behavior

  1. Start the Spyder application properly.
  2. Start the anaconda-navigator properly.

Steps to Reproduce

  1. launch the spyder application, within the command line. (base) iMac-di-Marco:~ marcopuccetti$ spyder
  2. launch the anaconda-navigator command, within the command line. (base) iMac-di-Marco:~ marcopuccetti$ anaconda-navigator
Anaconda or Miniconda version:
Operating System:

MacOS High Sierra ver. 10.13.6

conda info
``` active environment : base active env location : /Applications/anaconda3 shell level : 1 user config file : /Users/marcopuccetti/.condarc populated config files : conda version : 4.10.3 conda-build version : 3.21.4 python version : 3.8.10.final.0 virtual packages : __osx=10.13.6=0 __unix=0=0 __archspec=1=x86_64 base environment : /Applications/anaconda3 (writable) conda av data dir : /Applications/anaconda3/etc/conda conda av metadata url : None 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 : /Applications/anaconda3/pkgs /Users/marcopuccetti/.conda/pkgs envs directories : /Applications/anaconda3/envs /Users/marcopuccetti/.conda/envs platform : osx-64 user-agent : conda/4.10.3 requests/2.25.1 CPython/3.8.10 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 /Applications/anaconda3: # # Name Version Build Channel _anaconda_depends 2020.07 py38_0 _ipyw_jlab_nb_ext_conf 0.1.0 py38_0 alabaster 0.7.12 pyhd3eb1b0_0 anaconda custom py38_1 anaconda-client 1.8.0 py38hecd8cb5_0 anaconda-navigator 2.0.3 py38_0 anaconda-project 0.10.0 pyhd3eb1b0_0 anyio 2.2.0 py38hecd8cb5_1 appdirs 1.4.4 py_0 applaunchservices 0.2.1 py_0 appnope 0.1.2 py38hecd8cb5_1001 appscript 1.1.2 py38h9ed2024_0 argh 0.26.2 py38_0 argon2-cffi 20.1.0 py38h9ed2024_1 asn1crypto 1.4.0 py_0 astroid 2.6.2 py38hecd8cb5_0 astropy 4.2.1 py38h9ed2024_1 async_generator 1.10 pyhd3eb1b0_0 atomicwrites 1.4.0 py_0 attrs 21.2.0 pyhd3eb1b0_0 autopep8 1.5.3 py_0 babel 2.9.1 pyhd3eb1b0_0 backcall 0.2.0 pyhd3eb1b0_0 backports 1.0 pyhd3eb1b0_2 backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0 backports.shutil_get_terminal_size 1.0.0 pyhd3eb1b0_3 backports.tempfile 1.0 pyhd3eb1b0_1 backports.weakref 1.0.post1 py_1 beautifulsoup4 4.9.3 pyha847dfd_0 bitarray 2.1.0 py38h9ed2024_1 bkcharts 0.2 py38_0 black 19.10b0 py_0 blas 1.0 mkl bleach 3.3.0 pyhd3eb1b0_0 blosc 1.21.0 h2842e9f_0 bokeh 2.3.3 py38hecd8cb5_0 boto 2.49.0 py38_0 bottleneck 1.3.2 py38hf1fa96c_1 brotlipy 0.7.0 py38h9ed2024_1003 bzip2 1.0.8 h1de35cc_0 c-ares 1.17.1 h9ed2024_0 ca-certificates 2021.7.5 hecd8cb5_1 certifi 2021.5.30 py38hecd8cb5_0 cffi 1.14.6 py38h2125817_0 chardet 4.0.0 py38hecd8cb5_1003 click 8.0.1 pyhd3eb1b0_0 cloudpickle 1.6.0 py_0 clyent 1.2.2 py38_1 colorama 0.4.4 pyhd3eb1b0_0 conda 4.10.3 py38hecd8cb5_0 conda-build 3.21.4 py38hecd8cb5_0 conda-content-trust 0.1.1 pyhd3eb1b0_0 conda-env 2.6.0 1 conda-pack 0.6.0 pyhd3eb1b0_0 conda-package-handling 1.7.3 py38h9ed2024_1 conda-repo-cli 1.0.4 pyhd3eb1b0_0 conda-token 0.3.0 pyhd3eb1b0_0 conda-verify 3.4.2 py_1 contextlib2 0.6.0.post1 py_0 cryptography 3.4.7 py38h2fd3fbb_0 curl 7.71.1 hb0a8c7a_1 cycler 0.10.0 py38_0 cython 0.29.23 py38h23ab428_0 cytoolz 0.11.0 py38haf1e3a3_0 dask 2021.6.2 pyhd3eb1b0_0 dask-core 2021.6.2 pyhd3eb1b0_0 dbus 1.13.18 h18a8e69_0 decorator 4.4.2 pyhd3eb1b0_0 defusedxml 0.7.1 pyhd3eb1b0_0 diff-match-patch 20200713 py_0 distributed 2021.6.2 py38hecd8cb5_0 docutils 0.17.1 py38hecd8cb5_1 entrypoints 0.3 py38_0 et_xmlfile 1.1.0 py38hecd8cb5_0 expat 2.4.1 h23ab428_2 fastcache 1.1.0 py38h1de35cc_0 filelock 3.0.12 pyhd3eb1b0_1 flake8 3.8.3 py_0 flask 1.1.2 pyhd3eb1b0_0 freetype 2.10.4 ha233b18_0 fsspec 2021.6.0 pyhd3eb1b0_0 future 0.18.2 py38_1 get_terminal_size 1.0.0 h7520d66_0 gettext 0.21.0 h7535e17_0 gevent 21.1.2 py38h9ed2024_1 glib 2.69.0 hdf23fa2_0 glob2 0.7 pyhd3eb1b0_0 gmp 6.2.1 h23ab428_2 gmpy2 2.0.8 py38h6ef4df4_3 greenlet 1.1.0 py38h23ab428_0 h5py 2.10.0 py38h3134771_0 hdf5 1.10.4 hfa1e0ec_0 heapdict 1.0.1 py_0 html5lib 1.1 py_0 icu 58.2 h0a44026_3 idna 2.10 pyhd3eb1b0_0 imageio 2.9.0 pyhd3eb1b0_0 imagesize 1.2.0 pyhd3eb1b0_0 importlib-metadata 3.10.0 py38hecd8cb5_0 importlib_metadata 3.10.0 hd3eb1b0_0 iniconfig 1.1.1 pyhd3eb1b0_0 intel-openmp 2021.2.0 hecd8cb5_564 intervaltree 3.1.0 py_0 ipykernel 5.3.4 py38h5ca1d4c_0 ipython 7.22.0 py38h01d92e1_0 ipython_genutils 0.2.0 pyhd3eb1b0_1 ipywidgets 7.6.3 pyhd3eb1b0_1 isort 5.9.2 pyhd3eb1b0_0 itsdangerous 2.0.1 pyhd3eb1b0_0 jbig 2.1 h4d881f8_0 jdcal 1.4.1 py_0 jedi 0.17.2 py38hecd8cb5_1 jinja2 3.0.1 pyhd3eb1b0_0 joblib 1.0.1 pyhd3eb1b0_0 jpeg 9b he5867d9_2 json5 0.9.6 pyhd3eb1b0_0 jsonschema 3.2.0 py_2 jupyter 1.0.0 py38_7 jupyter-packaging 0.7.12 pyhd3eb1b0_0 jupyter_client 6.1.12 pyhd3eb1b0_0 jupyter_console 6.4.0 pyhd3eb1b0_0 jupyter_core 4.7.1 py38hecd8cb5_0 jupyter_server 1.4.1 py38hecd8cb5_0 jupyterlab 3.0.14 pyhd3eb1b0_1 jupyterlab_pygments 0.1.2 py_0 jupyterlab_server 2.4.0 pyhd3eb1b0_0 jupyterlab_widgets 1.0.0 pyhd3eb1b0_1 keyring 23.0.1 py38hecd8cb5_0 kiwisolver 1.3.1 py38h23ab428_0 krb5 1.18.2 h75d18d8_0 lazy-object-proxy 1.6.0 py38h9ed2024_0 lcms2 2.12 hf1fd2bf_0 libarchive 3.4.2 haa3ed63_0 libcurl 7.71.1 h8a08a2b_1 libcxx 10.0.0 1 libedit 3.1.20210216 h9ed2024_1 libev 4.33 haf1e3a3_0 libffi 3.3 hb1e8313_2 libgfortran 3.0.1 h93005f0_2 libiconv 1.16 h1de35cc_0 liblief 0.10.1 h0a44026_0 libllvm10 10.0.1 h76017ad_5 libllvm9 9.0.1 h21ff451_1 libpng 1.6.37 ha441bb4_0 libsodium 1.0.18 h1de35cc_0 libspatialindex 1.9.3 h23ab428_0 libssh2 1.9.0 ha12b0ac_1 libtiff 4.2.0 h87d7836_0 libuv 1.40.0 haf1e3a3_0 libwebp-base 1.2.0 h9ed2024_0 libxml2 2.9.12 hcdb78fc_0 libxslt 1.1.34 h83b36ba_0 llvm-openmp 10.0.0 h28b9765_0 llvmlite 0.36.0 py38he4411ff_4 locket 0.2.1 py38hecd8cb5_1 lxml 4.6.3 py38h26b266a_0 lz4-c 1.9.3 h23ab428_0 lzo 2.10 haf1e3a3_2 markupsafe 2.0.1 py38h9ed2024_0 matplotlib 3.3.4 py38hecd8cb5_0 matplotlib-base 3.3.4 py38h8b3ea08_0 mccabe 0.6.1 py38_1 mistune 0.8.4 py38h1de35cc_1001 mkl 2021.2.0 hecd8cb5_269 mkl-service 2.3.0 py38h9ed2024_1 mkl_fft 1.3.0 py38h4a7008c_2 mkl_random 1.2.1 py38hb2f4e1b_2 mock 4.0.3 pyhd3eb1b0_0 more-itertools 8.8.0 pyhd3eb1b0_0 mpc 1.1.0 h6ef4df4_1 mpfr 4.0.2 h9066e36_1 mpmath 1.2.1 py38hecd8cb5_0 msgpack-python 1.0.2 py38hf7b0b51_1 multipledispatch 0.6.0 py38_0 mypy_extensions 0.4.3 py38_0 navigator-updater 0.2.1 py38_0 nbclassic 0.2.6 pyhd3eb1b0_0 nbclient 0.5.3 pyhd3eb1b0_0 nbconvert 6.1.0 py38hecd8cb5_0 nbformat 5.1.3 pyhd3eb1b0_0 ncurses 6.2 h0a44026_1 nest-asyncio 1.5.1 pyhd3eb1b0_0 networkx 2.5.1 pyhd3eb1b0_0 nltk 3.6.2 pyhd3eb1b0_0 nose 1.3.7 pyhd3eb1b0_1006 notebook 6.4.0 py38hecd8cb5_0 numba 0.53.1 py38hb2f4e1b_0 numexpr 2.7.3 py38h5873af2_1 numpy 1.20.2 py38h4b4dc7a_0 numpy-base 1.20.2 py38he0bd621_0 numpydoc 1.1.0 pyhd3eb1b0_1 olefile 0.46 py_0 openjpeg 2.3.0 hb95cd4c_1 openpyxl 3.0.7 pyhd3eb1b0_0 openssl 1.1.1k h9ed2024_0 packaging 21.0 pyhd3eb1b0_0 pandas 1.2.5 py38h23ab428_0 pandoc 2.12 hecd8cb5_0 pandocfilters 1.4.3 py38hecd8cb5_1 parso 0.7.0 py_0 partd 1.2.0 pyhd3eb1b0_0 path 16.0.0 py38hecd8cb5_0 path.py 12.5.0 0 pathlib2 2.3.6 py38hecd8cb5_2 pathspec 0.7.0 py_0 pathtools 0.1.2 py_1 patsy 0.5.1 py38_0 pcre 8.45 h23ab428_0 pep8 1.7.1 py38_0 pexpect 4.8.0 pyhd3eb1b0_3 pickleshare 0.7.5 pyhd3eb1b0_1003 pillow 8.3.1 py38ha4cf6ea_0 pip 21.1.3 py38hecd8cb5_0 pkginfo 1.7.0 py38hecd8cb5_0 pluggy 0.13.1 py38hecd8cb5_0 ply 3.11 py38_0 prometheus_client 0.11.0 pyhd3eb1b0_0 prompt-toolkit 3.0.17 pyh06a4308_0 prompt_toolkit 3.0.17 hd3eb1b0_0 psutil 5.8.0 py38h9ed2024_1 ptyprocess 0.7.0 pyhd3eb1b0_2 py 1.10.0 pyhd3eb1b0_0 py-lief 0.10.1 py38haf313ee_0 pycodestyle 2.6.0 pyhd3eb1b0_0 pycosat 0.6.3 py38h1de35cc_1 pycparser 2.20 py_2 pycurl 7.43.0.6 py38hddc9c9b_0 pydocstyle 6.1.1 pyhd3eb1b0_0 pyerfa 2.0.0 py38h9ed2024_0 pyflakes 2.2.0 pyhd3eb1b0_0 pygments 2.9.0 pyhd3eb1b0_0 pylint 2.9.3 py38hecd8cb5_1 pyls-black 0.4.6 hd3eb1b0_0 pyls-spyder 0.3.2 pyhd3eb1b0_0 pyodbc 4.0.31 py38h23ab428_0 pyopenssl 20.0.1 pyhd3eb1b0_1 pyparsing 2.4.7 pyhd3eb1b0_0 pyqt 5.9.2 py38h655552a_2 pyrsistent 0.17.3 py38haf1e3a3_0 pysocks 1.7.1 py38_1 pytables 3.6.1 py38h4727e94_0 pytest 6.2.4 py38hecd8cb5_2 python 3.8.10 h88f2d9e_7 python-dateutil 2.8.1 pyhd3eb1b0_0 python-jsonrpc-server 0.4.0 py_0 python-language-server 0.36.2 pyhd3eb1b0_0 python-libarchive-c 2.9 pyhd3eb1b0_1 python.app 3 py38h9ed2024_0 pytz 2021.1 pyhd3eb1b0_0 pywavelets 1.1.1 py38haf1e3a3_2 pyyaml 5.4.1 py38h9ed2024_1 pyzmq 20.0.0 py38h23ab428_1 qdarkstyle 2.8.1 py_0 qt 5.9.7 h468cd18_1 qtawesome 1.0.2 pyhd3eb1b0_0 qtconsole 5.1.0 pyhd3eb1b0_0 qtpy 1.9.0 py_0 readline 8.1 h9ed2024_0 regex 2021.7.6 py38h9ed2024_0 requests 2.25.1 pyhd3eb1b0_0 ripgrep 12.1.1 0 rope 0.19.0 pyhd3eb1b0_0 rtree 0.9.7 py38hecd8cb5_1 ruamel_yaml 0.15.100 py38h9ed2024_0 scikit-image 0.16.2 py38h6c726b0_0 scikit-learn 0.24.2 py38hb2f4e1b_0 scipy 1.6.2 py38hd5f7400_1 seaborn 0.11.1 pyhd3eb1b0_0 send2trash 1.5.0 pyhd3eb1b0_1 setuptools 52.0.0 py38hecd8cb5_0 simplegeneric 0.8.1 py38_2 singledispatch 3.6.2 pyhd3eb1b0_1001 sip 4.19.8 py38h0a44026_0 six 1.16.0 pyhd3eb1b0_0 snappy 1.1.8 hb1e8313_0 sniffio 1.2.0 py38hecd8cb5_1 snowballstemmer 2.1.0 pyhd3eb1b0_0 sortedcollections 2.1.0 pyhd3eb1b0_0 sortedcontainers 2.4.0 pyhd3eb1b0_0 soupsieve 2.2.1 pyhd3eb1b0_0 sphinx 4.0.2 pyhd3eb1b0_0 sphinxcontrib 1.0 py38_1 sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0 sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0 sphinxcontrib-htmlhelp 2.0.0 pyhd3eb1b0_0 sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0 sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0 sphinxcontrib-serializinghtml 1.1.5 pyhd3eb1b0_0 sphinxcontrib-websupport 1.2.4 py_0 spyder 4.2.5 py38hecd8cb5_0 spyder-kernels 1.10.2 py38hecd8cb5_0 sqlalchemy 1.4.19 py38h9ed2024_0 sqlite 3.36.0 hce871da_0 statsmodels 0.12.2 py38h9ed2024_0 sympy 1.8 py38hecd8cb5_0 tbb 2020.3 h879752b_0 tblib 1.7.0 py_0 terminado 0.9.4 py38hecd8cb5_0 testpath 0.5.0 pyhd3eb1b0_0 textdistance 4.2.1 pyhd3eb1b0_0 threadpoolctl 2.1.0 pyh5ca1d4c_0 three-merge 0.1.1 pyhd3eb1b0_0 tk 8.6.10 hb0a8c7a_0 toml 0.10.2 pyhd3eb1b0_0 toolz 0.11.1 pyhd3eb1b0_0 tornado 6.1 py38h9ed2024_0 tqdm 4.61.2 pyhd3eb1b0_1 traitlets 5.0.5 pyhd3eb1b0_0 typed-ast 1.4.3 py38h9ed2024_1 typing_extensions 3.10.0.0 pyh06a4308_0 ujson 4.0.2 py38h23ab428_0 unicodecsv 0.14.1 py38_0 unixodbc 2.3.9 haf1e3a3_0 urllib3 1.26.6 pyhd3eb1b0_1 watchdog 1.0.2 py38h9ed2024_1 wcwidth 0.2.5 py_0 webencodings 0.5.1 py38_1 werkzeug 1.0.1 pyhd3eb1b0_0 wheel 0.36.2 pyhd3eb1b0_0 widgetsnbextension 3.5.1 py38_0 wrapt 1.12.1 py38haf1e3a3_1 wurlitzer 2.1.0 py38hecd8cb5_0 xlrd 2.0.1 pyhd3eb1b0_0 xlsxwriter 1.4.4 pyhd3eb1b0_0 xlwings 0.24.2 py38hecd8cb5_0 xlwt 1.3.0 py38_0 xmltodict 0.12.0 py_0 xz 5.2.5 h1de35cc_0 yaml 0.2.5 haf1e3a3_0 yapf 0.31.0 pyhd3eb1b0_0 zeromq 4.3.4 h23ab428_0 zict 2.0.0 pyhd3eb1b0_0 zipp 3.5.0 pyhd3eb1b0_0 zlib 1.2.11 h1de35cc_3 zope 1.0 py38_1 zope.event 4.5.0 py38_0 zope.interface 5.4.0 py38h9ed2024_0 zstd 1.4.9 h322a384_0 ```
mpuccetti commented 3 years ago

Hi, now started to do the following steps to fix the problem:

  1. Removing conda using the command: conda remove conda;

And this is the result was this: 

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: failed

RemoveError: This operation will remove conda without replacing it with
another version of conda.

So i decided to get an updated version of Anaconda command line installer (verified), Anaconda3-4.0.0-MacOSX-x86_64.sh.

But i ask now what could happen overinstalling the .sh installer on the dmg base installation?

Thanks Marco