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Unable to register environment - during installation error #11148

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Deena-B opened this issue Jul 25, 2019 · 27 comments · Fixed by conda/conda#9215
Closed

Unable to register environment - during installation error #11148

Deena-B opened this issue Jul 25, 2019 · 27 comments · Fixed by conda/conda#9215
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@Deena-B
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Deena-B commented Jul 25, 2019

Actual Behavior

I followed instructions to download anaconda using command line from here.

I accepted the license terms & confirmed the default location ~/anaconda3 for installation

Everything looks okay, except /Users/drb/.conda/environments.txt was NOT made!

[/Users/drb/anaconda3] >>>
PREFIX=/Users/drb/anaconda3
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/drb/anaconda3

  added / updated specs:
    - _ipyw_jlab_nb_ext_conf==0.1.0=py37_0
    - alabaster==0.7.12=py37_0
    - anaconda-client==1.7.2=py37_0
...

- zipp==0.5.1=py_0
    - zlib==1.2.11=h1de35cc_3
    - zstd==1.3.7=h5bba6e5_0


The following NEW packages will be INSTALLED:

  _ipyw_jlab_nb_ext~ pkgs/main/osx-64::_ipyw_jlab_nb_ext_conf-0.1.0-py37_0
  alabaster          pkgs/main/osx-64::alabaster-0.7.12-py37_0
  anaconda           pkgs/main/osx-64::anaconda-2019.07-py37_0
...

zipp               pkgs/main/noarch::zipp-0.5.1-py_0
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3
  zstd               pkgs/main/osx-64::zstd-1.3.7-h5bba6e5_0


Preparing transaction: done
Executing transaction: | b''
/ WARNING conda.core.envs_manager:register_env(46): Unable to register environment. Path not writable or missing.
  environment location: /Users/drb/anaconda3
  registry file: /Users/drb/.conda/environments.txt
done
installation finished.
Do you wish the installer to initialize Anaconda3
by running conda init? [yes|no]
[yes] >>> yes

/Users/drb/.conda/environments.txt was NOT made!

Expected Behavior

It seems like /Users/drb/.conda/environments.txt should have been made.

Steps to Reproduce

see what actually happened

Anaconda or Miniconda version:

I downloaded, and installed from, the file: Anaconda3-2019.07-MacOSX-x86_64.sh

Operating System:

macOS Mojave, version 10.14.6

conda info
     active environment : base
    active env location : /Users/drb/anaconda3
            shell level : 1
       user config file : /Users/drb/.condarc
 populated config files :
          conda version : 4.7.10
    conda-build version : 3.18.8
         python version : 3.7.3.final.0
       virtual packages :
       base environment : /Users/drb/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/drb/anaconda3/pkgs
                          /Users/drb/.conda/pkgs
       envs directories : /Users/drb/anaconda3/envs
                          /Users/drb/.conda/envs
               platform : osx-64
             user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Darwin/18.7.0 OSX/10.14.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False
conda list --show-channel-urls
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0    defaults
alabaster                 0.7.12                   py37_0    defaults
anaconda                  2019.07                  py37_0    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            4.7.1                    py37_1    defaults
bitarray                  0.9.3            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                     1.2.0                    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                     0    defaults
certifi                   2019.6.16                py37_0    defaults
cffi                      1.12.3           py37hb5b8e2f_0    defaults
chardet                   3.0.4                    py37_1    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                     4.7.10                   py37_0    defaults
conda-build               3.18.8                   py37_0    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                      7.65.2               ha441bb4_0    defaults
cycler                    0.10.0                   py37_0    defaults
cython                    0.29.12          py37h0a44026_0    defaults
cytoolz                   0.10.0           py37h1de35cc_0    defaults
dask                      2.1.0                      py_0    defaults
dask-core                 2.1.0                      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               2.1.0                      py_0    defaults
docutils                  0.14                     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
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        0.17                     py37_1    defaults
intel-openmp              2019.4                      233    defaults
ipykernel                 5.1.1            py37h39e3cac_0    defaults
ipython                   7.6.1            py37h39e3cac_0    defaults
ipython_genutils          0.2.0                    py37_0    defaults
ipywidgets                7.5.0                      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                      0.13.3                   py37_0    defaults
jinja2                    2.10.1                   py37_0    defaults
joblib                    0.13.2                   py37_0    defaults
jpeg                      9b                   he5867d9_2    defaults
json5                     0.8.4                      py_0    defaults
jsonschema                3.0.1                    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_0    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         1.4.1            py37h1de35cc_0    defaults
libarchive                3.3.3                h786848e_5    defaults
libcurl                   7.65.2               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                      4.3.4            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                3.1.0            py37h54f8f79_0    defaults
mccabe                    0.6.1                    py37_1    defaults
mistune                   0.8.4            py37h1de35cc_0    defaults
mkl                       2019.4                      233    defaults
mkl-service               2.0.2            py37h1de35cc_0    defaults
mkl_fft                   1.0.12           py37h5e564d8_0    defaults
mkl_random                1.0.2            py37h27c97d8_0    defaults
mock                      3.0.5                    py37_0    defaults
more-itertools            7.0.0                    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                      3.4.4                    py37_0    defaults
nose                      1.3.7                    py37_2    defaults
notebook                  6.0.0                    py37_0    defaults
numba                     0.44.1           py37h6440ff4_0    defaults
numexpr                   2.6.9            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                   1.1.1c               h1de35cc_1    defaults
packaging                 19.0                     py37_0    defaults
pandas                    0.24.2           py37h0a44026_0    defaults
pandoc                    2.2.3.2                       0    defaults
pandocfilters             1.4.2                    py37_1    defaults
parso                     0.5.0                      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                       19.1.1                   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                    4.0.26           py37h0a44026_0    defaults
pyopenssl                 19.0.0                   py37_0    defaults
pyparsing                 2.4.0                      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         0.3.1                    py37_0    defaults
python                    3.7.3                h359304d_0    defaults
python-dateutil           2.8.0                    py37_0    defaults
python-libarchive-c       2.8                     py37_11    defaults
python.app                2                        py37_9    defaults
pytz                      2019.1                     py_0    defaults
pywavelets                1.0.3            py37h1d22016_1    defaults
pyyaml                    5.1.1            py37h1de35cc_0    defaults
pyzmq                     18.0.0           py37h0a44026_0    defaults
qt                        5.9.7                h468cd18_1    defaults
qtawesome                 0.5.7                    py37_1    defaults
qtconsole                 4.5.1                      py_0    defaults
qtpy                      1.8.0                      py_0    defaults
readline                  7.0                  h1de35cc_5    defaults
requests                  2.22.0                   py37_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                     1.3.0            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                 1.8                      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                1.3.5            py37h1de35cc_0    defaults
sqlite                    3.29.0               ha441bb4_0    defaults
statsmodels               0.10.0           py37h1d22016_0    defaults
sympy                     1.4                      py37_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                  0.15.4                     py_0    defaults
wheel                     0.33.4                   py37_0    defaults
widgetsnbextension        3.5.0                    py37_0    defaults
wrapt                     1.11.2           py37h1de35cc_0    defaults
wurlitzer                 1.0.2                    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                      0.5.1                      py_0    defaults
zlib                      1.2.11               h1de35cc_3    defaults
zstd                      1.3.7                h5bba6e5_0    defaults
@msarahan
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Contributor

That is definitely an odd error, and we didn't see this during our QA process. Can you verify if the ~/.conda folder already exists? If so, is the environments.txt present, but not writable? Have you had an anaconda installation earlier that may have left that file in a strange state?

It looks like your installation is otherwise intact. Can you create new environments?

conda create -n test python

@dustinfreeman
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Field Report: I observed an identical error to the above, and for me the ~/.conda folder did not exist after I ran the install script.

@dustinfreeman
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FYI, I observed an identical error to the above, and my ~/.conda folder did not appear on first run. I ran the install script again with the -u option, then created a conda environment, and the ~/.conda folder finally appeared.

@MaryoHg
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MaryoHg commented Aug 1, 2019

Hi,

Recently, I was trying to install the Miniconda2-latest-Linux-x86_64.sh (as usually do).
I'm getting the same error/warning from above:

Preparing transaction: done
Executing transaction: / WARNING conda.core.envs_manager:register_env(46): Unable to register environment. Path not writable or missing.
environment location: /home/me/bioinformatics/miniconda2
registry file: /home/me/.conda/environments.txt
done
installation finished.

Did you install into the same path as before when using the -u update an existing installation ? @dustinfreeman

Thanks,

Maryo.

@dustinfreeman
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@MaryoHg yes, the install path was identical. My command was the same except for the addition of -u

@Furqan136
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I had the same error.
OS: Ubuntu 18.04
Version: Anaconda3-2019.07
The ~/.conda and ~/.anaconda folders appear after running anaconda-navigator

@MaryoHg
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MaryoHg commented Aug 2, 2019

Thanks @dustinfreeman.

After manually source the base conda environment (I do not initialize it from start) and creating some environments without any issue, I realized the hidden folders were created.

So I guess I'm fine until now. Hope all goes OK.

@frankang
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frankang commented Aug 4, 2019

same issue with latest miniconda, currently switching to the old version installer would help.
https://repo.continuum.io/miniconda/

@aparente-nurix
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aparente-nurix commented Aug 5, 2019

I just experienced this issue while trying to install Anaconda3 on a Centos7 machine. Anaconda is already installed for a different user on this same machine, but there shouldn't be any path overlaps with existing installs.

I first attempted to fix this issue by using that -u option, but it still couldn't create the directory.

The .conda folder only appeared after running the following, similar to @Furqan136 :

source anaconda3/bin/activate
source ~/.bashrc
anaconda-navigator (failed to launch because of X11 connection errors, but still created .conda directory)

@MaickonPrebianca
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Try before install create .conda path in the same path will install anaconda

mkdir /home/youruser/.conda

@RaghuSpaceRajan
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I have the same error with Anaconda3-2019.07-Linux-x86_64.sh. I had a previous Anaconda 2 installation. I see that ~/.conda exists now after creation of 2 environments. I don't know if the .conda folder existed before/after install but I don't see .anaconda.

@joelkuiper
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Note that I had the same problem using Docker 19.* but not Docker 18.*, creating the .conda folder before executing the command fixed it weirdly.

@schmidtl4
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schmidtl4 commented Aug 14, 2019

I have encountered the same issue except on a windows 64-bit install.
The error is "Unable to register environment. Path not writable or missing."
I've installed, uninstalled, rebooted several times including simply using the defaults all the way through the installation process. No joy, same error every time.
From the installer details it looks like the trouble starts here: (replacing my actual user directory name with my_user_directory):

Preparing transaction: ...working... done
Executing transaction: ...working... DEBUG menuinst_win32:init(199): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}', prefix: 'C:\Users\my_user_directory\Anaconda3', env_name: 'Anaconda3', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(324): Shortcut cmd is %windir%\System32\cmd.exe, args are ['"/K"', 'C:\Users\my_user_directory\Anaconda3\Scripts\activate.bat', 'C:\Users\my_user_directory\Anaconda3']
DEBUG menuinst_win32:init(199): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}', prefix: 'C:\Users\my_user_directory\Anaconda3', env_name: 'Anaconda3', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(324): Shortcut cmd is %windir%\System32\WindowsPowerShell\v1.0\powershell.exe, args are ['-ExecutionPolicy', 'ByPass', '-NoExit', '-Command', '"& 'C:\Users\my_user_directory\Anaconda3\shell\condabin\conda-hook.ps1' ; conda activate 'C:\Users\my_user_directory\Anaconda3' "']
DEBUG menuinst_win32:init(199): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}', prefix: 'C:\Users\my_user_directory\Anaconda3', env_name: 'Anaconda3', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(324): Shortcut cmd is C:\Users\my_user_directory\Anaconda3\pythonw.exe, args are ['C:\Users\my_user_directory\Anaconda3\cwp.py', 'C:\Users\my_user_directory\Anaconda3', 'C:\Users\my_user_directory\Anaconda3\pythonw.exe', 'C:\Users\my_user_directory\Anaconda3\Scripts\anaconda-navigator-script.py']
DEBUG menuinst_win32:init(199): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}', prefix: 'C:\Users\my_user_directory\Anaconda3', env_name: 'Anaconda3', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(324): Shortcut cmd is C:\Users\my_user_directory\Anaconda3\pythonw.exe, args are ['C:\Users\my_user_directory\Anaconda3\cwp.py', 'C:\Users\my_user_directory\Anaconda3', 'C:\Users\my_user_directory\Anaconda3\pythonw.exe', 'C:\Users\my_user_directory\Anaconda3\Scripts\spyder-script.py']
DEBUG menuinst_win32:create(324): Shortcut cmd is C:\Users\my_user_directory\Anaconda3\python.exe, args are ['C:\Users\my_user_directory\Anaconda3\cwp.py', 'C:\Users\my_user_directory\Anaconda3', 'C:\Users\my_user_directory\Anaconda3\python.exe', 'C:\Users\my_user_directory\Anaconda3\Scripts\spyder-script.py', '--reset']
DEBUG menuinst_win32:init(199): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}', prefix: 'C:\Users\my_user_directory\Anaconda3', env_name: 'Anaconda3', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(324): Shortcut cmd is C:\Users\my_user_directory\Anaconda3\python.exe, args are ['C:\Users\my_user_directory\Anaconda3\cwp.py', 'C:\Users\my_user_directory\Anaconda3', 'C:\Users\my_user_directory\Anaconda3\python.exe', 'C:\Users\my_user_directory\Anaconda3\Scripts\jupyter-notebook-script.py', '"%USERPROFILE%/"']
WARNING conda.core.envs_manager:register_env(46): Unable to register environment. Path not writable or missing.
environment location: C:\Users\my_user_directory\Anaconda3
registry file: C:\Users\my_user_directory.conda\environments.txt
done
Delete file: C:\Users\my_user_directory\Anaconda3\pkgs\env.txt
Output folder: C:\Users\my_user_directory\Anaconda3\conda-meta
Extract: history
Creating Anaconda3 menus...
Processed C:\Users\my_user_directory\Anaconda3\Menu\anaconda-navigator.json successfully.
Processed C:\Users\my_user_directory\Anaconda3\Menu\console_shortcut.json successfully.
Processed C:\Users\my_user_directory\Anaconda3\Menu\notebook.json successfully.
Processed C:\Users\my_user_directory\Anaconda3\Menu\powershell_shortcut.json successfully.
Processed C:\Users\my_user_directory\Anaconda3\Menu\spyder_shortcut.json successfully.
Execute: "C:\Users\my_user_directory\Anaconda3\pythonw.exe" -E -s "C:\Users\my_user_directory\Anaconda3\Lib_nsis.py" mkdirs
Running post install...
Execute: "C:\Users\my_user_directory\Anaconda3\pythonw.exe" -E -s "C:\Users\my_user_directory\Anaconda3\Lib_nsis.py" post_install
Execute: "C:\Users\my_user_directory\Anaconda3\pythonw.exe" -E -s "C:\Users\my_user_directory\Anaconda3\pkgs.cio-config.py" "C:\Users\my_user_directory\Downloads\python\Anaconda3-2019.07-Windows-x86_64.exe"
Created uninstaller: C:\Users\my_user_directory\Anaconda3\Uninstall-Anaconda3.exe
Completed


The bottom line is that I can not install Anaconda successfully. Help appreciated.

@joshua-theisen
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I am trying to use Conda to install a package that has failed under other installation methods. When installing Anaconda I received the same error as the OP:
Executing transaction: - WARNING conda.core.envs_manager:register_env(46): Unable to register environment. Path not writable or missing.

The ~/.conda folder was created, but is empty. How can I test if this Anaconda installation worked? Does anyone have a solution for this error?
Thanks
Josh

@akshaybabloo
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Creating ~/.conda folder before installing doesn't give me that problem anymore.

@drorata
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drorata commented Aug 20, 2019

I can also confirm the issue. Trying to install Anaconda on an EC2 instance using the following steps:

ANACONDA_INST_DIR=$HOME/anaconda3
rm -rf $ANACONDA_INST_DIR
rm -rf $HOME/tmp
mkdir $HOME/tmp
ANACONDA_INST_NAME=Anaconda3-2019.07-Linux-x86_64.sh
wget https://repo.anaconda.com/archive/${ANACONDA_INST_NAME} -O $HOME/tmp/$ANACONDA_INST_NAME
bash $HOME/tmp/$ANACONDA_INST_NAME -f -b -p $ANACONDA_INST_DIR

ended up with the following:

Preparing transaction: done
Executing transaction: - WARNING conda.core.envs_manager:register_env(46): Unable to register environment. Path not writable or missing.
  environment location: /home/ubuntu/anaconda3
  registry file: /home/ubuntu/.conda/environments.txt
done
installation finished.

If I create the directory ~/.conda before executing the installation steps, I get no warnings.

@csoja csoja added the type-bug label Aug 20, 2019
@jacob-lee
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I had this problem on Mac OS 10.14.6.

Creating the ~/.conda directory before running the script fixed it.

I deleted the ~/.conda and ~/miniconda directories and re-ran the installation script. The error re-appeared.

@freedom9393
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freedom9393 commented Aug 23, 2019

First way: Firstly, run this command to remove anaconda3 folder:

sudo rm -rf ~/anaconda3

Then, remove this line from your .bash_profile (or .bashrc):

export PATH="/Users/yourname/anaconda3/bin:$PATH"

Then reinstall anaconda :)

Second way: Create

/Users/drb/.conda/environments.txt

file and change the owner to drb from root user. If you don't have /Users/drb/.conda/environments.txt file, create it and change the owner to drb

@kemathur
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Have the same issue. MacOS Mojave 10.14.5

Same error as everyone above. The mention folder/ file not created.
Was using
bash ~/build/Miniconda3-latest-MacOSX-x86_64.sh

@AnotherSamWilson
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I am getting this error on arch linux

Preparing transaction: done
Executing transaction: - WARNING conda.core.envs_manager:register_env(46): Unable to register environment. Path not writable or missing.
  environment location: /home/sam/anaconda3
  registry file: /home/sam/.conda/environments.txt
done
installation finished.
Do you wish the installer to initialize Anaconda3
by running conda init? [yes|no]

Executed the .sh found here:
https://repo.anaconda.com/archive/Anaconda3-2019.07-Linux-x86_64.sh

System info:
OS: Arch Linux x86_64
Kernel Release: 5.2.5-arch1-1-ARCH
Packages: 546
RAM: 1616 MB / 32180 MB
Processor Type: AMD Ryzen 5 1600 Six-Core Processor

@msarahan
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Contributor

This seems like it's probably a race condition causing a permissions problem, but I haven't managed to isolate it yet. The code that is doing the registration (creation of that folder and file) is not run in parallel: https://github.com/conda/conda/blob/4.7.10/conda/core/link.py#L636-L642

The error you see is this one: https://github.com/conda/conda/blob/4.7.10/conda/core/path_actions.py#L955-L961

The path unfortunately does not appear to be configurable, because all of the calls to this function have no parameter: https://github.com/conda/conda/blob/4.7.10/conda/core/envs_manager.py#L21

As a workaround, please take the advice of many others here: mkdir ~/.conda and ignore the warning - that should allow you to move forward.

@raf2019
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raf2019 commented Aug 27, 2019

First way: Firstly, run this command to remove anaconda3 folder:

sudo rm -rf ~/anaconda3

Then, remove this line from your .bash_profile (or .bashrc):

export PATH="/Users/yourname/anaconda3/bin:$PATH"

Then reinstall anaconda :)

Second way: Create

/Users/drb/.conda/environments.txt

file and change the ownet to drb from root user. If you don't have /Users/drb/.conda/environments.txt file, create it and change the owner to drb

Same occurs to me during installation and freedom9393 solution works.
My settings:
SO: Linux MX 18.3 x64
Installation: running from usb with persistence - "persist_static" mode
HW (pendrive): sandisk 64GB usb 3.0 formatted for only this distro installation
HW (laptop): Lenovo Thinkpad T440

Thank you all

vangj added a commit to oneoffcoder/vagrant-boxes that referenced this issue Aug 27, 2019
@hyperknot
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I can replicate this by running conda in stall in a Docker image.

RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda
Preparing transaction: ...working... done
Executing transaction: ...working... WARNING conda.core.envs_manager:register_env(46): Unable to register environment. Path not writable or missing.
  environment location: /opt/conda
  registry file: /root/.conda/environments.txt
done
installation finished.

In an Ubuntu 16.04 image. After the install and update however the environments.txt file does actually get created.

@msarahan
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msarahan commented Sep 6, 2019

This will be fixed in conda 4.7.12 and later, but unfortunately we can't retroactively fix existing installers. If you see this problem, please take the advice of many others here: mkdir ~/.conda and ignore the warning - that should allow you to move forward.

@SreeChandan
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SreeChandan commented Sep 9, 2019

This will be fixed in conda 4.7.12 and later, but unfortunately we can't retroactively fix existing installers. If you see this problem, please take the advice of many others here: mkdir ~/.conda and ignore the warning - that should allow you to move forward.

creating the ~/.conda made the installation run without any errors/warnings. But I still can't directly run conda or anaconda-navigator.
If I give the full path it works.
That is:
. "anaconda-navigator" doesn't work
. "/home/[insert username]/anaconda3/bin/anaconda-navigator" works
. same for conda

[edit: Solution]
nvm sorry. I just had to close and reopen the terminal. Not sure if it was mentioned in the installation process. If it's not mentioned, add it please for us newbies :)

@phil-blain
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I had this problem today installing Miniconda3 ; it appears the miniconda installer is still at version 4.7.10, as can be seen at https://docs.conda.io/en/latest/miniconda_hashes.html or by doing

grep -a '4\.7\.10' Miniconda3-latest-Linux-x86_64.sh

after downloading the installer from https://docs.conda.io/en/latest/miniconda.html.
will this be fixed soon ?

@msarahan
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Contributor

Yes, in the next 1-2 weeks

@ContinuumIO ContinuumIO locked as resolved and limited conversation to collaborators Sep 27, 2019
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