I needed to update the matplotlib when I encountered the following error:

conda update matplotlib
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /home/gpu-server/anaconda3

  added / updated specs:
    - matplotlib

The following NEW packages will be INSTALLED:

  libopenblas        pkgs/main/linux-64::libopenblas-0.3.3-h5a2b251_3
  setuptools         pkgs/main/linux-64::setuptools-40.6.3-py37_0

The following packages will be UPDATED:

  matplotlib                conda-forge::matplotlib-3.0.0-2 --> pkgs/main::matplotlib-3.0.2-py37h5429711_0
  numpy              conda-forge::numpy-1.15.1-py36_blas_o~ --> pkgs/main::numpy-1.15.4-py37h99e49ec_0
  numpy-base                          1.15.3-py36h81de0dd_0 --> 1.15.4-py37h2f8d375_0
  pyparsing          conda-forge/noarch::pyparsing-2.2.2-p~ --> pkgs/main/linux-64::pyparsing-2.3.1-py37_0
  python                                   3.6.8-h0371630_0 --> 3.7.2-h0371630_0
  pytz                 conda-forge/noarch::pytz-2018.6-py_0 --> pkgs/main/linux-64::pytz-2018.9-py37_0
  six                     conda-forge::six-1.11.0-py36_1001 --> pkgs/main::six-1.12.0-py37_0
  wheel                    conda-forge::wheel-0.32.2-py36_0 --> pkgs/main::wheel-0.32.3-py37_0

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            conda-forge::certifi-2018.11.29-py36_~ --> pkgs/main::certifi-2018.11.29-py37_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_1 --> pkgs/main/linux-64::cycler-0.10.0-py37_0
  kiwisolver         conda-forge::kiwisolver-1.0.1-py36h2d~ --> pkgs/main::kiwisolver-1.0.1-py37hf484d3e_0
  pip                       conda-forge::pip-18.1-py36_1000 --> pkgs/main::pip-18.1-py37_0
  python-dateutil    conda-forge/noarch::python-dateutil-2~ --> pkgs/main/linux-64::python-dateutil-2.7.5-py37_0
  sip                conda-forge::sip-4.19.8-py36hfc679d8_0 --> pkgs/main::sip-4.19.8-py37hf484d3e_0
  tornado            conda-forge::tornado-5.1.1-py36h470a2~ --> pkgs/main::tornado-5.1.1-py37h7b6447c_0

The following packages will be DOWNGRADED:

  pyqt                                 5.9.2-py36h05f1152_2 --> 5.9.2-py37h05f1152_2

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: failed

RemoveError: 'setuptools' is a dependency of conda and cannot be removed from
conda's operating environment.

After that I tried updating all conda packages, uninstalling matplotlib, installing setuptools with conda and I always get the same error:

RemoveError: 'setuptools' is a dependency of conda and cannot be removed from
conda's operating environment.

It seems like anything to do with conda's install/update/remove functionality leads to this error. Then I tried uninstalling and reinstalling the setuptools with pip. Re-installation worked but the RemoveError persisted. I have no more clue of what is going on below is my conda list output and conda env list .I have also tried switching from the base environment but the error was still there.

conda list:

(base) gpu-server@gpuserver:~$ conda list
# packages in environment at /home/gpu-server/anaconda3:
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py36_0  
absl-py                   0.6.0                    py36_0    conda-forge
alabaster                 0.7.12                     py_0    conda-forge
algopy                    0.5.7                    pypi_0    pypi
anaconda-client           1.7.1                      py_0    conda-forge
anaconda-navigator        1.9.2                    py36_0  
anaconda-project          0.8.2                      py_1    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
asn1crypto                0.24.0                py36_1003    conda-forge
astor                     0.7.1                      py_0    conda-forge
astroid                   2.0.3                    py36_0    conda-forge
astropy                   3.0.5            py36h470a237_0    conda-forge
atomicwrites              1.2.1                      py_0    conda-forge
attrs                     18.2.0                     py_0    conda-forge
automat                   0.7.0                      py_1    conda-forge
babel                     2.6.0                      py_1    conda-forge
backcall                  0.1.0                      py_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.os              0.1.1                 py36_1000    conda-forge
backports.shutil_get_terminal_size 1.0.0                      py_3    conda-forge
beautifulsoup4            4.6.3                 py36_1000    conda-forge
bitarray                  0.8.3            py36h470a237_0    conda-forge
bkcharts                  0.2                      py36_0    conda-forge
blas                      1.1                    openblas    conda-forge
blaze                     0.11.3                   py36_0    conda-forge
bleach                    3.0.2                    pypi_0    pypi
blinker                   1.4                        py_1    conda-forge
blosc                     1.14.4               hdbcaa40_0  
bokeh                     1.0.0                 py36_1000    conda-forge
boto                      2.49.0                   py36_0  
boto3                     1.9.32                     py_0    conda-forge
botocore                  1.12.33                    py_0    conda-forge
bottleneck                1.2.1            py36h7eb728f_1    conda-forge
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.6                h14c3975_5  
c-ares                    1.15.0               h470a237_0    conda-forge
ca-certificates           2018.12.5                     0  
cairo                     1.14.12              h8948797_3  
certifi                   2018.11.29            py36_1000    conda-forge
cffi                      1.11.5           py36h5e8e0c9_1    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
click                     7.0                        py_0    conda-forge
cloudpickle               0.6.1                      py_0    conda-forge
clyent                    1.2.2                      py_1    conda-forge
colorama                  0.4.0                      py_0    conda-forge
conda                     4.6.2                    py36_0  
conda-build               3.16.1                   py36_0    conda-forge
conda-env                 2.6.0                         1  
constantly                15.1.0                     py_0    conda-forge
contextlib2               0.5.5                      py_2    conda-forge
cryptography              2.4.2            py36h1ba5d50_0  
cryptography-vectors      2.3.1                 py36_1000    conda-forge
cuda92                    1.0                           0    pytorch
cudatoolkit               9.0                  h13b8566_0  
cudnn                     7.1.2                 cuda9.0_0  
curl                      7.63.0            hbc83047_1000  
cycler                    0.10.0                   pypi_0    pypi
cython                    0.29             py36hfc679d8_0    conda-forge
cytoolz                   py36h470a237_1    conda-forge
dash                      0.35.1                   pypi_0    pypi
dash-core-components      0.42.1                   pypi_0    pypi
dash-html-components      0.13.4                   pypi_0    pypi
dash-renderer             0.17.0                   pypi_0    pypi
dash-table                3.1.11                   pypi_0    pypi
dask                      0.20.0                     py_0    conda-forge
dask-core                 0.20.0                     py_0    conda-forge
datashape                 0.5.4                    py36_0    conda-forge
dbus                      1.13.2               h714fa37_1  
decorator                 4.3.0                      py_0    conda-forge
defusedxml                0.5.0                      py_1    conda-forge
distributed               1.24.0                py36_1000    conda-forge
docutils                  0.14                  py36_1001    conda-forge
entrypoints               0.2.3                 py36_1002    conda-forge
et_xmlfile                1.0.1                    py36_0    conda-forge
expat                     2.2.6                he6710b0_0  
fastcache                 1.0.2            py36h470a237_1    conda-forge
filelock                  3.0.9                      py_0    conda-forge
flask                     1.0.2                      py_2    conda-forge
flask-compress            1.4.0                    pypi_0    pypi
flask-cors                3.0.6                      py_0    conda-forge
fontconfig                2.13.0               h9420a91_0  
freetype                  2.9.1                h8a8886c_1  
fribidi                   1.0.5                h7b6447c_0  
gast                      0.2.0                      py_0    conda-forge
gensim                    3.5.0                    py36_0    conda-forge
get_terminal_size         1.0.0                haa9412d_0  
gevent                    1.3.6            py36h470a237_0    conda-forge
glib                      2.56.2               hd408876_0  
glob2                     0.6                        py_0    conda-forge
gmp                       6.1.2                h6c8ec71_1  
gmpy2                     2.0.8            py36hb705a9b_2    conda-forge
graphite2                 1.3.12               h23475e2_2  
greenlet                  0.4.13                   py36_0    conda-forge
grpcio                    1.16.1           py36hf8bcb03_1  
gst-plugins-base          1.14.0               hbbd80ab_1  
gstreamer                 1.14.0               hb453b48_1  
h5py                      2.8.0            py36h7eb728f_3    conda-forge
harfbuzz                  1.8.8                hffaf4a1_0  
hdf5                      1.10.2               hba1933b_1  
heapdict                  1.0.0                 py36_1000    conda-forge
html5lib                  1.0.1                      py_0    conda-forge
hyperlink                 17.3.1                     py_0    conda-forge
icu                       58.2                 h9c2bf20_1  
idna                      2.7                   py36_1002    conda-forge
imageio                   2.3.0                      py_1    conda-forge
imagesize                 1.1.0                      py_0    conda-forge
importlib_metadata        0.6                      py36_0    conda-forge
incremental               17.5.0                     py_0    conda-forge
intel-openmp              2019.0                      118  
ipykernel                 5.1.0              pyh24bf2e0_0    conda-forge
ipython                   7.1.1           py36h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
isort                     4.3.4                 py36_1000    conda-forge
itsdangerous              1.1.0                      py_0    conda-forge
jbig                      2.1                  hdba287a_0  
jdcal                     1.4                        py_1    conda-forge
jedi                      0.13.1                py36_1000    conda-forge
jeepney                   0.4                        py_0    conda-forge
jinja2                    2.10                       py_1    conda-forge
jmespath                  0.9.3                      py_1    conda-forge
jpeg                      9b                   h024ee3a_2  
jsonschema                2.6.0                 py36_1002    conda-forge
jupyter                   1.0.0                      py_1    conda-forge
jupyter_client            5.2.3                      py_1    conda-forge
jupyter_console           6.0.0                      py_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyterlab                0.35.3                   py36_0    conda-forge
jupyterlab_launcher       0.13.1                     py_2    conda-forge
jupyterlab_server         0.2.0                      py_0    conda-forge
keras-applications        1.0.6                    pypi_0    pypi
keras-preprocessing       1.0.5                    pypi_0    pypi
keyring                   16.0.0                   py36_0    conda-forge
kiwisolver                1.0.1            py36h2d50403_2    conda-forge
krb5                      1.16.1               h173b8e3_7  
lazy-object-proxy         1.3.1            py36h470a237_0    conda-forge
libarchive                3.3.3                h5d8350f_5  
libcurl                   7.63.0            h20c2e04_1000  
libedit                   3.1.20170329         h6b74fdf_2  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 8.2.0                hdf63c60_1  
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.3.0                hdf63c60_0  
libiconv                  1.15                 h470a237_3    conda-forge
libpng                    1.6.36               hbc83047_0  
libprotobuf               3.6.1                hd28b015_0    conda-forge
libsodium                 1.0.16               h1bed415_0  
libssh2                   1.8.0                h1ba5d50_4  
libstdcxx-ng              8.2.0                hdf63c60_1  
libtiff                   4.0.9                he85c1e1_2  
libtool                   2.4.6                h544aabb_3  
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.13                 h1bed415_1  
libxml2                   2.9.8                h26e45fe_1  
libxslt                   1.1.32               h1312cb7_0  
llvmlite                  0.25.0           py36hd28b015_1    conda-forge
locket                    0.2.0                      py_2    conda-forge
lxml                      4.2.5            py36hc9114bc_0    conda-forge
lz4-c                         h14c3975_0  
lzo                       2.10                 h49e0be7_2  
markdown                  2.6.11                     py_0    conda-forge
markupsafe                1.0              py36h470a237_1    conda-forge
matplotlib                3.0.0                         2    conda-forge
matplotlib-base           3.0.0            py36hc039c98_2    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
mistune                   0.8.4            py36h470a237_0    conda-forge
mkl                       2019.0                      118  
mkl-service               1.1.2            py36h90e4bf4_5  
mkl_fft                   1.0.6                    py36_0    conda-forge
mkl_random                1.0.1                    py36_0    conda-forge
more-itertools            4.3.0                 py36_1000    conda-forge
mpc                       1.1.0                h10f8cd9_1  
mpfr                      4.0.1                hdf1c602_3  
mpmath                    1.0.0                      py_1    conda-forge
msgpack-python            0.5.6            py36h2d50403_3    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
navigator-updater         0.2.1                    py36_0  
nbconvert                 5.4.0                         1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
nccl                      1.3.5                 cuda9.0_0  
ncurses                   6.1                  hf484d3e_0  
networkx                  2.2                        py_1    conda-forge
ninja                     1.8.2                h2d50403_1    conda-forge
nltk                      3.2.5                      py_0    conda-forge
nose                      1.3.7                 py36_1002    conda-forge
notebook                  5.7.0                 py36_1000    conda-forge
numba                     0.40.0           py36hf8a1672_0    conda-forge
numdifftools              0.9.20                   pypi_0    pypi
numexpr                   2.6.8            py36hf8a1672_0    conda-forge
numpy                     1.15.1          py36_blas_openblashd3ea46f_0    conda-forge
numpy-base                1.15.3           py36h81de0dd_0  
numpydoc                  0.8.0                      py_1    conda-forge
oauthlib                  2.1.0                      py_0    conda-forge
odo                       0.5.1                      py_1    conda-forge
olefile                   0.46                       py_0    conda-forge
openblas                  0.2.20                        8    conda-forge
openpyxl                  2.5.9                      py_0    conda-forge
openssl                   1.1.1a               h7b6447c_0  
packaging                 18.0                       py_0    conda-forge
pandas                    0.23.4           py36hf8a1672_0    conda-forge
pandoc                       hea2e7c5_1  
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.42.4               h049681c_0  
parso                     0.3.1                      py_0    conda-forge
partd                     0.3.9                      py_0    conda-forge
patchelf                  0.9                  hf484d3e_2  
path.py                   11.5.0                     py_0    conda-forge
pathlib2                  2.3.2                 py36_1000    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.42                 h439df22_0  
pep8                      1.7.1                      py_0    conda-forge
pexpect                   4.6.0                 py36_1000    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
pillow                    5.3.0            py36h34e0f95_0  
pip                       18.1                  py36_1000    conda-forge
pixman                    0.34.0               hceecf20_3  
pkginfo                   1.4.2                      py_1    conda-forge
plotly                    3.6.0                    py36_0    plotly
pluggy                    0.8.0                      py_0    conda-forge
ply                       3.11                       py_1    conda-forge
prometheus_client         0.4.2                      py_0    conda-forge
prompt_toolkit            2.0.6                      py_0    conda-forge
protobuf                  3.6.1            py36hfc679d8_1    conda-forge
psutil                    5.4.7            py36h470a237_1    conda-forge
ptyprocess                0.6.0                 py36_1000    conda-forge
py                        1.7.0                      py_0    conda-forge
pyasn1                    0.4.4                      py_1    conda-forge
pyasn1-modules            0.2.1                      py_0    conda-forge
pycodestyle               2.4.0                      py_1    conda-forge
pycosat                   0.6.3            py36h470a237_1    conda-forge
pycparser                 2.19                       py_0    conda-forge
pycrypto                  2.6.1            py36h470a237_2    conda-forge
pycurl                   py36h1ba5d50_0  
pyflakes                  2.0.0                      py_0    conda-forge
pyflux                    0.4.15                   pypi_0    pypi
pygments                  2.2.0                      py_1    conda-forge
pyhamcrest                1.9.0                      py_2    conda-forge
pyjwt                     1.6.4                      py_0    conda-forge
pylint                    2.1.1                    py36_0    conda-forge
pyodbc                    4.0.24           py36hfc679d8_0    conda-forge
pyopenssl                 18.0.0                py36_1000    conda-forge
pyparsing                 2.3.0                    pypi_0    pypi
pyqt                      5.9.2            py36h05f1152_2  
pysocks                   1.6.8                 py36_1002    conda-forge
pytables                  3.4.4            py36h4f72b40_1    conda-forge
pytest                    3.9.3                 py36_1000    conda-forge
pytest-arraydiff          0.2                        py_0    conda-forge
pytest-astropy            0.4.0                      py_0    conda-forge
pytest-doctestplus        0.1.3                      py_0    conda-forge
pytest-openfiles          0.3.0                      py_0    conda-forge
pytest-remotedata         0.3.0                      py_0    conda-forge
python                    3.6.8                h0371630_0  
python-crfsuite           0.9.6            py36h2d50403_0    conda-forge
python-dateutil           2.7.5                      py_0    conda-forge
python-libarchive-c       2.8                   py36_1004    conda-forge
pytorch                   0.4.1            py36ha74772b_0  
pytz                      2018.6                     py_0    conda-forge
pywavelets                1.0.1            py36h7eb728f_0    conda-forge
pyyaml                    3.13             py36h470a237_1    conda-forge
pyzmq                     17.1.2           py36hae99301_1    conda-forge
qt                        5.9.7                h5867ecd_1  
qtawesome                 0.5.2              pyh8a2030e_0    conda-forge
qtconsole                 4.4.2                      py_1    conda-forge
qtpy                      1.5.2              pyh8a2030e_0    conda-forge
readline                  7.0                  h7b6447c_5  
requests                  2.20.0                py36_1000    conda-forge
requests-oauthlib         1.0.0                      py_1    conda-forge
retrying                  1.3.3                    py36_2  
rope                      0.10.7                     py_1    conda-forge
ruamel_yaml               0.15.71          py36h470a237_0    conda-forge
s3transfer                0.1.13                py36_1001    conda-forge
scikit-image              0.14.1           py36hfc679d8_0    conda-forge
scikit-learn              0.20.0           py36h4989274_1  
scipy                     1.1.0           py36_blas_openblash7943236_201    conda-forge
seaborn                   0.9.0                    pypi_0    pypi
secretstorage             3.1.0                 py36_1001    conda-forge
send2trash                1.5.0                      py_0    conda-forge
service_identity          17.0.0                     py_0    conda-forge
setuptools                40.7.3                   pypi_0    pypi
simplegeneric             0.8.1                      py_1    conda-forge
singledispatch                 py36_1000    conda-forge
sip                       4.19.8           py36hfc679d8_0    conda-forge
six                       1.11.0                   pypi_0    pypi
smart_open                1.7.1                      py_0    conda-forge
snappy                    1.1.7                hbae5bb6_3  
snowballstemmer           1.2.1                      py_1    conda-forge
sortedcollections         1.0.1                      py_1    conda-forge
sortedcontainers          2.0.5                      py_0    conda-forge
sphinx                    1.8.1                 py36_1000    conda-forge
sphinxcontrib             1.0                      py36_1  
sphinxcontrib-websupport  1.1.0                      py_1    conda-forge
spyder                    3.2.8                    py36_0    conda-forge
spyder-kernels            1.1.0                      py_0    conda-forge
sqlalchemy                1.2.12           py36h470a237_0    conda-forge
sqlite                    3.26.0               h7b6447c_0  
statsmodels               0.9.0            py36h7eb728f_0    conda-forge
sympy                     1.3                   py36_1000    conda-forge
tblib                     1.3.2                      py_1    conda-forge
tensorboard               1.11.0                   pypi_0    pypi
tensorflow                1.10.0                   py36_0    conda-forge
tensorflow-gpu            1.11.0                   pypi_0    pypi
termcolor                 1.1.0                      py_2    conda-forge
terminado                 0.8.1                 py36_1001    conda-forge
testpath                  0.4.2                 py36_1000    conda-forge
tk                        8.6.8                hbc83047_0  
toolz                     0.9.0                      py_1    conda-forge
torchfile                 0.1.0                      py_0    conda-forge
torchvision               0.2.1                 py36_1000    conda-forge
tornado                   5.1.1            py36h470a237_0    conda-forge
tqdm                      4.28.1                     py_0    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
twisted                   18.9.0           py36h470a237_0    conda-forge
twython                   3.7.0                      py_0    conda-forge
typed-ast                 1.1.0                    py36_0    conda-forge
unicodecsv                0.14.1                     py_1    conda-forge
unidecode                 1.0.23                   py36_0  
unixodbc                  2.3.7                h14c3975_0  
urllib3                   1.23                  py36_1001    conda-forge
visdom                                 0    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                    pypi_0    pypi
websocket-client          0.54.0                py36_1000    conda-forge
werkzeug                  0.14.1                     py_0    conda-forge
wheel                     0.32.2                   py36_0    conda-forge
widgetsnbextension        3.4.2                 py36_1000    conda-forge
wrapt                     1.10.11          py36h470a237_1    conda-forge
xlrd                      1.1.0                      py_2    conda-forge
xlsxwriter                1.1.2                      py_0    conda-forge
xlwt                      1.3.0                      py_1    conda-forge
xz                        5.2.4                h14c3975_4  
yaml                      0.1.7                had09818_2  
zeromq                    4.2.5                hf484d3e_1  
zict                      0.1.3                      py_0    conda-forge
zlib                      1.2.11               ha838bed_2  
zope                      1.0                      py36_1  
zope.interface            4.6.0            py36h470a237_0    conda-forge
zstd                      1.3.7                h0b5b093_0

conda env list:

(base) gpu-server@gpuserver:~$ conda env list
# conda environments:
base                  *  /home/gpu-server/anaconda3

Any help or insight about what could be wrong is appreciated.

6 Answers 6


I think this issue in github may be related. This response mentions doing an update of conda using the force flag, which seemed to also work for users who reported that a normal update without the flag didn't work:

conda update --force conda

I'm not sure why the above answer had negative rating.

I had conda running for some time ... tonight I updated, and then resulted in every conda action resulting in:

RemoveError: 'setuptools' is a dependency of conda and cannot be removed from
conda's operating environment.

The only thing that actually worked was

conda install -c anaconda setuptools

After which sanity was restored. In between correction attempts I tried to create a new environment which always failed with the same error. After the fix above, I found that the desired environment did not exist in 'conda env list' but it refused to create it giving an error that it already existed. I needed to go into my ~/miniconda3/envs directory where I found the offending directory, deleted it, and was able to create a desired.

  • This worked for me as well. Thanks! Aug 28, 2019 at 15:50

setuptools is not installed by conda but pip, so you need to uninstall setuptools by pip

pip uninstall setuptools

and reinstall it though conda:

conda install setuptools

Try to reinstall the dependency:

conda install -c anaconda setuptools


This was the only thing that worked for me, when using miniconda in pwsh on a Win8 machine.

# Remove index cache, lock files, unused cache packages, and tarballs.
conda clean -a -vv

conda deactivate
conda update -y -n base -c defaults conda --force
conda activate
conda update -y --force conda
pip install -U setuptools
  • 1
    Old post, but just to say this is the only solution that worked for me when I encountered this problem just now.
    – os1
    Feb 8 at 20:03

Adding the potentially obvious, which is the only solution that worked for me (I tried all of the above to no avail):

conda update -n base conda setuptools

Essentially, tell conda to not remove setuptools if it's so precious.

Note: It's possible that if setuptools was installed before using pip instead of conda, you need to apply easton's solution before this one.

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