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The following packages will be SUPERSEDED by a higher-priority channel: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 0.9.0.1 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 1.8.1.2 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 1.19.2.1 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 7.43.0.2 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 3.4.0.3 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 0.1.8.5 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.
