Jupyter-notebook exploding after command conda install -c conda-forge

Question

I hope this post brings you well. I have environment issues that I would love to get assistance on.

I installed geopandas with command: conda install -c conda-forge geopandas

Then typed jupyter-notebook and got a nasty error, here is what it reads:

Traceback (most recent call last): File "/home/mathlizard/anaconda3/lib/python3.6/site-packages/notebook/services/sessions/sessionmanager.py", line 10, in import sqlite3 File "/home/mathlizard/anaconda3/lib/python3.6/sqlite3/init.py", line 23, in from sqlite3.dbapi2 import * File "/home/mathlizard/anaconda3/lib/python3.6/sqlite3/dbapi2.py", line 27, in from _sqlite3 import * ImportError: libncurses.so.6: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/mathlizard/anaconda3/bin/jupyter-notebook", line 7, in from notebook.notebookapp import main File "/home/mathlizard/anaconda3/lib/python3.6/site-packages/notebook/notebookapp.py", line 84, in from .services.sessions.sessionmanager import SessionManager File "/home/mathlizard/anaconda3/lib/python3.6/site-packages/notebook/services/sessions/sessionmanager.py", line 13, in from pysqlite2 import dbapi2 as sqlite3 ModuleNotFoundError: No module named 'pysqlite2'

My attempts

wrote the following commands:
- pip install pysqlite2
- pip install libsqlite3-dev
- sudo apt-get install libsqlite3-dev
- pip install pysqlite
- conda install pysqlite2
- conda install pysqlite
created and edited .condarc file in root directory with following lines of code:

channels: - conda-forge - defaults

UPDATES

installed pysqlite with conda install -c kbchoi pysqlite and now the error after typing jupyter-notebook is the following:

Traceback (most recent call last): File "/home/mathlizard/anaconda3/bin/jupyter-notebook", line 7, in from notebook.notebookapp import main File "/home/mathlizard/anaconda3/lib/python2.7/site-packages/notebook/notebookapp.py", line 85, in from .services.sessions.sessionmanager import SessionManager File "/home/mathlizard/anaconda3/lib/python2.7/site-packages/notebook/services/sessions/sessionmanager.py", line 13, in from pysqlite2 import dbapi2 as sqlite3 File "/home/mathlizard/anaconda3/lib/python2.7/site-packages/pysqlite2/dbapi2.py", line 28, in from pysqlite2._sqlite import * ImportError: libncurses.so.6: cannot open shared object file: No such file or directory

Background info:

which python outputs this: /home/mathlizard/anaconda3/bin/python
which jupyter outputs this: /home/mathlizard/anaconda3/bin/jupyter
my .bashrc file contains these lines of code: export PATH="/home/mathlizard/anaconda3/bin:$PATH" and export PATH="/home/mathlizard/anaconda2/bin:$PATH"
conda list generates:
Name Version Build Channel

_ipyw_jlab_nb_ext_conf 0.1.0 py27h08a7f0c_0
alabaster 0.7.10 py27he5a193a_0
anaconda 5.2.0 py27_3
anaconda-client 1.6.14 py27_0
anaconda-navigator 1.8.7 py27_0
anaconda-project 0.8.2 py27h236b58a_0
asn1crypto 0.24.0 py27_0
astroid 1.6.3 py27_0
astropy 2.0.6 py27h3010b51_1
attrs 18.1.0 py27_0
babel 2.5.3 py27_0
backports 1.0 py27h63c9359_1
backports.functools_lru_cache 1.5 py27_1
backports.shutil_get_terminal_size 1.0.0 py27h5bc021e_2
backports_abc 0.5 py27h7b3c97b_0
beautifulsoup4 4.6.0 py27h3f86ba9_1
bitarray 0.8.1 py27h14c3975_1
bkcharts 0.2 py27h241ae91_0
blas 1.0 mkl
blaze 0.11.3 py27h5f341da_0
bleach 2.1.3 py27_0
blosc 1.14.3 hdbcaa40_0
bokeh 0.12.16 py27_0
boto 2.48.0 py27h9556ac2_1
bottleneck 1.2.1 py27h21b16a3_0
bzip2 1.0.6 h14c3975_5
ca-certificates 2018.03.07 0
cairo 1.14.12 h7636065_2
cdecimal 2.3 py27h14c3975_3
certifi 2018.4.16 py27_0
cffi 1.11.5 py27h9745a5d_0
chardet 3.0.4 py27hfa10054_1
click 6.7 py27h4225b90_0
cloudpickle 0.5.3 py27_0
clyent 1.2.2 py27h7276e6c_1
colorama 0.3.9 py27h5cde069_0
conda 4.5.11 py27_0
conda-build 3.10.5 py27_0
conda-env 2.6.0 h36134e3_1
conda-verify 2.0.0 py27hf052a9d_0
configparser 3.5.0 py27h5117587_0
contextlib2 0.5.5 py27hbf4c468_0
cryptography 2.2.2 py27h14c3975_0
curl 7.60.0 h84994c4_0
cycler 0.10.0 py27hc7354d3_0
cython 0.28.2 py27h14c3975_0
cytoolz 0.9.0.1 py27h14c3975_0
dask 0.17.5 py27_0
dask-core 0.17.5 py27_0
datashape 0.5.4 py27hf507385_0
dbus 1.13.2 h714fa37_1
decorator 4.3.0 py27_0
distributed 1.21.8 py27_0
docutils 0.14 py27hae222c1_0
entrypoints 0.2.3 py27h502b47d_2
enum34 1.1.6 py27h99a27e9_1
et_xmlfile 1.0.1 py27h75840f5_0
expat 2.2.5 he0dffb1_0
fastcache 1.0.2 py27h14c3975_2
filelock 3.0.4 py27_0
flask 1.0.2 py27_1
flask-cors 3.0.4 py27_0
fontconfig 2.12.6 h49f89f6_0
freetype 2.8 hab7d2ae_1
funcsigs 1.0.2 py27h83f16ab_0
functools32 3.2.3.2 py27h4ead58f_1
futures 3.2.0 py27h7b459c0_0
get_terminal_size 1.0.0 haa9412d_0
gevent 1.3.0 py27h14c3975_0
glib 2.56.1 h000015b_0
glob2 0.6 py27hcea9cbd_0
gmp 6.1.2 h6c8ec71_1
gmpy2 2.0.8 py27h4cf3fa8_2
graphite2 1.3.11 h16798f4_2
greenlet 0.4.13 py27h14c3975_0
grin 1.2.1 py27_4
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
h5py 2.7.1 py27ha1f6525_2
harfbuzz 1.7.6 h5f0a787_1
hdf5 1.10.2 hba1933b_1
heapdict 1.0.0 py27_2
html5lib 1.0.1 py27h5233db4_0
icu 58.2 h9c2bf20_1
idna 2.6 py27h5722d68_1
imageio 2.3.0 py27_0
imagesize 1.0.0 py27_0
intel-openmp 2018.0.0 8
ipaddress 1.0.22 py27_0
ipykernel 4.8.2 py27_0
ipython 5.7.0 py27_0
ipython_genutils 0.2.0 py27h89fb69b_0
ipywidgets 7.2.1 py27_0
isort 4.3.4 py27_0
itsdangerous 0.24 py27hb8295c1_1
jbig 2.1 hdba287a_0
jdcal 1.4 py27_0
jedi 0.12.0 py27_1
jinja2 2.10 py27h4114e70_0
jpeg 9b h024ee3a_2
jsonschema 2.6.0 py27h7ed5aa4_0
jupyter 1.0.0 py27_4
jupyter_client 5.2.3 py27_0
jupyter_console 5.2.0 py27hc6bee7e_1
jupyter_core 4.4.0 py27h345911c_0
jupyterlab 0.32.1 py27_0
jupyterlab_launcher 0.10.5 py27_0
kiwisolver 1.0.1 py27hc15e7b5_0
lazy-object-proxy 1.3.1 py27h682c727_0
libcurl 7.60.0 h1ad7b7a_0
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc-ng 7.2.0 hdf63c60_3
libgfortran-ng 7.2.0 hdf63c60_3
libpng 1.6.34 hb9fc6fc_0
libsodium 1.0.16 h1bed415_0
libssh2 1.8.0 h9cfc8f7_4
libstdcxx-ng 7.2.0 hdf63c60_3
libtiff 4.0.9 he85c1e1_1
libtool 2.4.6 h544aabb_3
libxcb 1.13 h1bed415_1
libxml2 2.9.8 h26e45fe_1
libxslt 1.1.32 h1312cb7_0
llvmlite 0.23.1 py27hdbcaa40_0
locket 0.2.0 py27h73929a2_1
lxml 4.2.1 py27h23eabaa_0
lzo 2.10 h49e0be7_2
markupsafe 1.0 py27h97b2822_1
matplotlib 2.2.2 py27h0e671d2_1
mccabe 0.6.1 py27h0e7c7be_1
mistune 0.8.3 py27h14c3975_1
mkl 2018.0.2 1
mkl-service 1.1.2 py27hb2d42c5_4
mkl_fft 1.0.1 py27h3010b51_0
mkl_random 1.0.1 py27h629b387_0
more-itertools 4.1.0 py27_0
mpc 1.0.3 hec55b23_5
mpfr 3.1.5 h11a74b3_2
mpmath 1.0.0 py27h9669132_2
msgpack-python 0.5.6 py27h6bb024c_0
multipledispatch 0.5.0 py27_0
navigator-updater 0.2.1 py27_0
nbconvert 5.3.1 py27he041f76_0
nbformat 4.4.0 py27hed7f2b2_0
ncurses 6.1 hf484d3e_0
networkx 2.1 py27_0
nltk 3.3.0 py27_0
nose 1.3.7 py27heec2199_2
notebook 5.5.0 py27_0
numba 0.38.0 py27h637b7d7_0
numexpr 2.6.5 py27h7bf3b9c_0
numpy 1.14.3 py27hcd700cb_1
numpy-base 1.14.3 py27h9be14a7_1
numpydoc 0.8.0 py27_0
odo 0.5.1 py27h9170de3_0
olefile 0.45.1 py27_0
openpyxl 2.5.3 py27_0
openssl 1.0.2o h20670df_0
packaging 17.1 py27_0
pandas 0.23.0 py27h637b7d7_0
pandoc 1.19.2.1 hea2e7c5_1
pandocfilters 1.4.2 py27h428e1e5_1
pango 1.41.0 hd475d92_0
parso 0.2.0 py27_0
partd 0.3.8 py27h4e55004_0
patchelf 0.9 hf79760b_2
path.py 11.0.1 py27_0
pathlib2 2.3.2 py27_0
patsy 0.5.0 py27_0
pcre 8.42 h439df22_0
pep8 1.7.1 py27_0
pexpect 4.5.0 py27_0
pickleshare 0.7.4 py27h09770e1_0
pillow 5.1.0 py27h3deb7b8_0
pip 10.0.1 py27_0
pixman 0.34.0 hceecf20_3
pkginfo 1.4.2 py27_1
pluggy 0.6.0 py27h1f4f128_0
ply 3.11 py27_0
prompt_toolkit 1.0.15 py27h1b593e1_0
psutil 5.4.5 py27h14c3975_0
ptyprocess 0.5.2 py27h4ccb14c_0
py 1.5.3 py27_0
pycairo 1.15.4 py27h1b9232e_1
pycodestyle 2.4.0 py27_0
pycosat 0.6.3 py27ha4109ae_0
pycparser 2.18 py27hefa08c5_1
pycrypto 2.6.1 py27h14c3975_8
pycurl 7.43.0.1 py27hb7f436b_0
pyflakes 1.6.0 py27h904a57d_0
pygments 2.2.0 py27h4a8b6f5_0
pylint 1.8.4 py27_0
pyodbc 4.0.23 py27hf484d3e_0
pyopenssl 18.0.0 py27_0
pyparsing 2.2.0 py27hf1513f8_1
pyqt 5.9.2 py27h751905a_0
pysocks 1.6.8 py27_0
pytables 3.4.3 py27h02b9ad4_2
pytest 3.5.1 py27_0
python 2.7.15 h1571d57_0
python-dateutil 2.7.3 py27_0
pytz 2018.4 py27_0
pywavelets 0.5.2 py27hecda097_0
pyyaml 3.12 py27h2d70dd7_1
pyzmq 17.0.0 py27h14c3975_1
qt 5.9.5 h7e424d6_0
qtawesome 0.4.4 py27hd7914c3_0
qtconsole 4.3.1 py27hc444b0d_0
qtpy 1.4.1 py27_0
readline 7.0 ha6073c6_4
requests 2.18.4 py27hc5b0589_1
rope 0.10.7 py27hfe459b0_0
ruamel_yaml 0.15.35 py27h14c3975_1
scandir 1.7 py27h14c3975_0
scikit-image 0.13.1 py27h14c3975_1
scikit-learn 0.19.1 py27h445a80a_0
scipy 1.1.0 py27hfc37229_0
seaborn 0.8.1 py27h633ea1e_0
send2trash 1.5.0 py27_0
setuptools 39.1.0 py27_0
simplegeneric 0.8.1 py27_2
singledispatch 3.4.0.3 py27h9bcb476_0
sip 4.19.8 py27hf484d3e_0
six 1.11.0 py27h5f960f1_1
snappy 1.1.7 hbae5bb6_3
snowballstemmer 1.2.1 py27h44e2768_0
sortedcollections 0.6.1 py27_0
sortedcontainers 1.5.10 py27_0
sphinx 1.7.4 py27_0
sphinxcontrib 1.0 py27h1512b58_1
sphinxcontrib-websupport 1.0.1 py27hf906f22_1
spyder 3.2.8 py27_0
sqlalchemy 1.2.7 py27h6b74fdf_0
sqlite 3.23.1 he433501_0
ssl_match_hostname 3.5.0.1 py27h4ec10b9_2
statsmodels 0.9.0 py27h3010b51_0
subprocess32 3.5.0 py27h14c3975_0
sympy 1.1.1 py27hc28188a_0
tblib 1.3.2 py27h51fe5ba_0
terminado 0.8.1 py27_1
testpath 0.3.1 py27hc38d2c4_0
tk 8.6.7 hc745277_3
toolz 0.9.0 py27_0
tornado 5.0.2 py27_0
traitlets 4.3.2 py27hd6ce930_0
typing 3.6.4 py27_0
unicodecsv 0.14.1 py27h5062da9_0
unixodbc 2.3.6 h1bed415_0
urllib3 1.22 py27ha55213b_0
wcwidth 0.1.7 py27h9e3e1ab_0
webencodings 0.5.1 py27hff10b21_1
werkzeug 0.14.1 py27_0
wheel 0.31.1 py27_0
widgetsnbextension 3.2.1 py27_0
wrapt 1.10.11 py27h04f6869_0
xlrd 1.1.0 py27ha77178f_1
xlsxwriter 1.0.4 py27_0
xlwt 1.3.0 py27h3d85d97_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zeromq 4.2.5 h439df22_0
zict 0.1.3 py27h12c336c_0
zlib 1.2.11 ha838bed_2

Diego Quinchavil Diego Quinchavil · Accepted Answer · 2019-02-12T19:37:35

This steps works for me:

Jupyter Instance

!source activate python3( or other env. , not root )
!conda config --remove channels defaults
!conda config --add channels conda-forge
!conda install "your library"
!conda list
import "your library"

Jupyter-notebook exploding after command conda install -c conda-forge

Name Version Build Channel

1 Answers