segfault when opening any R notebook

[stevenpur]

No description provided.

[stevenpur]

Behavior:
Jupyter kernal stuck at: "kernel starting, please wait..." whenever I open a R kernel jupyter notebook.

Error message from the terminal:

jupyter notebook ~/OneDrive\ -\ OnTheHub\ -\ The\ University\ of\ Oxford/hbv_covar\ \(original\)/Produce_association_test.ipynb
[I 21:50:40.465 NotebookApp] The port 8888 is already in use, trying another port.
[I 21:50:40.512 NotebookApp] JupyterLab extension loaded from /Users/stevenlin/anaconda3/lib/python3.7/site-packages/jupyterlab
[I 21:50:40.512 NotebookApp] JupyterLab application directory is /Users/stevenlin/anaconda3/share/jupyter/lab
[I 21:50:40.514 NotebookApp] Serving notebooks from local directory: /Users/stevenlin/OneDrive - OnTheHub - The University of Oxford/hbv_covar (original)
[I 21:50:40.514 NotebookApp] The Jupyter Notebook is running at:
[I 21:50:40.514 NotebookApp] http://localhost:8889/?token=315d5c5b0dcfde7b1c063f4fa90d584257df00e48a6c8b10
[I 21:50:40.514 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 21:50:40.526 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///Users/stevenlin/Library/Jupyter/runtime/nbserver-14280-open.html
    Or copy and paste one of these URLs:
        http://localhost:8889/?token=315d5c5b0dcfde7b1c063f4fa90d584257df00e48a6c8b10
[W 21:50:42.811 NotebookApp] Notebook Produce_association_test.ipynb is not trusted
[I 21:50:43.840 NotebookApp] Kernel started: 0889f887-70be-4433-9fc9-b0d974c151ec

 caught segfault
address 0x18, cause 'memory not mapped'

Traceback:
 1: UUIDgenerate()
 2: new_reply(msg_type, parent_msg)
 3: send_response("status", msg, "iopub", list(execution_state = "busy"))
 4: handle_shell()
 5: kernel$run()
 6: IRkernel::main()
An irrecoverable exception occurred. R is aborting now ...

operating system: macos 10.14.3

conda version: conda 4.6.7

conda info

    active environment : base
    active env location : /Users/stevenlin/anaconda3
            shell level : 1
       user config file : /Users/stevenlin/.condarc
 populated config files : /Users/stevenlin/.condarc
          conda version : 4.6.7
    conda-build version : 3.17.8
         python version : 3.7.2.final.0
       base environment : /Users/stevenlin/anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/stevenlin/anaconda3/pkgs
                          /Users/stevenlin/.conda/pkgs
       envs directories : /Users/stevenlin/anaconda3/envs
                          /Users/stevenlin/.conda/envs
               platform : osx-64
             user-agent : conda/4.6.7 requests/2.21.0 CPython/3.7.2 Darwin/18.2.0 OSX/10.14.3
                UID:GID : 501:20
             netrc file : None
           offline mode : False

conda list --show-channel-urls

# packages in environment at /Users/stevenlin/anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0    defaults
_r-mutex                  1.0.0               anacondar_1    defaults
alabaster                 0.7.12                   py37_0    defaults
anaconda                  custom                   py37_0    defaults
anaconda-client           1.7.2                    py37_0    defaults
anaconda-navigator        1.9.6                    py37_0    defaults
anaconda-project          0.8.2                    py37_0    defaults
appnope                   0.1.0                    py37_0    defaults
appscript                 1.1.0            py37h1de35cc_0    defaults
asn1crypto                0.24.0                   py37_0    defaults
astroid                   2.1.0                    py37_0    defaults
astropy                   3.1.2            py37h1de35cc_0    defaults
atomicwrites              1.3.0                      py_0    defaults
attrs                     18.2.0           py37h28b3542_0    defaults
babel                     2.6.0                    py37_0    defaults
backcall                  0.1.0                    py37_0    defaults
backports                 1.0                      py37_1    defaults
backports.os              0.1.1                    py37_0    defaults
backports.shutil_get_terminal_size 1.0.0                    py37_2    defaults
beautifulsoup4            4.7.1                    py37_1    defaults
bitarray                  0.8.3            py37h1de35cc_0    defaults
bkcharts                  0.2                      py37_0    defaults
blas                      1.0                         mkl    defaults
blaze                     0.11.3                   py37_0    defaults
bleach                    3.1.0                    py37_0    defaults
blosc                     1.15.0               hd9629dc_0    defaults
bokeh                     1.0.4                    py37_0    defaults
boto                      2.49.0                   py37_0    defaults
bottleneck                1.2.1            py37h1d22016_1    defaults
bwidget                   1.9.11                        1    defaults
bzip2                     1.0.6                h1de35cc_5    defaults
ca-certificates           2019.1.23                     0    defaults
cairo                     1.14.12              hc4e6be7_4    defaults
cctools                   895                           1    defaults
certifi                   2018.11.29               py37_0    defaults
cffi                      1.12.1           py37hb5b8e2f_0    defaults
chardet                   3.0.4                    py37_1    defaults
clang                     4.0.1                         1    defaults
clang_osx-64              4.0.1               h1ce6c1d_11    defaults
clangxx                   4.0.1                         1    defaults
clangxx_osx-64            4.0.1               h22b1bf0_11    defaults
click                     7.0                      py37_0    defaults
cloudpickle               0.8.0                    py37_0    defaults
clyent                    1.2.2                    py37_1    defaults
colorama                  0.4.1                    py37_0    defaults
compiler-rt               4.0.1                hcfea43d_1    defaults
conda                     4.6.7                    py37_0    defaults
conda-build               3.17.8                   py37_0    defaults
conda-env                 2.6.0                         1    defaults
conda-verify              3.1.1                    py37_0    defaults
contextlib2               0.5.5                    py37_0    defaults
cryptography              2.5              py37ha12b0ac_0    defaults
curl                      7.63.0            ha441bb4_1000    defaults
cycler                    0.10.0                   py37_0    defaults
cython                    0.29.5           py37h0a44026_0    defaults
cytoolz                   0.9.0.1          py37h1de35cc_1    defaults
dask                      1.1.3                      py_0    defaults
dask-core                 1.1.3                      py_0    defaults
datashape                 0.5.4                    py37_1    defaults
dbus                      1.13.6               h90a0687_0    defaults
decorator                 4.3.2                    py37_0    defaults
defusedxml                0.5.0                    py37_1    defaults
distributed               1.26.0                   py37_1    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                 1.0.2            py37h1de35cc_2    defaults
filelock                  3.0.10                   py37_0    defaults
flask                     1.0.2                    py37_1    defaults
flask-cors                3.0.7                    py37_0    defaults
fontconfig                2.13.0               h5d5b041_1    defaults
freetype                  2.9.1                hb4e5f40_0    defaults
fribidi                   1.0.5                h1de35cc_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
gfortran_osx-64           4.8.5                h22b1bf0_8    defaults
glib                      2.56.2               hd9629dc_0    defaults
glob2                     0.6                      py37_1    defaults
gmp                       6.1.2                hb37e062_1    defaults
gmpy2                     2.0.8            py37h6ef4df4_2    defaults
graphite2                 1.3.13               h2098e52_0    defaults
greenlet                  0.4.15           py37h1de35cc_0    defaults
gsl                       2.4                  h1de35cc_4    defaults
h5py                      2.9.0            py37h3134771_0    defaults
harfbuzz                  1.8.8                hb8d4a28_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        0.7                      py37_0    defaults
intel-openmp              2019.1                      144    defaults
ipykernel                 5.1.0            py37h39e3cac_0    defaults
ipython                   7.3.0            py37h39e3cac_0    defaults
ipython_genutils          0.2.0                    py37_0    defaults
ipywidgets                7.4.2                    py37_0    defaults
isort                     4.3.8                    py37_0    defaults
itsdangerous              1.1.0                    py37_0    defaults
jbig                      2.1                  h4d881f8_0    defaults
jdcal                     1.4                      py37_0    defaults
jedi                      0.13.3                   py37_0    defaults
jinja2                    2.10                     py37_0    defaults
jpeg                      9b                   he5867d9_2    defaults
jsonschema                2.6.0                    py37_0    defaults
jupyter                   1.0.0                    py37_7    defaults
jupyter_client            5.2.4                    py37_0    defaults
jupyter_console           6.0.0                    py37_0    defaults
jupyter_core              4.4.0                    py37_0    defaults
jupyterlab                0.35.3                   py37_0    defaults
jupyterlab_server         0.2.0                    py37_0    defaults
keyring                   18.0.0                   py37_0    defaults
kiwisolver                1.0.1            py37h0a44026_0    defaults
krb5                      1.16.1               hddcf347_7    defaults
lazy-object-proxy         1.3.1            py37h1de35cc_2    defaults
ld64                      274.2                         1    defaults
libarchive                3.3.3                h786848e_5    defaults
libcurl                   7.63.0            h051b688_1000    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
libopenblas               0.3.3                hdc02c5d_3    defaults
libpng                    1.6.36               ha441bb4_0    defaults
libsodium                 1.0.16               h3efe00b_0    defaults
libssh2                   1.8.0                ha12b0ac_4    defaults
libtiff                   4.0.10               hcb84e12_2    defaults
libxml2                   2.9.9                hab757c2_0    defaults
libxslt                   1.1.33               h33a18ac_0    defaults
llvm                      4.0.1                         1    defaults
llvm-lto-tapi             4.0.1                         1    defaults
llvm-openmp               4.0.1                hcfea43d_1    defaults
llvmlite                  0.27.0           py37h8c7ce04_0    defaults
locket                    0.2.0                    py37_1    defaults
lxml                      4.3.1            py37hef8c89e_0    defaults
lz4-c                     1.8.1.2              h1de35cc_0    defaults
lzo                       2.10                 h362108e_2    defaults
make                      4.2.1                h3efe00b_1    defaults
markupsafe                1.1.1            py37h1de35cc_0    defaults
matplotlib                3.0.2            py37h54f8f79_0    defaults
mccabe                    0.6.1                    py37_1    defaults
mistune                   0.8.4            py37h1de35cc_0    defaults
mkl                       2019.1                      144    defaults
mkl-service               1.1.2            py37hfbe908c_5    defaults
mkl_fft                   1.0.10           py37h5e564d8_0    defaults
mkl_random                1.0.2            py37h27c97d8_0    defaults
more-itertools            5.0.0                    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                 5.3.1                    py37_0    defaults
nbformat                  4.4.0                    py37_0    defaults
ncurses                   6.1                  h0a44026_1    defaults
networkx                  2.2                      py37_1    defaults
nltk                      3.4                      py37_1    defaults
nose                      1.3.7                    py37_2    defaults
notebook                  5.7.4                    py37_0    defaults
numba                     0.42.0           py37h6440ff4_0    defaults
numexpr                   2.6.9            py37h7413580_0    defaults
numpy                     1.16.2           py37hacdab7b_0    defaults
numpy-base                1.16.2           py37h6575580_0    defaults
numpydoc                  0.8.0                    py37_0    defaults
odo                       0.5.1                    py37_0    defaults
olefile                   0.46                     py37_0    defaults
openpyxl                  2.6.0                    py37_0    defaults
openssl                   1.1.1b               h1de35cc_1    defaults
packaging                 19.0                     py37_0    defaults
pandas                    0.24.1           py37h0a44026_0    defaults
pandoc                    2.2.3.2                       0    defaults
pandocfilters             1.4.2                    py37_1    defaults
pango                     1.42.4               h060686c_0    defaults
parso                     0.3.4                    py37_0    defaults
partd                     0.3.9                    py37_0    defaults
path.py                   11.5.0                   py37_0    defaults
pathlib2                  2.3.3                    py37_0    defaults
patsy                     0.5.1                    py37_0    defaults
pcre                      8.42                 h378b8a2_0    defaults
pep8                      1.7.1                    py37_0    defaults
pexpect                   4.6.0                    py37_0    defaults
pickleshare               0.7.5                    py37_0    defaults
pillow                    5.4.1            py37hb68e598_0    defaults
pip                       19.0.3                   py37_0    defaults
pixman                    0.36.0               h1de35cc_0    defaults
pkginfo                   1.5.0.1                  py37_0    defaults
pluggy                    0.9.0                    py37_0    defaults
ply                       3.11                     py37_0    defaults
prometheus_client         0.6.0                    py37_0    defaults
prompt_toolkit            2.0.9                    py37_0    defaults
psutil                    5.5.0            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                    7.43.0.2         py37ha12b0ac_0    defaults
pyflakes                  2.1.0                    py37_0    defaults
pygments                  2.3.1                    py37_0    defaults
pylint                    2.2.2                    py37_0    defaults
pyodbc                    4.0.26           py37h0a44026_0    defaults
pyopenssl                 19.0.0                   py37_0    defaults
pyparsing                 2.3.1                    py37_0    defaults
pyqt                      5.9.2            py37h655552a_2    defaults
pysocks                   1.6.8                    py37_0    defaults
pytables                  3.4.4            py37h5bccee9_0    defaults
pytest                    4.3.0                    py37_0    defaults
pytest-arraydiff          0.3              py37h39e3cac_0    defaults
pytest-astropy            0.5.0                    py37_0    defaults
pytest-doctestplus        0.2.0                    py37_0    defaults
pytest-openfiles          0.3.2                    py37_0    defaults
pytest-remotedata         0.3.1                    py37_0    defaults
python                    3.7.2                haf84260_0    defaults
python-dateutil           2.8.0                    py37_0    defaults
python-libarchive-c       2.8                      py37_6    defaults
python.app                2                        py37_9    defaults
pytz                      2018.9                   py37_0    defaults
pywavelets                1.0.1            py37h1d22016_0    defaults
pyyaml                    3.13             py37h1de35cc_0    defaults
pyzmq                     17.1.2           py37h1de35cc_0    defaults
qt                        5.9.7                h468cd18_1    defaults
qtawesome                 0.5.6                      py_0    defaults
qtconsole                 4.4.3                    py37_0    defaults
qtpy                      1.6.0                      py_0    defaults
r                         3.5.1                    r351_0    r
r-abind                   1.4_5            r351hf348343_0    r
r-assertthat              0.2.0            r351hf348343_0    r
r-backports               1.1.2            r351h6402f54_0    r
r-base                    3.5.1                h539fb6c_1    r
r-base64enc               0.1_3            r351h6402f54_4    r
r-bh                      1.66.0_1         r351hf348343_0    r
r-bindr                   0.1.1            r351hf348343_0    r
r-bindrcpp                0.2.2            r351h32998d9_0    r
r-boot                    1.3_20           r351hf348343_0    r
r-broom                   0.5.0            r351hf348343_0    r
r-callr                   2.0.4            r351hf348343_0    r
r-caret                   6.0_80           r351h6402f54_0    r
r-cellranger              1.1.0            r351hf348343_0    r
r-class                   7.3_14           r351h6402f54_4    r
r-cli                     1.0.0            r351h6115d3f_0    r
r-clipr                   0.4.1            r351hf348343_0    r
r-cluster                 2.0.7_1          r351h0b560c1_0    r
r-codetools               0.2_15           r351hf348343_0    r
r-colorspace              1.3_2            r351h6402f54_0    r
r-crayon                  1.3.4            r351hf348343_0    r
r-curl                    3.2              r351h6402f54_0    r
r-cvst                    0.2_2            r351hf348343_0    r
r-data.table              1.11.4           r351h6402f54_0    r
r-dbi                     1.0.0            r351hf348343_0    r
r-dbplyr                  1.2.2            r351hf348343_0    r
r-ddalpha                 1.3.4            r351h4496799_0    r
r-deoptimr                1.0_8            r351hf348343_0    r
r-dichromat               2.0_0            r351hf348343_4    r
r-digest                  0.6.15           r351h6402f54_0    r
r-dimred                  0.1.0            r351hf348343_0    r
r-dplyr                   0.7.6            r351h32998d9_0    r
r-drr                     0.0.3            r351hf348343_0    r
r-essentials              3.5.1                    r351_0    r
r-evaluate                0.11             r351hf348343_0    r
r-fansi                   0.2.3            r351h6402f54_0    r
r-forcats                 0.3.0            r351hf348343_0    r
r-foreach                 1.4.4            r351hf348343_0    r
r-foreign                 0.8_71           r351h6402f54_0    r
r-formatr                 1.5              r351hf348343_0    r
r-geometry                0.3_6            r351h6402f54_0    r
r-ggplot2                 3.0.0            r351hf348343_0    r
r-glmnet                  2.0_16           r351h0b560c1_0    r
r-glue                    1.3.0            r351h6402f54_0    r
r-gower                   0.1.2            r351h6402f54_0    r
r-gtable                  0.2.0            r351hf348343_0    r
r-haven                   1.1.2            r351h32998d9_0    r
r-hexbin                  1.27.2           r351h0b560c1_0    r
r-highr                   0.7              r351hf348343_0    r
r-hms                     0.4.2            r351hf348343_0    r
r-htmltools               0.3.6            r351h32998d9_0    r
r-htmlwidgets             1.2              r351hf348343_0    r
r-httpuv                  1.4.5            r351h32998d9_0    r
r-httr                    1.3.1            r351hf348343_0    r
r-ipred                   0.9_6            r351h6402f54_0    r
r-irdisplay               0.5.0            r351hf348343_0    r
r-irkernel                0.8.12                   r351_0    r
r-iterators               1.0.10           r351hf348343_0    r
r-jsonlite                1.5              r351h6402f54_0    r
r-kernlab                 0.9_26           r351h46e27c5_0    r
r-kernsmooth              2.23_15          r351h0b560c1_4    r
r-knitr                   1.20             r351hf348343_0    r
r-labeling                0.3              r351hf348343_4    r
r-later                   0.7.3            r351h32998d9_0    r
r-lattice                 0.20_35          r351h6402f54_0    r
r-lava                    1.6.2            r351hf348343_0    r
r-lazyeval                0.2.1            r351h6402f54_0    r
r-lubridate               1.7.4            r351h32998d9_0    r
r-magic                   1.5_8            r351hf348343_0    r
r-magrittr                1.5              r351hf348343_4    r
r-maps                    3.3.0            r351h6402f54_0    r
r-markdown                0.8              r351h6402f54_0    r
r-mass                    7.3_50           r351h6402f54_0    r
r-matrix                  1.2_14           r351h6402f54_0    r
r-mgcv                    1.8_24           r351h6402f54_0    r
r-mime                    0.5              r351h6402f54_0    r
r-modelmetrics            1.1.0            r351h32998d9_0    r
r-modelr                  0.1.2            r351hf348343_0    r
r-munsell                 0.5.0            r351hf348343_0    r
r-nlme                    3.1_137          r351h0b560c1_0    r
r-nnet                    7.3_12           r351h6402f54_0    r
r-numderiv                2016.8_1         r351hf348343_0    r
r-openssl                 1.0.2            r351h46e59ec_1    r
r-pbdzmq                  0.3_3            r351h32998d9_0    r
r-pillar                  1.3.0            r351hf348343_0    r
r-pkgconfig               2.0.1            r351hf348343_0    r
r-plogr                   0.2.0            r351hf348343_0    r
r-pls                     2.6_0            r351hf348343_0    r
r-plyr                    1.8.4            r351h32998d9_0    r
r-praise                  1.0.0            r351hf348343_4    r
r-processx                3.1.0            r351h32998d9_0    r
r-prodlim                 2018.04.18       r351h32998d9_0    r
r-promises                1.0.1            r351h32998d9_0    r
r-purrr                   0.2.5            r351h6402f54_0    r
r-quantmod                0.4_13           r351hf348343_0    r
r-r6                      2.2.2            r351hf348343_0    r
r-randomforest            4.6_14           r351h0b560c1_0    r
r-rbokeh                  0.6.3                    r351_0    r
r-rcolorbrewer            1.1_2            r351hf348343_0    r
r-rcpp                    0.12.18          r351h32998d9_0    r
r-rcpproll                0.3.0            r351h32998d9_0    r
r-readr                   1.1.1            r351h32998d9_0    r
r-readxl                  1.1.0            r351h32998d9_0    r
r-recipes                 0.1.3            r351hf348343_0    r
r-recommended             3.5.1                    r351_0    r
r-rematch                 1.0.1            r351hf348343_0    r
r-repr                    0.15.0           r351hf348343_0    r
r-reprex                  0.2.0            r351hf348343_0    r
r-reshape2                1.4.3            r351h32998d9_0    r
r-rlang                   0.2.1            r351h6402f54_0    r
r-rmarkdown               1.10             r351hf348343_0    r
r-robustbase              0.93_2           r351h0b560c1_0    r
r-rpart                   4.1_13           r351h6402f54_0    r
r-rprojroot               1.3_2            r351hf348343_0    r
r-rstudioapi              0.7              r351hf348343_0    r
r-rvest                   0.3.2            r351hf348343_0    r
r-scales                  0.5.0            r351h32998d9_0    r
r-selectr                 0.4_1            r351hf348343_0    r
r-sfsmisc                 1.1_2            r351hf348343_0    r
r-shiny                   1.1.0            r351hf348343_0    r
r-sourcetools             0.1.7            r351h32998d9_0    r
r-spatial                 7.3_11           r351h6402f54_4    r
r-squarem                 2017.10_1        r351hf348343_0    r
r-stringi                 1.2.4            r351h32998d9_0    r
r-stringr                 1.3.1            r351hf348343_0    r
r-survival                2.42_6           r351h6402f54_0    r
r-testthat                2.0.0            r351h32998d9_0    r
r-tibble                  1.4.2            r351h6402f54_0    r
r-tidyr                   0.8.1            r351h32998d9_0    r
r-tidyselect              0.2.4            r351h32998d9_0    r
r-tidyverse               1.2.1            r351hf348343_0    r
r-timedate                3043.102         r351hf348343_0    r
r-tinytex                 0.6              r351hf348343_0    r
r-ttr                     0.23_3           r351h0b560c1_0    r
r-utf8                    1.1.4            r351h6402f54_0    r
r-uuid                    0.1_2            r351h6402f54_4    r
r-viridislite             0.3.0            r351hf348343_0    r
r-whisker                 0.3_2            r351hf348343_4    r
r-withr                   2.1.2            r351hf348343_0    r
r-xfun                    0.3              r351hf348343_0    r
r-xml2                    1.2.0            r351h32998d9_0    r
r-xtable                  1.8_2            r351hf348343_0    r
r-xts                     0.11_0           r351h6402f54_0    r
r-yaml                    2.2.0            r351h6402f54_0    r
r-zoo                     1.8_3            r351h6402f54_0    r
readline                  7.0                  h1de35cc_5    defaults
requests                  2.21.0                   py37_0    defaults
rope                      0.12.0                   py37_0    defaults
ruamel_yaml               0.15.46          py37h1de35cc_0    defaults
scikit-image              0.14.1           py37h0a44026_0    defaults
scikit-learn              0.20.2           py37h27c97d8_0    defaults
scipy                     1.2.1            py37h1410ff5_0    defaults
seaborn                   0.9.0                    py37_0    defaults
send2trash                1.5.0                    py37_0    defaults
setuptools                40.8.0                   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           1.2.1                    py37_0    defaults
sortedcollections         1.1.2                    py37_0    defaults
sortedcontainers          2.1.0                    py37_0    defaults
soupsieve                 1.7.1                    py37_0    defaults
sphinx                    1.8.4                    py37_0    defaults
sphinxcontrib             1.0                      py37_1    defaults
sphinxcontrib-websupport  1.1.0                    py37_1    defaults
spyder                    3.3.3                    py37_0    defaults
spyder-kernels            0.4.2                    py37_0    defaults
sqlalchemy                1.2.18           py37h1de35cc_0    defaults
sqlite                    3.26.0               ha441bb4_0    defaults
statsmodels               0.9.0            py37h1d22016_0    defaults
sympy                     1.3                      py37_0    defaults
tblib                     1.3.2                    py37_0    defaults
terminado                 0.8.1                    py37_1    defaults
testpath                  0.4.2                    py37_0    defaults
tk                        8.6.8                ha441bb4_0    defaults
tktable                   2.10                 h1de35cc_0    defaults
toolz                     0.9.0                    py37_0    defaults
tornado                   5.1.1            py37h1de35cc_0    defaults
tqdm                      4.31.1                     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                   1.24.1                   py37_0    defaults
wcwidth                   0.1.7                    py37_0    defaults
webencodings              0.5.1                    py37_1    defaults
werkzeug                  0.14.1                   py37_0    defaults
wheel                     0.33.1                   py37_0    defaults
widgetsnbextension        3.4.2                    py37_0    defaults
wrapt                     1.11.1           py37h1de35cc_0    defaults
wurlitzer                 1.0.2                    py37_0    defaults
xlrd                      1.2.0                    py37_0    defaults
xlsxwriter                1.1.5                    py37_0    defaults
xlwings                   0.15.3                   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                    4.2.5                h0a44026_1    defaults
zict                      0.1.3                    py37_0    defaults
zlib                      1.2.11               h1de35cc_3    defaults
zstd                      1.3.7                h5bba6e5_0    defaults

Tried:
reinstalling anaconda3, updating all packages. The same error occurs. What is weird is that jupyter notebook for R was working flawlessly for me for many months, but it suddenly stop working recently, and I can not figure out why.

Many thanks.