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Dead Kernel happens everytime I try to run a command (OSX) #3316

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jolespin opened this issue Aug 18, 2016 · 21 comments
Closed

Dead Kernel happens everytime I try to run a command (OSX) #3316

jolespin opened this issue Aug 18, 2016 · 21 comments
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locked [bot] locked due to inactivity

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@jolespin
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I get this error:

[I 14:48:47.243 NotebookApp] Kernel started: ced3c457-52f1-4d0e-a2f4-5183dfc066ff
[1] "Got unhandled msg_type:" "comm_open"
Error in unlockBinding("base_display", displayenv) :
  no binding for "base_display"
Calls: <Anonymous> ... <Anonymous> -> handle_shell -> <Anonymous> -> unlockBinding
Execution halted
[I 14:48:50.246 NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING:root:kernel ced3c457-52f1-4d0e-a2f4-5183dfc066ff restarted

screen shot 2016-08-17 at 2 52 26 pm

Here's some specs:

$ which R
/Users/jespinoz/anaconda/bin/R

from command line

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin11.0.0 (64-bit)

Jupyter version

$ jupyter --version
4.1.0

conda version

$ conda --version
conda 4.1.11

IRKernel

$ conda update r-irkernel
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata ...........
# All requested packages already installed.
# packages in environment at /Users/jespinoz/anaconda:
#
r-irkernel                0.6.1                  r3.3.1_0    r
jespinozlt-osx:~ jespinoz$

IRDisplay

$ conda update r-irdisplay
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata ...........
# All requested packages already installed.
# packages in environment at /Users/jespinoz/anaconda:
#
r-irdisplay               0.3                    r3.3.1_2    r

Originally here: IRkernel/IRkernel#396 but on IRkernel/IRkernel#204 (comment) they told me to migrate it to conda.
@jolespin
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I had to move to RStudio but here's a link to get RStudio to work w/ conda installed R for anyone interested:
http://stackoverflow.com/questions/38534383/how-to-set-up-conda-installed-r-for-use-with-rstudio

@Z-Shiyi
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Z-Shiyi commented Aug 21, 2016

Thanks for sharing, for me, I add those settings to shell rc file, i.e. .zshrc

#Rstudio setting

RSTUDIO_WHICH_R=$HOME/bin/bin/R

launchctl setenv RSTUDIO_WHICH_R $RSTUDIO_WHICH_R

and then you restart your rstudio, and you will see which version R is using from Rstudio console.

From: "Josh L. Espinoza" notifications@github.com
Reply-To: conda/conda reply@reply.github.com
Date: Sunday, August 21, 2016 at 00:42
To: conda/conda conda@noreply.github.com
Subject: Re: [conda/conda] Dead Kernel happens everytime I try to run a command (OSX) (#3316)

I had to move to RStudio but here's a link to get RStudio to work w/ conda installed R for anyone interested:
http://stackoverflow.com/questions/38534383/how-to-set-up-conda-installed-r-for-use-with-rstudio

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@jolespin jolespin mentioned this issue Aug 25, 2016
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@mingwandroid
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Hi @jolespin, can you please show me the output of:

conda list --show-channel-urls | grep zeromq

Then can you try conda update zeromq and again show the output of the above (and also test if your R/Jupyter issues are then resolved)?

Finally, conda install -c defaults zeromq should see you right if the above doesn't work.

@jolespin
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jolespin commented Aug 25, 2016 •
edited 

jespinozlt-osx:~ jespinoz$ conda list --show-channel-urls | grep zeromq
Using Anaconda Cloud api site https://api.anaconda.org
zeromq                    4.1.3                         0    defaults
jespinozlt-osx:~ jespinoz$ conda update zeromq
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata ...........
# All requested packages already installed.
# packages in environment at /Users/jespinoz/anaconda:
#
zeromq                    4.1.3                         0
jespinozlt-osx:~ jespinoz$ conda install -c defaults zeromq
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata ...........
Solving package specifications: ..........

# All requested packages already installed.
# packages in environment at /Users/jespinoz/anaconda:
#
zeromq                    4.1.3                         0

I just ran those 3 and then tried the R kernel again :/ Thanks for the help tho.
screen shot 2016-08-25 at 2 51 31 pm

with this as my error in the terminal

[I 14:51:22.527 NotebookApp] Kernel started: 47c1daca-a108-47c2-b014-db6a848d59eb
[1] "Got unhandled msg_type:" "comm_open"
Error in unlockBinding("base_display", displayenv) :
  no binding for "base_display"
Calls: <Anonymous> ... <Anonymous> -> handle_shell -> <Anonymous> -> unlockBinding
Execution halted
[I 14:51:28.530 NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING:root:kernel 47c1daca-a108-47c2-b014-db6a848d59eb restarted

@mingwandroid
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OK, please show:

conda list --show-channel-urls

@jolespin
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I put it on http://pastebin.com/4bdXE9m7 b/c it's kind of long

@tatarsky tatarsky mentioned this issue Sep 19, 2016
Closed
@sandhujasmine
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@jolespin - did you get this working.

I just did a clean install of r-essentials and ran into the same issue. Updating r-irkernel fixed it for me:

> conda update -c r r-irkernel
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /Users/jsandhu/miniconda/envs/r_env:

The following NEW packages will be INSTALLED:

    r-crayon:   1.3.1-r3.3.1_0 r
    r-memoise:  1.0.0-r3.3.1_0 r

The following packages will be UPDATED:

    r-irkernel: 0.7-r3.3.1_0   r --> 0.7-r3.3.1_2 r

@jolespin
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I will try it when I get to work on Monday. I gave up on it when I found out how to route RStudio to use conda R.

Sent from my iPhone

On Oct 14, 2016, at 9:43 PM, Minna notifications@github.com wrote:

@jolespin - did you get this working.

I just did a clean install of r-essentials and ran into the same issue. Updating r-irkernel fixed it for me:

conda update -c r r-irkernel
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /Users/jsandhu/miniconda/envs/r_env:

The following NEW packages will be INSTALLED:

r-crayon:   1.3.1-r3.3.1_0 r
r-memoise:  1.0.0-r3.3.1_0 r

The following packages will be UPDATED:

r-irkernel: 0.7-r3.3.1_0   r --> 0.7-r3.3.1_2 r

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@ggrrll
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ggrrll commented Jan 16, 2017

@sandhujasmine

I am having the same issue here on macOS 10.12.2 (16C67)

I run conda update r-irkernel in the root env and didn't work for me...
my version now is:
r-irkernel 0.7.1 r3.3.2_0 defaults

@mingwandroid

I also get
zeromq 4.1.3 0

after conda install -c defaults zeromq

any hints?

@mingwandroid
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Please show the output from:
conda info
and:
conda list --show-channel-urls

@ggrrll
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ggrrll commented Jan 16, 2017 •
edited

conda_list.txt

conda_info

r_kernel_issue

@mingwandroid
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Screenshots and attachments are not as user-friendly as inline text. Here are the contents of your text file:

# packages in environment at /Users/lazzari/anaconda:
#
alabaster                 0.7.7                    py27_0    defaults
anaconda                  custom                   py27_0    defaults
anaconda-client           1.4.0                    py27_0    defaults
anaconda-navigator        1.2.3                    py27_0    defaults
appnope                   0.1.0                    py27_0    defaults
appscript                 1.0.1                    py27_0    defaults
argcomplete               1.0.0                    py27_1    defaults
astroid                   1.4.7                    py27_0    defaults
astropy                   1.2.1               np111py27_0    defaults
babel                     2.2.0                    py27_0    defaults
backports_abc             0.4                      py27_0    defaults
beautifulsoup4            4.5.1                    py27_0    defaults
bitarray                  0.8.1                    py27_0    defaults
blaze                     0.9.1                    py27_0    defaults
bokeh                     0.11.1                   py27_0    defaults
boto                      2.39.0                   py27_0    defaults
bottleneck                1.1.0               np111py27_0    defaults
bz2file                   0.98                     py27_0    defaults
cachecontrol              0.11.5                   py27_0    defaults
cairo                     1.14.6                        0    defaults
cdecimal                  2.3                      py27_0    defaults
cffi                      1.5.2                    py27_0    defaults
chest                     0.2.3                    py27_0    defaults
cloudpickle               0.1.1                    py27_0    defaults
clyent                    1.2.1                    py27_0    defaults
colorama                  0.3.7                    py27_0    defaults
conda                     4.3.4                    py27_0    defaults
conda-build               1.20.0                   py27_0    defaults
conda-env                 2.6.0                         0    defaults
conda-manager             0.4.0                    py27_0    defaults
configobj                 5.0.6                    py27_0    defaults
contextlib2               0.4.0                    py27_0    defaults
cryptography              1.7.1                    py27_0    defaults
curl                      7.45.0                        0    defaults
cycler                    0.10.0                   py27_0    defaults
cython                    0.23.4                   py27_1    defaults
cytoolz                   0.7.5                    py27_0    defaults
dask                      0.8.1                    py27_0    defaults
datashape                 0.5.1                    py27_0    defaults
decorator                 4.0.9                    py27_0    defaults
dill                      0.2.4                    py27_0    defaults
docutils                  0.12                     py27_0    defaults
dynd-python               0.7.2                    py27_0    defaults
enum34                    1.1.2                    py27_0    defaults
et_xmlfile                1.0.1                    py27_0    defaults
fastcache                 1.0.2                    py27_0    defaults
flask                     0.10.1                   py27_1    defaults
flask-cors                2.1.2                    py27_0    defaults
folium                    0.2.1                     <pip>
fontconfig                2.12.1                        0    defaults
freetype                  2.5.5                         0    defaults
funcsigs                  0.4                      py27_0    defaults
future                    0.15.2                   py27_0    defaults
futures                   3.0.3                    py27_0    defaults
gensim                    0.12.4              np111py27_0    defaults
gettext                   0.19.8                        1    defaults
gevent                    1.1.0                    py27_0    defaults
glib                      2.50.2                        0    defaults
glueviz                   0.8.2                    py27_0    defaults
greenlet                  0.4.9                    py27_0    defaults
grin                      1.2.1                    py27_1    defaults
gsl                       1.16                          2    r
h5py                      2.6.0               np111py27_2    defaults
harfbuzz                  0.9.39                        1    defaults
hdf5                      1.8.17                        1    defaults
heapdict                  1.0.0                    py27_0    defaults
icu                       54.1                          0    defaults
idna                      2.0                      py27_0    defaults
ipaddress                 1.0.14                   py27_0    defaults
ipykernel                 4.3.1                    py27_0    defaults
ipython                   4.1.2                    py27_1    defaults
ipython_genutils          0.1.0                    py27_0    defaults
ipywidgets                4.1.1                    py27_0    defaults
itsdangerous              0.24                     py27_0    defaults
jbig                      2.1                           0    defaults
jdcal                     1.2                      py27_0    defaults
jedi                      0.9.0                    py27_0    defaults
jinja2                    2.8                      py27_0    defaults
jpeg                      8d                            1    defaults
jsonschema                2.4.0                    py27_0    defaults
jupyter                   1.0.0                    py27_2    defaults
jupyter_client            4.2.2                    py27_0    defaults
jupyter_console           4.1.1                    py27_0    defaults
jupyter_contrib_core      0.3.0                    py27_1    conda-forge
jupyter_contrib_nbextensions 0.2.3                    py27_0    conda-forge
jupyter_core              4.1.0                    py27_0    defaults
jupyter_highlight_selected_word 0.0.7                    py27_0    conda-forge
jupyter_latex_envs        1.3.6                    py27_0    conda-forge
jupyter_nbextensions_configurator 0.2.3                    py27_0    conda-forge
lazy-object-proxy         1.2.1                    py27_0    defaults
libdynd                   0.7.2                         0    defaults
libffi                    3.2.1                         1    defaults
libgcc                    4.8.5                         1    r
libiconv                  1.14                          0    defaults
libpng                    1.6.17                        0    defaults
libtiff                   4.0.6                         2    defaults
libxml2                   2.9.2                         0    defaults
libxslt                   1.1.28                        2    defaults
llvmlite                  0.13.0                   py27_0    defaults
locket                    0.2.0                    py27_0    defaults
lockfile                  0.12.2                   py27_0    defaults
lxml                      3.6.0                    py27_0    defaults
markupsafe                0.23                     py27_0    defaults
matplotlib                1.5.1               np111py27_0    defaults
mistune                   0.7.2                    py27_1    defaults
mkl                       11.3.3                        0    defaults
mkl-rt                    11.1                         p0    defaults
mkl-service               1.1.0                   py27_p0    defaults
mpmath                    0.19                     py27_0    defaults
multipledispatch          0.4.8                    py27_0    defaults
natsort                   4.0.3                    py27_0    defaults
nbconvert                 4.1.0                    py27_0    defaults
nbformat                  4.0.1                    py27_0    defaults
ncurses                   5.9                           8    r
networkx                  1.11                     py27_0    defaults
nltk                      3.2                      py27_0    defaults
nose                      1.3.7                    py27_0    defaults
notebook                  4.3.1                    py27_0    defaults
numba                     0.28.1              np111py27_0    defaults
numexpr                   2.6.1               np111py27_1    defaults
numpy                     1.11.2                   py27_0    defaults
odo                       0.4.2                    py27_0    defaults
openpyxl                  2.3.2                    py27_0    defaults
openssl                   1.0.2g                        0    defaults
orange                    2.7.8                    py27_3    defaults
orange-app                1.0.1                    py27_0    defaults
pandas                    0.19.0              np111py27_0    defaults
pango                     1.40.3                        0    defaults
partd                     0.3.2                    py27_1    defaults
pastedeploy               1.5.2                    py27_1    defaults
path.py                   8.1.2                    py27_1    defaults
patsy                     0.4.1                    py27_0    defaults
pcre                      8.39                          1    defaults
pep8                      1.7.0                    py27_0    defaults
pexpect                   4.0.1                    py27_0    defaults
pickleshare               0.5                      py27_0    defaults
pillow                    3.1.1                    py27_0    defaults
pip                       8.1.1                    py27_1    defaults
pixman                    0.34.0                        0    defaults
ply                       3.8                      py27_0    defaults
psutil                    4.1.0                    py27_1    defaults
ptyprocess                0.5                      py27_0    defaults
py                        1.4.31                   py27_0    defaults
pyasn1                    0.1.9                    py27_0    defaults
pyaudio                   0.2.7                    py27_0    defaults
pycosat                   0.6.1                    py27_0    defaults
pycparser                 2.14                     py27_0    defaults
pycrypto                  2.6.1                    py27_0    defaults
pycurl                    7.19.5.3                 py27_0    defaults
pyflakes                  1.1.0                    py27_0    defaults
pygments                  2.1.1                    py27_0    defaults
pylint                    1.5.4                    py27_1    defaults
pyopenssl                 16.2.0                   py27_0    defaults
pyparsing                 2.0.3                    py27_0    defaults
pyqt                      4.11.4                   py27_1    defaults
pyramid                   1.5.7                    py27_0    defaults
pyramid_jinja2            2.5                      py27_1    defaults
pytables                  3.2.3.1             np111py27_0    defaults
pytest                    2.8.5                    py27_0    defaults
python                    2.7.11                        0    defaults
python-dateutil           2.5.1                    py27_0    defaults
python.app                1.2                      py27_4    defaults
pytz                      2016.2                   py27_0    defaults
pyyaml                    3.11                     py27_1    defaults
pyzmq                     15.2.0                   py27_0    defaults
qt                        4.8.7                         1    defaults
qtawesome                 0.3.2                    py27_0    defaults
qtconsole                 4.2.1                    py27_0    defaults
qtpy                      1.1.2                    py27_0    defaults
r                         3.3.2                  r3.3.2_0    defaults
r-assertthat              0.1                    r3.3.2_4    defaults
r-backports               1.0.4                  r3.3.2_0    defaults
r-base                    3.3.2                         0    defaults
r-base64enc               0.1_3                  r3.3.2_0    defaults
r-bh                      1.62.0_1               r3.3.2_0    defaults
r-bitops                  1.0_6                  r3.3.2_2    defaults
r-boot                    1.3_18                 r3.3.2_0    defaults
r-car                     2.1_4                  r3.3.2_0    defaults
r-caret                   6.0_73                 r3.3.2_0    defaults
r-catools                 1.17.1                       1a    r
r-chron                   2.3_47                 r3.3.2_0    defaults
r-class                   7.3_14                 r3.3.2_0    defaults
r-cluster                 2.0.5                  r3.3.2_0    defaults
r-codetools               0.2_15                 r3.3.2_0    defaults
r-colorspace              1.3_1                  r3.3.2_0    defaults
r-crayon                  1.3.2                  r3.3.2_0    defaults
r-curl                    2.3                    r3.3.2_0    defaults
r-data.table              1.10.0                 r3.3.2_0    defaults
r-dbi                     0.5_1                  r3.3.2_0    defaults
r-dichromat               2.0_0                  r3.3.2_2    defaults
r-digest                  0.6.10                 r3.3.2_0    defaults
r-dplyr                   0.5.0                  r3.3.2_0    defaults
r-essentials              1.4                           0    defaults
r-evaluate                0.10                   r3.3.2_0    defaults
r-foreach                 1.4.3                  r3.3.2_0    defaults
r-foreign                 0.8_67                 r3.3.2_0    defaults
r-formatr                 1.4                    r3.3.2_0    defaults
r-ggplot2                 2.2.0                  r3.3.2_0    defaults
r-gistr                   0.3.6                  r3.3.2_0    defaults
r-glmnet                  2.0_5                  r3.3.2_0    defaults
r-gtable                  0.2.0                  r3.3.2_0    defaults
r-hexbin                  1.27.1                 r3.3.2_0    defaults
r-highr                   0.6                    r3.3.2_0    defaults
r-htmltools               0.3.5                  r3.3.2_0    defaults
r-htmlwidgets             0.8                    r3.3.2_0    defaults
r-httpuv                  1.3.3                  r3.3.2_0    defaults
r-httr                    1.2.1                  r3.3.2_0    defaults
r-irdisplay               0.4.4                  r3.3.2_0    defaults
r-irkernel                0.7.1                  r3.3.2_0    defaults
r-iterators               1.0.8                  r3.3.2_0    defaults
r-jsonlite                1.1                    r3.3.2_0    defaults
r-kernsmooth              2.23_15                r3.3.2_0    defaults
r-knitr                   1.15.1                 r3.3.2_0    defaults
r-labeling                0.3                    r3.3.2_2    defaults
r-lattice                 0.20_34                r3.3.2_0    defaults
r-lazyeval                0.2.0                  r3.3.2_0    defaults
r-lme4                    1.1_12                 r3.3.2_0    defaults
r-magrittr                1.5                    r3.3.2_2    defaults
r-maps                    3.1.1                  r3.3.2_0    defaults
r-markdown                0.7.7                  r3.3.2_2    defaults
r-mass                    7.3_45                 r3.3.2_0    defaults
r-matrix                  1.2_7.1                r3.3.2_0    defaults
r-matrixmodels            0.4_1                  r3.3.2_0    defaults
r-memoise                 1.0.0                  r3.3.2_0    defaults
r-mgcv                    1.8_16                 r3.3.2_0    defaults
r-mime                    0.5                    r3.3.2_0    defaults
r-minqa                   1.2.4                  r3.3.2_2    defaults
r-modelmetrics            1.1.0                  r3.3.2_0    defaults
r-munsell                 0.4.3                  r3.3.2_0    defaults
r-nlme                    3.1_128                r3.3.2_0    defaults
r-nloptr                  1.0.4                  r3.3.2_2    defaults
r-nnet                    7.3_12                 r3.3.2_0    defaults
r-openssl                 0.9.5                  r3.3.2_0    defaults
r-pbdzmq                  0.2_4                  r3.3.2_0    defaults
r-pbkrtest                0.4_6                  r3.3.2_0    defaults
r-plyr                    1.8.4                  r3.3.2_0    defaults
r-pryr                    0.1.2                  r3.3.2_0    defaults
r-quantmod                0.4_7                  r3.3.2_0    defaults
r-quantreg                5.29                   r3.3.2_0    defaults
r-r6                      2.2.0                  r3.3.2_0    defaults
r-randomforest            4.6_12                 r3.3.2_0    defaults
r-rbokeh                  0.5.0                  r3.3.2_0    defaults
r-rcolorbrewer            1.1_2                        2a    r
r-rcpp                    0.12.8                 r3.3.2_0    defaults
r-rcppeigen               0.3.2.9.0              r3.3.2_0    defaults
r-recommended             3.3.2                  r3.3.2_0    defaults
r-repr                    0.10                   r3.3.2_0    defaults
r-reshape2                1.4.1                        1a    r
r-rmarkdown               1.2                    r3.3.2_0    defaults
r-rpart                   4.1_10                 r3.3.2_0    defaults
r-rprojroot               1.1                    r3.3.2_0    defaults
r-scales                  0.4.1                  r3.3.2_0    defaults
r-shiny                   0.14.2                 r3.3.2_0    defaults
r-sourcetools             0.1.5                  r3.3.2_0    defaults
r-sparsem                 1.74                   r3.3.2_0    defaults
r-spatial                 7.3_11                 r3.3.2_0    defaults
r-stringi                 1.1.2                  r3.3.2_0    defaults
r-stringr                 1.1.0                  r3.3.2_0    defaults
r-survival                2.40_1                 r3.3.2_0    defaults
r-tibble                  1.2                    r3.3.2_0    defaults
r-tidyr                   0.6.0                  r3.3.2_0    defaults
r-ttr                     0.23_1                 r3.3.2_0    defaults
r-uuid                    0.1_2                  r3.3.2_0    defaults
r-xtable                  1.8_2                  r3.3.2_0    defaults
r-xts                     0.9_7                  r3.3.2_2    defaults
r-yaml                    2.1.14                 r3.3.2_0    defaults
r-zoo                     1.7_13                 r3.3.2_0    defaults
readline                  6.2                           2    defaults
redis                     2.6.9                         0    defaults
redis-py                  2.10.3                   py27_0    defaults
repoze.lru                0.6                      py27_0    defaults
requests                  2.12.4                   py27_0    defaults
rope                      0.9.4                    py27_1    defaults
ruamel_yaml               0.11.14                  py27_0    defaults
scikit-bio                0.4.0               np111py27_0    defaults
scikit-image              0.12.3              np111py27_1    defaults
scikit-learn              0.18.1              np111py27_0    defaults
scipy                     0.18.1              np111py27_0    defaults
seaborn                   0.7.1                    py27_0    defaults
setuptools                20.3                     py27_0    defaults
simplegeneric             0.8.1                    py27_0    defaults
singledispatch            3.4.0.3                  py27_0    defaults
sip                       4.16.9                   py27_0    defaults
six                       1.10.0                   py27_0    defaults
smart_open                1.3.5                    py27_0    defaults
snowballstemmer           1.2.1                    py27_0    defaults
sockjs-tornado            1.0.1                    py27_0    defaults
sphinx                    1.3.5                    py27_0    defaults
sphinx_rtd_theme          0.1.9                    py27_0    defaults
spyder                    3.0.2                    py27_0    defaults
sqlalchemy                1.0.12                   py27_0    defaults
sqlite                    3.9.2                         0    defaults
ssl_match_hostname        3.4.0.2                  py27_0    defaults
statsmodels               0.6.1               np111py27_1    defaults
sympy                     1.0                      py27_0    defaults
terminado                 0.5                      py27_1    defaults
tk                        8.5.18                        0    defaults
toolz                     0.7.4                    py27_0    defaults
tornado                   4.3                      py27_0    defaults
traitlets                 4.2.1                    py27_0    defaults
translationstring         1.3                      py27_0    defaults
unicodecsv                0.14.1                   py27_0    defaults
venusian                  1.0                      py27_0    defaults
webob                     1.4.1                    py27_0    defaults
werkzeug                  0.11.4                   py27_0    defaults
wheel                     0.29.0                   py27_0    defaults
wrapt                     1.10.8                   py27_0    defaults
xlrd                      0.9.4                    py27_0    defaults
xlsxwriter                0.8.4                    py27_0    defaults
xlwings                   0.7.0                    py27_0    defaults
xlwt                      1.0.0                    py27_0    defaults
xz                        5.2.2                         0    defaults
yaml                      0.1.6                         0    defaults
zeromq                    4.1.3                         0    defaults
zlib                      1.2.8                         0    defaults
zope                      1.0                      py27_0    defaults
zope.deprecation          4.1.2                    py27_1    defaults
zope.interface            4.1.2                    py27_1    defaults

@mingwandroid
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Contributor

You've mixed conda-defaults packages and conda-forge packages:

jupyter_contrib_core      0.3.0                    py27_1    conda-forge
jupyter_contrib_nbextensions 0.2.3                    py27_0    conda-forge
jupyter_core              4.1.0                    py27_0    defaults
jupyter_highlight_selected_word 0.0.7                    py27_0    conda-forge
jupyter_latex_envs        1.3.6                    py27_0    conda-forge
jupyter_nbextensions_configurator 0.2.3                    py27_0    conda-forge

Can you try creating an env without any conda-forge packages?

@ggrrll
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ggrrll commented Jan 17, 2017

I re installed conda - with python 3 - and these is the output

#
_license                  1.1                      py35_1    defaults
_nb_ext_conf              0.3.0                    py35_0    defaults
alabaster                 0.7.9                    py35_0    defaults
anaconda                  4.2.0               np111py35_0    defaults
anaconda-clean            1.0.0                    py35_0    defaults
anaconda-client           1.5.1                    py35_0    defaults
anaconda-navigator        1.3.2                    py35_0    defaults
appnope                   0.1.0                    py35_0    defaults
appscript                 1.0.1                    py35_0    defaults
argcomplete               1.0.0                    py35_1    defaults
astroid                   1.4.7                    py35_0    defaults
astropy                   1.2.1               np111py35_0    defaults
babel                     2.3.4                    py35_0    defaults
backports                 1.0                      py35_0    defaults
beautifulsoup4            4.5.1                    py35_0    defaults
bitarray                  0.8.1                    py35_0    defaults
blaze                     0.10.1                   py35_0    defaults
bokeh                     0.12.2                   py35_0    defaults
boto                      2.42.0                   py35_0    defaults
bottleneck                1.1.0               np111py35_0    defaults
cairo                     1.14.6                        0    defaults
cffi                      1.7.0                    py35_0    defaults
chest                     0.2.3                    py35_0    defaults
click                     6.6                      py35_0    defaults
cloudpickle               0.2.1                    py35_0    defaults
clyent                    1.2.2                    py35_0    defaults
colorama                  0.3.7                    py35_0    defaults
conda                     4.3.4                    py35_0    defaults
conda-build               2.0.2                    py35_0    defaults
conda-env                 2.6.0                         0    defaults
configobj                 5.0.6                    py35_0    defaults
contextlib2               0.5.3                    py35_0    defaults
cryptography              1.5                      py35_0    defaults
curl                      7.49.0                        1    defaults
cycler                    0.10.0                   py35_0    defaults
cython                    0.24.1                   py35_0    defaults
cytoolz                   0.8.0                    py35_0    defaults
dask                      0.11.0                   py35_0    defaults
datashape                 0.5.2                    py35_0    defaults
decorator                 4.0.10                   py35_0    defaults
dill                      0.2.5                    py35_0    defaults
docutils                  0.12                     py35_2    defaults
dynd-python               0.7.2                    py35_0    defaults
entrypoints               0.2.2                    py35_0    defaults
et_xmlfile                1.0.1                    py35_0    defaults
fastcache                 1.0.2                    py35_1    defaults
filelock                  2.0.6                    py35_0    defaults
flask                     0.11.1                   py35_0    defaults
flask-cors                2.1.2                    py35_0    defaults
fontconfig                2.12.1                        0    defaults
freetype                  2.5.5                         1    defaults
get_terminal_size         1.0.0                    py35_0    defaults
gettext                   0.19.8                        1    defaults
gevent                    1.1.2                    py35_0    defaults
glib                      2.50.2                        0    defaults
greenlet                  0.4.10                   py35_0    defaults
gsl                       2.2.1                         0    defaults
h5py                      2.6.0               np111py35_2    defaults
harfbuzz                  0.9.39                        1    defaults
hdf5                      1.8.17                        1    defaults
heapdict                  1.0.0                    py35_1    defaults
icu                       54.1                          0    defaults
idna                      2.1                      py35_0    defaults
imagesize                 0.7.1                    py35_0    defaults
ipykernel                 4.5.0                    py35_0    defaults
ipython                   5.1.0                    py35_0    defaults
ipython_genutils          0.1.0                    py35_0    defaults
ipywidgets                5.2.2                    py35_0    defaults
itsdangerous              0.24                     py35_0    defaults
jbig                      2.1                           0    defaults
jdcal                     1.2                      py35_1    defaults
jedi                      0.9.0                    py35_1    defaults
jinja2                    2.8                      py35_1    defaults
jpeg                      8d                            2    defaults
jsonschema                2.5.1                    py35_0    defaults
jupyter                   1.0.0                    py35_3    defaults
jupyter_client            4.4.0                    py35_0    defaults
jupyter_console           5.0.0                    py35_0    defaults
jupyter_core              4.2.0                    py35_0    defaults
lazy-object-proxy         1.2.1                    py35_0    defaults
libdynd                   0.7.2                         0    defaults
libffi                    3.2.1                         1    defaults
libgcc                    4.8.5                         1    defaults
libiconv                  1.14                          0    defaults
libpng                    1.6.22                        0    defaults
libtiff                   4.0.6                         2    defaults
libxml2                   2.9.2                         0    defaults
libxslt                   1.1.28                        2    defaults
llvmlite                  0.13.0                   py35_0    defaults
locket                    0.2.0                    py35_1    defaults
lxml                      3.6.4                    py35_0    defaults
markupsafe                0.23                     py35_2    defaults
matplotlib                1.5.3               np111py35_0    defaults
mistune                   0.7.3                    py35_1    defaults
mkl                       11.3.3                        0    defaults
mkl-service               1.1.2                    py35_2    defaults
mpmath                    0.19                     py35_1    defaults
multipledispatch          0.4.8                    py35_0    defaults
nb_anacondacloud          1.2.0                    py35_0    defaults
nb_conda                  2.0.0                    py35_0    defaults
nb_conda_kernels          2.0.0                    py35_0    defaults
nbconvert                 4.2.0                    py35_0    defaults
nbformat                  4.1.0                    py35_0    defaults
nbpresent                 3.0.2                    py35_0    defaults
ncurses                   5.9                          10    defaults
networkx                  1.11                     py35_0    defaults
nltk                      3.2.1                    py35_0    defaults
nose                      1.3.7                    py35_1    defaults
notebook                  4.3.1                    py35_0    defaults
numba                     0.28.1              np111py35_0    defaults
numexpr                   2.6.1               np111py35_0    defaults
numpy                     1.11.1                   py35_0    defaults
odo                       0.5.0                    py35_1    defaults
openpyxl                  2.3.2                    py35_0    defaults
openssl                   1.0.2j                        0    defaults
pandas                    0.18.1              np111py35_0    defaults
pango                     1.40.3                        0    defaults
partd                     0.3.6                    py35_0    defaults
path.py                   8.2.1                    py35_0    defaults
pathlib2                  2.1.0                    py35_0    defaults
patsy                     0.4.1                    py35_0    defaults
pcre                      8.39                          1    defaults
pep8                      1.7.0                    py35_0    defaults
pexpect                   4.0.1                    py35_0    defaults
pickleshare               0.7.4                    py35_0    defaults
pillow                    3.3.1                    py35_0    defaults
pip                       8.1.2                    py35_0    defaults
pixman                    0.34.0                        0    defaults
pkginfo                   1.3.2                    py35_0    defaults
ply                       3.9                      py35_0    defaults
prompt_toolkit            1.0.3                    py35_0    defaults
psutil                    4.3.1                    py35_0    defaults
ptyprocess                0.5.1                    py35_0    defaults
py                        1.4.31                   py35_0    defaults
pyasn1                    0.1.9                    py35_0    defaults
pycosat                   0.6.1                    py35_1    defaults
pycparser                 2.14                     py35_1    defaults
pycrypto                  2.6.1                    py35_4    defaults
pycurl                    7.43.0                   py35_0    defaults
pyflakes                  1.3.0                    py35_0    defaults
pygments                  2.1.3                    py35_0    defaults
pylint                    1.5.4                    py35_1    defaults
pyopenssl                 16.2.0                   py35_0    defaults
pyparsing                 2.1.4                    py35_0    defaults
pyqt                      5.6.0                    py35_0    defaults
pytables                  3.2.3.1             np111py35_0    defaults
pytest                    2.9.2                    py35_0    defaults
python                    3.5.2                         0    defaults
python-dateutil           2.5.3                    py35_0    defaults
python.app                1.2                      py35_4    defaults
pytz                      2016.6.1                 py35_0    defaults
pyyaml                    3.12                     py35_0    defaults
pyzmq                     15.4.0                   py35_0    defaults
qt                        5.6.0                         0    defaults
qtawesome                 0.3.3                    py35_0    defaults
qtconsole                 4.2.1                    py35_1    defaults
qtpy                      1.1.2                    py35_0    defaults
r-assertthat              0.1                    r3.3.2_4    r
r-backports               1.0.4                  r3.3.2_0    r
r-base                    3.3.2                         0    r
r-base64enc               0.1_3                  r3.3.2_0    r
r-bh                      1.62.0_1               r3.3.2_0    r
r-bitops                  1.0_6                  r3.3.2_2    r
r-boot                    1.3_18                 r3.3.2_0    r
r-broom                   0.4.1                  r3.3.2_0    r
r-car                     2.1_4                  r3.3.2_0    r
r-caret                   6.0_73                 r3.3.2_0    r
r-catools                 1.17.1                 r3.3.2_2    r
r-class                   7.3_14                 r3.3.2_0    r
r-cluster                 2.0.5                  r3.3.2_0    r
r-codetools               0.2_15                 r3.3.2_0    r
r-colorspace              1.3_1                  r3.3.2_0    r
r-crayon                  1.3.2                  r3.3.2_0    r
r-curl                    2.3                    r3.3.2_0    r
r-data.table              1.10.0                 r3.3.2_0    r
r-dbi                     0.5_1                  r3.3.2_0    r
r-dichromat               2.0_0                  r3.3.2_2    r
r-digest                  0.6.10                 r3.3.2_0    r
r-dplyr                   0.5.0                  r3.3.2_0    r
r-essentials              1.5.1                         0    r
r-evaluate                0.10                   r3.3.2_0    r
r-forcats                 0.1.1                  r3.3.2_0    r
r-foreach                 1.4.3                  r3.3.2_0    r
r-foreign                 0.8_67                 r3.3.2_0    r
r-formatr                 1.4                    r3.3.2_0    r
r-ggplot2                 2.2.0                  r3.3.2_0    r
r-gistr                   0.3.6                  r3.3.2_0    r
r-glmnet                  2.0_5                  r3.3.2_0    r
r-gtable                  0.2.0                  r3.3.2_0    r
r-haven                   1.0.0                  r3.3.2_0    r
r-hexbin                  1.27.1                 r3.3.2_0    r
r-highr                   0.6                    r3.3.2_0    r
r-hms                     0.3                    r3.3.2_0    r
r-htmltools               0.3.5                  r3.3.2_0    r
r-htmlwidgets             0.8                    r3.3.2_0    r
r-httpuv                  1.3.3                  r3.3.2_0    r
r-httr                    1.2.1                  r3.3.2_0    r
r-irdisplay               0.4.4                  r3.3.2_0    r
r-irkernel                0.7.1                  r3.3.2_0    r
r-iterators               1.0.8                  r3.3.2_0    r
r-jsonlite                1.1                    r3.3.2_0    r
r-kernsmooth              2.23_15                r3.3.2_0    r
r-knitr                   1.15.1                 r3.3.2_0    r
r-labeling                0.3                    r3.3.2_2    r
r-lattice                 0.20_34                r3.3.2_0    r
r-lazyeval                0.2.0                  r3.3.2_0    r
r-lme4                    1.1_12                 r3.3.2_0    r
r-lubridate               1.6.0                  r3.3.2_0    r
r-magrittr                1.5                    r3.3.2_2    r
r-maps                    3.1.1                  r3.3.2_0    r
r-markdown                0.7.7                  r3.3.2_2    r
r-mass                    7.3_45                 r3.3.2_0    r
r-matrix                  1.2_7.1                r3.3.2_0    r
r-matrixmodels            0.4_1                  r3.3.2_0    r
r-mgcv                    1.8_16                 r3.3.2_0    r
r-mime                    0.5                    r3.3.2_0    r
r-minqa                   1.2.4                  r3.3.2_2    r
r-mnormt                  1.5_5                  r3.3.2_0    r
r-modelmetrics            1.1.0                  r3.3.2_0    r
r-modelr                  0.1.0                  r3.3.2_0    r
r-munsell                 0.4.3                  r3.3.2_0    r
r-nlme                    3.1_128                r3.3.2_0    r
r-nloptr                  1.0.4                  r3.3.2_2    r
r-nnet                    7.3_12                 r3.3.2_0    r
r-openssl                 0.9.5                  r3.3.2_0    r
r-pbdzmq                  0.2_4                  r3.3.2_0    r
r-pbkrtest                0.4_6                  r3.3.2_0    r
r-plyr                    1.8.4                  r3.3.2_0    r
r-pryr                    0.1.2                  r3.3.2_0    r
r-psych                   1.6.9                  r3.3.2_0    r
r-purrr                   0.2.2                  r3.3.2_0    r
r-quantmod                0.4_7                  r3.3.2_0    r
r-quantreg                5.29                   r3.3.2_0    r
r-r6                      2.2.0                  r3.3.2_0    r
r-randomforest            4.6_12                 r3.3.2_0    r
r-rbokeh                  0.5.0                  r3.3.2_0    r
r-rcolorbrewer            1.1_2                  r3.3.2_3    r
r-rcpp                    0.12.8                 r3.3.2_0    r
r-rcppeigen               0.3.2.9.0              r3.3.2_0    r
r-readr                   1.0.0                  r3.3.2_0    r
r-readxl                  0.1.1                  r3.3.2_0    r
r-recommended             3.3.2                  r3.3.2_0    r
r-repr                    0.10                   r3.3.2_0    r
r-reshape2                1.4.2                  r3.3.2_0    r
r-rmarkdown               1.2                    r3.3.2_0    r
r-rpart                   4.1_10                 r3.3.2_0    r
r-rprojroot               1.1                    r3.3.2_0    r
r-rvest                   0.3.2                  r3.3.2_0    r
r-scales                  0.4.1                  r3.3.2_0    r
r-selectr                 0.3_0                  r3.3.2_0    r
r-shiny                   0.14.2                 r3.3.2_0    r
r-sourcetools             0.1.5                  r3.3.2_0    r
r-sparsem                 1.74                   r3.3.2_0    r
r-spatial                 7.3_11                 r3.3.2_0    r
r-stringi                 1.1.2                  r3.3.2_0    r
r-stringr                 1.1.0                  r3.3.2_0    r
r-survival                2.40_1                 r3.3.2_0    r
r-tibble                  1.2                    r3.3.2_0    r
r-tidyr                   0.6.0                  r3.3.2_0    r
r-tidyverse               1.0.0                  r3.3.2_0    r
r-ttr                     0.23_1                 r3.3.2_0    r
r-uuid                    0.1_2                  r3.3.2_0    r
r-xml2                    1.0.0                  r3.3.2_0    r
r-xtable                  1.8_2                  r3.3.2_0    r
r-xts                     0.9_7                  r3.3.2_2    r
r-yaml                    2.1.14                 r3.3.2_0    r
r-zoo                     1.7_13                 r3.3.2_0    r
readline                  6.2                           2    defaults
redis                     3.2.0                         0    defaults
redis-py                  2.10.5                   py35_0    defaults
requests                  2.12.4                   py35_0    defaults
rope                      0.9.4                    py35_1    defaults
ruamel_yaml               0.11.14                  py35_0    defaults
scikit-image              0.12.3              np111py35_1    defaults
scikit-learn              0.17.1              np111py35_2    defaults
scipy                     0.18.1              np111py35_0    defaults
setuptools                27.2.0                   py35_0    defaults
simplegeneric             0.8.1                    py35_1    defaults
singledispatch            3.4.0.3                  py35_0    defaults
sip                       4.18                     py35_0    defaults
six                       1.10.0                   py35_0    defaults
snowballstemmer           1.2.1                    py35_0    defaults
sockjs-tornado            1.0.3                    py35_0    defaults
sphinx                    1.4.6                    py35_0    defaults
spyder                    3.0.0                    py35_0    defaults
sqlalchemy                1.0.13                   py35_0    defaults
sqlite                    3.13.0                        0    defaults
statsmodels               0.6.1               np111py35_1    defaults
sympy                     1.0                      py35_0    defaults
terminado                 0.6                      py35_0    defaults
tk                        8.5.18                        0    defaults
toolz                     0.8.0                    py35_0    defaults
tornado                   4.4.1                    py35_0    defaults
traitlets                 4.3.0                    py35_0    defaults
unicodecsv                0.14.1                   py35_0    defaults
wcwidth                   0.1.7                    py35_0    defaults
werkzeug                  0.11.11                  py35_0    defaults
wheel                     0.29.0                   py35_0    defaults
widgetsnbextension        1.2.6                    py35_0    defaults
wrapt                     1.10.6                   py35_0    defaults
xlrd                      1.0.0                    py35_0    defaults
xlsxwriter                0.9.3                    py35_0    defaults
xlwings                   0.10.0                   py35_0    defaults
xlwt                      1.1.2                    py35_0    defaults
xz                        5.2.2                         0    defaults
yaml                      0.1.6                         0    defaults
zeromq                    4.1.3                         0    defaults
zlib                      1.2.8                         3    defaults```

@ggrrll
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ggrrll commented Jan 17, 2017

and conda-info


               platform : osx-64
          conda version : 4.3.4
       conda is private : False
      conda-env version : 4.3.4
    conda-build version : 2.0.2
         python version : 3.5.2.final.0
       requests version : 2.12.4
       root environment : /Users/lazzari/anaconda  (writable)
    default environment : /Users/lazzari/anaconda
       envs directories : /Users/lazzari/anaconda/envs
          package cache : /Users/lazzari/anaconda/pkgs
           channel URLs : https://repo.continuum.io/pkgs/free/osx-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/osx-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/osx-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : None
           offline mode : False
             user-agent : conda/4.3.4 requests/2.12.4 CPython/3.5.2 Darwin/16.3.0 OSX/10.12.2
                UID:GID : 140211:11347

@ggrrll
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ggrrll commented Jan 17, 2017 •
edited

ps: if you have a solution I guess would be useful...for the time being I just run r-kernel in jupyter without conda and it's fine

@jolespin
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Author

I never figured it out and just started using my conda installed R with RStudio. Here was my error:

Traceback (most recent call last):
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/notebook/base/handlers.py", line 481, in wrapper
    result = yield gen.maybe_future(method(self, *args, **kwargs))
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 1015, in run
    value = future.result()
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/concurrent.py", line 237, in result
    raise_exc_info(self._exc_info)
  File "<string>", line 3, in raise_exc_info
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 1021, in run
    yielded = self.gen.throw(*exc_info)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/notebook/services/sessions/handlers.py", line 75, in post
    type=mtype))
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 1015, in run
    value = future.result()
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/concurrent.py", line 237, in result
    raise_exc_info(self._exc_info)
  File "<string>", line 3, in raise_exc_info
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 1021, in run
    yielded = self.gen.throw(*exc_info)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/notebook/services/sessions/sessionmanager.py", line 79, in create_session
    kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 1015, in run
    value = future.result()
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/concurrent.py", line 237, in result
    raise_exc_info(self._exc_info)
  File "<string>", line 3, in raise_exc_info
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 1021, in run
    yielded = self.gen.throw(*exc_info)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/notebook/services/sessions/sessionmanager.py", line 92, in start_kernel_for_session
    self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 1015, in run
    value = future.result()
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/concurrent.py", line 237, in result
    raise_exc_info(self._exc_info)
  File "<string>", line 3, in raise_exc_info
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 285, in wrapper
    yielded = next(result)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/notebook/services/kernels/kernelmanager.py", line 87, in start_kernel
    super(MappingKernelManager, self).start_kernel(**kwargs)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/jupyter_client/multikernelmanager.py", line 110, in start_kernel
    km.start_kernel(**kwargs)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/jupyter_client/manager.py", line 243, in start_kernel
    **kw)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/jupyter_client/manager.py", line 189, in _launch_kernel
    return launch_kernel(kernel_cmd, **kw)
  File "/Users/jespinoz/anaconda/lib/python3.5/site-packages/jupyter_client/launcher.py", line 123, in launch_kernel
    proc = Popen(cmd, **kwargs)
  File "/Users/jespinoz/anaconda/lib/python3.5/subprocess.py", line 947, in __init__
    restore_signals, start_new_session)
  File "/Users/jespinoz/anaconda/lib/python3.5/subprocess.py", line 1551, in _execute_child
    raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: '/Users/jespinoz/anaconda/lib/R/bin/R'

@ggrrll
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ggrrll commented Jan 18, 2017 •
edited

@jolespin yeah, I saw...but what's the point of changing R version? you are still in R studio.
I wanted to switch to jupyter because I find it much more useful for keep your code readable and reproducible - that's a big concern in academic research, at least.

( maybe this post is a bit off-topic...we could continue this conversation somewhere else )

@jolespin
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I didn't change my R-version b/c my RStudio is using my conda-installed R that would be used via Jupyter. I agree 100% that using Jupyter would be better but I tried fixing it for a couple of days and I have stuff I need to work on. I want to be able to use R with Jupyter (I had it working before) and, ultimately, Beaker Notebook so I can use Python and R in the same notebook.

@mingwandroid
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@jolespin can you see if this is fixed now? A re-install might be good. Also, conda has its own RStudio packages and they do not require setting RSTUDIO_WHICH_R (but do require being launched from an activated conda environment or from Anaconda Navigator).

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Hi there, thank you for your contribution to Conda!

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@sandhujasmine @mingwandroid @kalefranz @jolespin @ggrrll @Z-Shiyi