rbokeh not displaying plots in Jupyter

[ijstokes]

Previously this code snippet with an R kernel in Jupyter worked for me in that it resulted in an in-notebook rbokeh plot. Now I get an error.

Here is the code:

library(dplyr)
library(rbokeh)
library(shiny)

z <- lm(dist ~ speed, data = cars)

p <- figure(width = 600, height = 600) %>%
  ly_points(cars, hover = cars) %>%
  ly_lines(lowess(cars), legend = "lowess") %>%
  ly_abline(z, type = 2, legend = "lm")
p

Here is the (new) output error message:

HTML widgets cannot be represented in plain text (need html)

Here is what I previously got out:

And if you care to watch a video version of it (not very illuminating: it is from an online training course, so it takes 2 minutes to go through 2 code cells -- all the action is at the very end):

https://screencast.com/t/jQigxkqJHw

[mingwandroid]

Can you show the output from:

$ ls -l /tmp/jupyter/envs/dspyr/lib/libintl.9.dylib
-rw-rw-r--  1 rdonnelly  wheel  79952 16 Feb 19:50 /tmp/jupyter/envs/dspyr/lib/libintl.9.dylib

$ md5 /tmp/jupyter/envs/dspyr/lib/libintl.9.dylib
MD5 (/tmp/jupyter/envs/dspyr/lib/libintl.9.dylib) = 9efd5b78a5bbbd12226ab8c5ec7e1621

And also: chmod +x /tmp/jupyter/envs/dspyr/lib/libintl.9.dylib then try again?

[mingwandroid]

Another thing to try is to just run R on its own then from another Terminal window get the list of shared libraries loaded outside of any jupyter kernel bits:

$ lsof -p $(ps aux | grep "exec/R" | sort | head -1 | tr -s " " | cut -f2 -d' ') | grep "\.so\|.dylib" | tr -s " " | cut -f9 -d' ' | sort | xargs md5
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/lib/libR.dylib) = 8ce46eed21723109e0995261078caf2b
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/grDevices/libs/grDevices.so) = 7ffb65a84922076bf9f9703927069d06
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/graphics/libs/graphics.so) = 36331432dd74e886e8aef01549318fdf
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/methods/libs/methods.so) = bce1dd21f4f13012d25aa1531ff60cbf
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/stats/libs/stats.so) = 58dedf3c5ee743de351c171a643c601b
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/utils/libs/utils.so) = d7cb98b69b34b681e604cf90041afad0
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libgcc_s.1.dylib) = b046bd07a9730dc2cc56e289530f98bc
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libgfortran.3.dylib) = 24ef24669e10025ec0575d7d2b7f9b91
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libiconv.2.dylib) = 876e5ca126d78f8f70d66aa59553068d
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicudata.54.1.dylib) = d159af09c65333f9bbb424a0eee4078d
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicui18n.54.1.dylib) = e581f6eaa56d5cc5a73871954fa27858
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicuuc.54.1.dylib) = 38a514e9bbb2c69fbe7ac0f050c62aa9
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libintl.9.dylib) = 9efd5b78a5bbbd12226ab8c5ec7e1621
MD5 (/private/tmp/jupyter/envs/dspyr/lib/liblzma.5.dylib) = bcac4111a08ef28530c77660640ed2d9
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libpcre.1.dylib) = ecfe2aef1bd19212b429444d66974689
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libquadmath.0.dylib) = c7ca60c64ec4f7e6031e08df717e9a75
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libreadline.6.2.dylib) = dcfc8bb9b615176679aa9097f5b8acb5
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libz.1.2.8.dylib) = e933057789e60406502f57c28ba7dcb8
MD5 (/usr/lib/libSystem.B.dylib) = 3e302c3d7a55d68f3d563af09096808e
MD5 (/usr/lib/system/libdyld.dylib) = f6098ab2aef1adebce43c6a4236b3699
MD5 (/usr/lib/system/libkxld.dylib) = be8dc101791da5da7204099fce61e330
MD5 (/usr/lib/system/libsystem_coretls.dylib) = c764f398a33330c9721185d6fefcc69f
MD5 (/usr/lib/system/libsystem_kernel.dylib) = 346c3820cf02cc12a7e56af07bc1e153
MD5 (/usr/lib/system/libsystem_networkextension.dylib) = 50360bb91fc7f160e2f07423d4a0ae77
MD5 (/usr/lib/system/libsystem_sandbox.dylib) = 05cddf1d2988e1366263f0080accde44
MD5 (/usr/lib/system/libsystem_symptoms.dylib) = 6ccbcfaf77560186e636561e795e7dde
MD5 (/usr/lib/system/libsystem_trace.dylib) = de9ddda018993f0d4a1031bfc93b47b8

[ijstokes]

This is interesting. libintl.9.dylib isn't there, but libintl.8.dylib is:

$  ls -l /tmp/jupyter/envs/dspyr/lib/libintl.9.dylib
ls: /tmp/jupyter/envs/dspyr/lib/libintl.9.dylib: No such file or directory
$  ls -l /tmp/jupyter/envs/dspyr/lib/libintl.
libintl.8.dylib  libintl.a        libintl.dylib    libintl.la

[mingwandroid]

conda info and conda list -e please!

[ijstokes]

My lsof ... | xargs md5 output is below:

$ lsof -p 41885 | grep "\.so\|.dylib" | tr -s " " | cut -f9 -d' ' | sort | xargs md5
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/lib/libR.dylib) = fa225d8d9305c998c42ebce879fb92db
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/grDevices/libs/grDevices.so) = c395fbec35311f6cfc148f88612c489d
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/graphics/libs/graphics.so) = 1ffff069298125b081af615803b21ee6
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/methods/libs/methods.so) = f06578e55ca987c0116637cc31b4131f
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/stats/libs/stats.so) = b10750ddb18ed7bf41438cd9f5d93a9b
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/utils/libs/utils.so) = af77665d3440260a4bf11cc0c07c1ee3
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libgcc_s.1.dylib) = b046bd07a9730dc2cc56e289530f98bc
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libgfortran.3.dylib) = 24ef24669e10025ec0575d7d2b7f9b91
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libiconv.2.dylib) = 263a1881df0ab6604b842a83d30ca439
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicudata.58.1.dylib) = cf206506c4b3fa212497ec0af9793bd2
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicui18n.58.1.dylib) = 76b38effeff0d352b272157f697d3c32
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicuuc.58.1.dylib) = 5bd91fba74f6456cc9f59b72936f72da
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libintl.8.dylib) = 2a0dfee7b2e5e62db8abd922f87f2c7f
MD5 (/private/tmp/jupyter/envs/dspyr/lib/liblzma.5.dylib) = e0bb032553485407bb5e0d297803d2a8
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libncurses.5.dylib) = a1e9fbd95339b689ed3f303319d60d12
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libpcre.1.dylib) = b7cfc6e7cec5f8eb128ab2385ec14039
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libquadmath.0.dylib) = c7ca60c64ec4f7e6031e08df717e9a75
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libreadline.6.2.dylib) = 38d576f05bc43e712a39ed919f560d38
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libtinfo.5.dylib) = e0167bf888808c5cb68e7fa9629d41da
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libz.1.2.8.dylib) = 266af1a5bf04d7c0690ce0273e8ef6b4
MD5 (/usr/lib/libSystem.B.dylib) = 3e302c3d7a55d68f3d563af09096808e
MD5 (/usr/lib/system/libdyld.dylib) = f6098ab2aef1adebce43c6a4236b3699
MD5 (/usr/lib/system/libkxld.dylib) = be8dc101791da5da7204099fce61e330
MD5 (/usr/lib/system/libsystem_coretls.dylib) = c764f398a33330c9721185d6fefcc69f
MD5 (/usr/lib/system/libsystem_kernel.dylib) = 346c3820cf02cc12a7e56af07bc1e153
MD5 (/usr/lib/system/libsystem_networkextension.dylib) = 50360bb91fc7f160e2f07423d4a0ae77
MD5 (/usr/lib/system/libsystem_sandbox.dylib) = 05cddf1d2988e1366263f0080accde44
MD5 (/usr/lib/system/libsystem_symptoms.dylib) = 6ccbcfaf77560186e636561e795e7dde
MD5 (/usr/lib/system/libsystem_trace.dylib) = de9ddda018993f0d4a1031bfc93b47b8

$ find . | grep libintl
./envs/dspyr/include/libintl.h
./envs/dspyr/lib/libintl.8.dylib
./envs/dspyr/lib/libintl.a
./envs/dspyr/lib/libintl.dylib
./envs/dspyr/lib/libintl.la
./envs/dspyr/share/gettext/intl/libintl.rc
./envs/dspyr/share/gettext/libintl.jar
./pkgs/gettext-0.19.7-1/include/libintl.h
./pkgs/gettext-0.19.7-1/lib/libintl.8.dylib
./pkgs/gettext-0.19.7-1/lib/libintl.a
./pkgs/gettext-0.19.7-1/lib/libintl.dylib
./pkgs/gettext-0.19.7-1/lib/libintl.la
./pkgs/gettext-0.19.7-1/share/gettext/intl/libintl.rc
./pkgs/gettext-0.19.7-1/share/gettext/libintl.jar

conda details:

(dspyr) ijstokes@0194-ijstokes jupyter $ conda info
Current conda install:

               platform : osx-64
          conda version : 4.3.11
       conda is private : False
      conda-env version : 4.3.11
    conda-build version : not installed
         python version : 3.6.0.final.0
       requests version : 2.12.4
       root environment : /tmp/jupyter  (writable)
    default environment : /tmp/jupyter/envs/dspyr
       envs directories : /tmp/jupyter/envs
                          /Users/ijstokes/.conda/envs
          package cache : /tmp/jupyter/pkgs
                          /Users/ijstokes/.conda/pkgs
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/anaconda-fusion/osx-64
                          https://conda.anaconda.org/anaconda-fusion/noarch
                          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 : /Users/ijstokes/.condarc
           offline mode : False
             user-agent : conda/4.3.11 requests/2.12.4 CPython/3.6.0 Darwin/16.4.0 OSX/10.12.3
                UID:GID : 502:20

(dspyr) ijstokes@0194-ijstokes jupyter $ conda list -e
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: osx-64
appnope=0.1.0=py35_0
bleach=1.5.0=py35_0
ca-certificates=2017.1.23=0
cairo=1.14.6=4
certifi=2017.1.23=py35_0
curl=7.52.1=0
decorator=4.0.11=py35_0
entrypoints=0.2.2=py35_1
fontconfig=2.12.1=4
freetype=2.7=1
gettext=0.19.7=1
glib=2.51.0=2
gsl=2.2.1=1
harfbuzz=1.3.4=2
html5lib=0.999=py35_0
icu=58.1=1
ipykernel=4.5.2=py35_0
ipython=5.2.2=py35_0
ipython_genutils=0.1.0=py35_0
jinja2=2.8=py35_1
jpeg=9b=0
jsonschema=2.5.1=py35_0
jupyter_client=4.4.0=py35_0
jupyter_core=4.2.1=py35_0
libffi=3.2.1=3
libgcc=4.8.5=1
libiconv=1.14=4
libpng=1.6.28=0
libsodium=1.0.10=0
libtiff=4.0.6=7
libxml2=2.9.4=4
markupsafe=0.23=py35_1
mistune=0.7.3=py35_1
nbconvert=5.1.1=py35_0
nbformat=4.2.0=py35_0
ncurses=5.9=10
notebook=4.4.1=py35_0
openssl=1.0.2h=3
pandoc=1.19.2=0
pandocfilters=1.4.1=py35_0
pango=1.40.3=3
pcre=8.39=0
pexpect=4.2.1=py35_0
pickleshare=0.7.3=py35_0
pip=9.0.1=py35_0
pixman=0.34.0=0
prompt_toolkit=1.0.13=py35_0
ptyprocess=0.5.1=py35_0
pygments=2.2.0=py35_0
python=3.5.3=1
pyzmq=16.0.2=py35_0
r-assertthat=0.1=r3.3.2_4
r-backports=1.0.4=r3.3.2_0
r-base=3.3.2=3
r-base64enc=0.1_3=r3.3.2_0
r-bh=1.62.0_1=r3.3.2_0
r-bitops=1.0_6=r3.3.2_2
r-boot=1.3_18=r3.3.2_0
r-broom=0.4.1=r3.3.2_0
r-car=2.1_4=r3.3.2_0
r-caret=6.0_73=r3.3.2_0
r-catools=1.17.1=r3.3.2_2
r-class=7.3_14=r3.3.2_0
r-cluster=2.0.5=r3.3.2_0
r-codetools=0.2_15=r3.3.2_0
r-colorspace=1.3_1=r3.3.2_0
r-crayon=1.3.2=r3.3.2_0
r-curl=2.3=r3.3.2_0
r-data.table=1.10.0=r3.3.2_0
r-dbi=0.5_1=r3.3.2_0
r-dichromat=2.0_0=r3.3.2_2
r-digest=0.6.10=r3.3.2_0
r-dplyr=0.5.0=r3.3.2_0
r-essentials=1.5.2=r3.3.2_0
r-evaluate=0.10=r3.3.2_0
r-forcats=0.1.1=r3.3.2_0
r-foreach=1.4.3=r3.3.2_0
r-foreign=0.8_67=r3.3.2_0
r-formatr=1.4=r3.3.2_0
r-ggplot2=2.2.0=r3.3.2_0
r-gistr=0.3.6=r3.3.2_0
r-glmnet=2.0_5=r3.3.2_0
r-gtable=0.2.0=r3.3.2_0
r-haven=1.0.0=r3.3.2_0
r-hexbin=1.27.1=r3.3.2_0
r-highr=0.6=r3.3.2_0
r-hms=0.3=r3.3.2_0
r-htmltools=0.3.5=r3.3.2_0
r-htmlwidgets=0.8=r3.3.2_0
r-httpuv=1.3.3=r3.3.2_0
r-httr=1.2.1=r3.3.2_0
r-irdisplay=0.4.4=r3.3.2_0
r-irkernel=0.7.1=r3.3.2_0
r-iterators=1.0.8=r3.3.2_0
r-jsonlite=1.1=r3.3.2_0
r-kernsmooth=2.23_15=r3.3.2_0
r-knitr=1.15.1=r3.3.2_0
r-labeling=0.3=r3.3.2_2
r-lattice=0.20_34=r3.3.2_0
r-lazyeval=0.2.0=r3.3.2_0
r-lme4=1.1_12=r3.3.2_0
r-lubridate=1.6.0=r3.3.2_0
r-magrittr=1.5=r3.3.2_2
r-maps=3.1.1=r3.3.2_0
r-markdown=0.7.7=r3.3.2_2
r-mass=7.3_45=r3.3.2_0
r-matrix=1.2_7.1=r3.3.2_0
r-matrixmodels=0.4_1=r3.3.2_0
r-mgcv=1.8_16=r3.3.2_0
r-mime=0.5=r3.3.2_0
r-minqa=1.2.4=r3.3.2_2
r-mnormt=1.5_5=r3.3.2_0
r-modelmetrics=1.1.0=r3.3.2_0
r-modelr=0.1.0=r3.3.2_0
r-munsell=0.4.3=r3.3.2_0
r-nlme=3.1_128=r3.3.2_0
r-nloptr=1.0.4=r3.3.2_2
r-nnet=7.3_12=r3.3.2_0
r-openssl=0.9.5=r3.3.2_0
r-pbdzmq=0.2_4=r3.3.2_0
r-pbkrtest=0.4_6=r3.3.2_0
r-plyr=1.8.4=r3.3.2_0
r-pryr=0.1.2=r3.3.2_0
r-psych=1.6.9=r3.3.2_0
r-purrr=0.2.2=r3.3.2_0
r-quantmod=0.4_7=r3.3.2_0
r-quantreg=5.29=r3.3.2_0
r-r6=2.2.0=r3.3.2_0
r-randomforest=4.6_12=r3.3.2_0
r-rbokeh=0.5.0=r3.3.2_0
r-rcolorbrewer=1.1_2=r3.3.2_3
r-rcpp=0.12.8=r3.3.2_0
r-rcppeigen=0.3.2.9.0=r3.3.2_0
r-readr=1.0.0=r3.3.2_0
r-readxl=0.1.1=r3.3.2_0
r-recommended=3.3.2=r3.3.2_0
r-repr=0.10=r3.3.2_0
r-reshape2=1.4.2=r3.3.2_0
r-rmarkdown=1.3=r3.3.2_0
r-rpart=4.1_10=r3.3.2_0
r-rprojroot=1.1=r3.3.2_0
r-rvest=0.3.2=r3.3.2_0
r-scales=0.4.1=r3.3.2_0
r-selectr=0.3_0=r3.3.2_0
r-shiny=0.14.2=r3.3.2_0
r-sourcetools=0.1.5=r3.3.2_0
r-sparsem=1.74=r3.3.2_0
r-spatial=7.3_11=r3.3.2_0
r-stringi=1.1.2=r3.3.2_0
r-stringr=1.1.0=r3.3.2_0
r-survival=2.40_1=r3.3.2_0
r-tibble=1.2=r3.3.2_0
r-tidyr=0.6.0=r3.3.2_0
r-tidyverse=1.0.0=r3.3.2_0
r-ttr=0.23_1=r3.3.2_0
r-uuid=0.1_2=r3.3.2_0
r-xml2=1.0.0=r3.3.2_0
r-xtable=1.8_2=r3.3.2_0
r-xts=0.9_7=r3.3.2_2
r-yaml=2.1.14=r3.3.2_0
r-zoo=1.7_13=r3.3.2_0
readline=6.2=0
setuptools=33.1.0=py35_0
simplegeneric=0.8.1=py35_0
six=1.10.0=py35_1
sqlite=3.13.0=1
terminado=0.6=py35_0
testpath=0.3=py35_0
tk=8.5.19=1
tornado=4.4.2=py35_0
traitlets=4.3.1=py35_0
wcwidth=0.1.7=py35_0
wheel=0.29.0=py35_0
xz=5.2.2=0
zeromq=4.1.5=0
zlib=1.2.8=3

[mingwandroid]

conda list -e --show-channel-urls please. I note you have conda-forge as your highest priority channel though!

[ijstokes]

I don't think that was going to give you what. you wanted so I did conda list -c instead. Yeah, conda-forge all over the place. Doh! Let me remove that and start again. I DID have it out of my .condarc but I added it back in for testing something else.

$ conda list -c
conda-forge::appnope-0.1.0-py35_0
conda-forge::bleach-1.5.0-py35_0
conda-forge::ca-certificates-2017.1.23-0
conda-forge::cairo-1.14.6-4
conda-forge::certifi-2017.1.23-py35_0
conda-forge::curl-7.52.1-0
conda-forge::decorator-4.0.11-py35_0
conda-forge::entrypoints-0.2.2-py35_1
conda-forge::fontconfig-2.12.1-4
conda-forge::freetype-2.7-1
conda-forge::gettext-0.19.7-1
conda-forge::glib-2.51.0-2
conda-forge::gsl-2.2.1-1
conda-forge::harfbuzz-1.3.4-2
defaults::html5lib-0.999-py35_0
conda-forge::icu-58.1-1
conda-forge::ipykernel-4.5.2-py35_0
conda-forge::ipython-5.2.2-py35_0
conda-forge::ipython_genutils-0.1.0-py35_0
conda-forge::jinja2-2.8-py35_1
conda-forge::jpeg-9b-0
conda-forge::jsonschema-2.5.1-py35_0
conda-forge::jupyter_client-4.4.0-py35_0
conda-forge::jupyter_core-4.2.1-py35_0
conda-forge::libffi-3.2.1-3
defaults::libgcc-4.8.5-1
conda-forge::libiconv-1.14-4
conda-forge::libpng-1.6.28-0
conda-forge::libsodium-1.0.10-0
conda-forge::libtiff-4.0.6-7
conda-forge::libxml2-2.9.4-4
conda-forge::markupsafe-0.23-py35_1
conda-forge::mistune-0.7.3-py35_1
conda-forge::nbconvert-5.1.1-py35_0
conda-forge::nbformat-4.2.0-py35_0
conda-forge::ncurses-5.9-10
conda-forge::notebook-4.4.1-py35_0
conda-forge::openssl-1.0.2h-3
conda-forge::pandoc-1.19.2-0
conda-forge::pandocfilters-1.4.1-py35_0
conda-forge::pango-1.40.3-3
conda-forge::pcre-8.39-0
conda-forge::pexpect-4.2.1-py35_0
conda-forge::pickleshare-0.7.3-py35_0
conda-forge::pip-9.0.1-py35_0
conda-forge::pixman-0.34.0-0
conda-forge::prompt_toolkit-1.0.13-py35_0
conda-forge::ptyprocess-0.5.1-py35_0
conda-forge::pygments-2.2.0-py35_0
conda-forge::python-3.5.3-1
conda-forge::pyzmq-16.0.2-py35_0
defaults::r-assertthat-0.1-r3.3.2_4
defaults::r-backports-1.0.4-r3.3.2_0
conda-forge::r-base-3.3.2-3
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
conda-forge::r-boot-1.3_18-r3.3.2_0
defaults::r-broom-0.4.1-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-r3.3.2_2
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-1.5.2-r3.3.2_0
defaults::r-evaluate-0.10-r3.3.2_0
defaults::r-forcats-0.1.1-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-haven-1.0.0-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-hms-0.3-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-lubridate-1.6.0-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-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-mnormt-1.5_5-r3.3.2_0
defaults::r-modelmetrics-1.1.0-r3.3.2_0
defaults::r-modelr-0.1.0-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-psych-1.6.9-r3.3.2_0
defaults::r-purrr-0.2.2-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-r3.3.2_3
defaults::r-rcpp-0.12.8-r3.3.2_0
defaults::r-rcppeigen-0.3.2.9.0-r3.3.2_0
defaults::r-readr-1.0.0-r3.3.2_0
defaults::r-readxl-0.1.1-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-reshape2-1.4.2-r3.3.2_0
defaults::r-rmarkdown-1.3-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-rvest-0.3.2-r3.3.2_0
defaults::r-scales-0.4.1-r3.3.2_0
defaults::r-selectr-0.3_0-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-tidyverse-1.0.0-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-xml2-1.0.0-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
conda-forge::readline-6.2-0
conda-forge::setuptools-33.1.0-py35_0
conda-forge::simplegeneric-0.8.1-py35_0
conda-forge::six-1.10.0-py35_1
conda-forge::sqlite-3.13.0-1
conda-forge::terminado-0.6-py35_0
conda-forge::testpath-0.3-py35_0
conda-forge::tk-8.5.19-1
conda-forge::tornado-4.4.2-py35_0
conda-forge::traitlets-4.3.1-py35_0
conda-forge::wcwidth-0.1.7-py35_0
conda-forge::wheel-0.29.0-py35_0
conda-forge::xz-5.2.2-0
conda-forge::zeromq-4.1.5-0
conda-forge::zlib-1.2.8-3

[ijstokes]

Started over, back to the original debug messages about "HTML widgets cannot be represented in plain text". No graphical output, only error output about dplyr. All packages now coming from defaults. No problems with libintl (picking up .9.dylib properly). Details below.

[I 06:16:37.275 NotebookApp] Kernel started: 19dcc1e9-7ae1-4e37-96c9-5551a659f236
DEBUG: Value output...
DEBUG: Message output: packageStartupMessage in packageStartupMessage(gettextf("\nAttaching package: %s\n", sQuote(package)), : 
Attaching package: ‘dplyr’

DEBUG: Stream output: 
Attaching package: ‘dplyr’

DEBUG: Sending msg stream
DEBUG: Message output: packageStartupMessage in packageStartupMessage(msg, domain = NA): The following objects are masked from ‘package:stats’:

    filter, lag

DEBUG: Stream output: The following objects are masked from ‘package:stats’:

    filter, lag

DEBUG: Sending msg stream
DEBUG: Message output: packageStartupMessage in packageStartupMessage(msg, domain = NA): The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

DEBUG: Stream output: The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

DEBUG: Sending msg stream
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Sending display_data: List of 2
 $ text/html : chr "<!DOCTYPE html>\n<html>\n<head>\n<meta charset=\"utf-8\" />\n<script src=\"data:application/x-javascript;base64,KGZ1bmN0aW9uKCk"| __truncated__
 $ text/plain: chr "HTML widgets cannot be represented in plain text (need html)"
DEBUG: Sending msg display_data

$ lsof -p $(ps aux | grep "exec/R" | sort | head -1 | tr -s " " | cut -f2 -d' ') | grep "\.so\|.dylib" | tr -s " " | cut -f9 -d' ' | sort | xargs md5
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/lib/libR.dylib) = 8ce46eed21723109e0995261078caf2b
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/Rcpp/libs/Rcpp.so) = 97519c675246d521c9ae89c86d1dd4c0
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/colorspace/libs/colorspace.so) = 4563da71ed233de27b9e21fc899c0b46
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/digest/libs/digest.so) = 0e4f7abe6cdb331c446e1a939808d55b
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/dplyr/libs/dplyr.so) = b5dc76ed53bf2edacc34b39f4edccbbe
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/grDevices/libs/grDevices.so) = 7ffb65a84922076bf9f9703927069d06
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/graphics/libs/graphics.so) = 36331432dd74e886e8aef01549318fdf
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/grid/libs/grid.so) = 11de18e98c5b0327880d06fdf50e3262
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/hexbin/libs/hexbin.so) = 9f6554c2e50b81266928953ebeb70ab7
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/htmltools/libs/htmltools.so) = 474984941ea1d1d1fc40e2aaa2f26f7f
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/jsonlite/libs/jsonlite.so) = cedf912a8744ed8350dd1b7de219101e
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/lattice/libs/lattice.so) = cb72876dac6edc330e0d2de9daa7e3fe
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/lazyeval/libs/lazyeval.so) = b107ff96a11a867e0ff2368e9e061d9d
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/maps/libs/maps.so) = 162883974c1fb07f21bc892d283fe6c1
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/methods/libs/methods.so) = bce1dd21f4f13012d25aa1531ff60cbf
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/pbdZMQ/libs/pbdZMQ.so) = 01017fbde6945d925e51ffb52f4fde99
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/plyr/libs/plyr.so) = 1f7aa928ec398d59fe286cfc801bf425
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/pryr/libs/pryr.so) = ffd1b91b7ef5cf9df274e090c38d57e3
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/scales/libs/scales.so) = 6379990a2a31c0b0706a53b884ba7da8
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/stats/libs/stats.so) = 58dedf3c5ee743de351c171a643c601b
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/stringi/libs/stringi.so) = 8a8de9d4269d8c4fed23bdaabd2ec74e
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/tibble/libs/tibble.so) = 30d7575eb80fd878bd7125be7130426d
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/tools/libs/tools.so) = fc3cf7e368f4b233cc69ac3b540981d5
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/utils/libs/utils.so) = d7cb98b69b34b681e604cf90041afad0
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/uuid/libs/uuid.so) = 63e3310c6abfd83a20c0cd07951ff6bd
MD5 (/private/tmp/jupyter/envs/dspyr/lib/R/library/yaml/libs/yaml.so) = 252a84f70c6bef9b38f8b4b6699bce88
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libgcc_s.1.dylib) = b046bd07a9730dc2cc56e289530f98bc
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libgfortran.3.dylib) = 24ef24669e10025ec0575d7d2b7f9b91
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libiconv.2.dylib) = 876e5ca126d78f8f70d66aa59553068d
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicudata.54.1.dylib) = d159af09c65333f9bbb424a0eee4078d
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicui18n.54.1.dylib) = e581f6eaa56d5cc5a73871954fa27858
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libicuuc.54.1.dylib) = 38a514e9bbb2c69fbe7ac0f050c62aa9
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libintl.9.dylib) = 9efd5b78a5bbbd12226ab8c5ec7e1621
MD5 (/private/tmp/jupyter/envs/dspyr/lib/liblzma.5.dylib) = bcac4111a08ef28530c77660640ed2d9
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libpcre.1.dylib) = ecfe2aef1bd19212b429444d66974689
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libquadmath.0.dylib) = c7ca60c64ec4f7e6031e08df717e9a75
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libreadline.6.2.dylib) = dcfc8bb9b615176679aa9097f5b8acb5
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libstdc++.6.dylib) = 18a3affdc57f95c1f06b0ab31278f5ca
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libz.1.2.8.dylib) = e933057789e60406502f57c28ba7dcb8
MD5 (/private/tmp/jupyter/envs/dspyr/lib/libzmq.5.dylib) = 1c00c63f6ac2402ae4722e44c07db6cf
MD5 (/usr/lib/libSystem.B.dylib) = 3e302c3d7a55d68f3d563af09096808e
MD5 (/usr/lib/system/libdyld.dylib) = f6098ab2aef1adebce43c6a4236b3699
MD5 (/usr/lib/system/libkxld.dylib) = be8dc101791da5da7204099fce61e330
MD5 (/usr/lib/system/libsystem_coretls.dylib) = c764f398a33330c9721185d6fefcc69f
MD5 (/usr/lib/system/libsystem_kernel.dylib) = 346c3820cf02cc12a7e56af07bc1e153
MD5 (/usr/lib/system/libsystem_networkextension.dylib) = 50360bb91fc7f160e2f07423d4a0ae77
MD5 (/usr/lib/system/libsystem_sandbox.dylib) = 05cddf1d2988e1366263f0080accde44
MD5 (/usr/lib/system/libsystem_symptoms.dylib) = 6ccbcfaf77560186e636561e795e7dde
MD5 (/usr/lib/system/libsystem_trace.dylib) = de9ddda018993f0d4a1031bfc93b47b8

$ conda list -c
defaults::appnope-0.1.0-py36_0
defaults::bleach-1.5.0-py36_0
defaults::cairo-1.14.8-0
defaults::curl-7.52.1-0
defaults::decorator-4.0.11-py36_0
defaults::entrypoints-0.2.2-py36_1
defaults::fontconfig-2.12.1-3
defaults::freetype-2.5.5-2
defaults::gettext-0.19.8-1
defaults::glib-2.50.2-1
defaults::gsl-2.2.1-0
defaults::harfbuzz-0.9.39-2
defaults::html5lib-0.999-py36_0
defaults::icu-54.1-0
defaults::ipykernel-4.5.2-py36_0
defaults::ipython-5.2.2-py36_0
defaults::ipython_genutils-0.1.0-py36_0
defaults::jbig-2.1-0
defaults::jinja2-2.9.4-py36_0
defaults::jpeg-9b-0
defaults::jsonschema-2.5.1-py36_0
defaults::jupyter_client-4.4.0-py36_0
defaults::jupyter_core-4.3.0-py36_0
defaults::libffi-3.2.1-1
defaults::libgcc-4.8.5-1
defaults::libiconv-1.14-0
defaults::libpng-1.6.27-0
defaults::libtiff-4.0.6-3
defaults::libxml2-2.9.4-0
defaults::markupsafe-0.23-py36_2
defaults::mistune-0.7.3-py36_1
defaults::nbconvert-5.1.1-py36_0
defaults::nbformat-4.2.0-py36_0
defaults::ncurses-5.9-10
defaults::notebook-4.3.1-py36_0
defaults::openssl-1.0.2k-0
defaults::pandoc-1.19.2.1-0
defaults::pandocfilters-1.4.1-py36_0
defaults::pango-1.40.3-1
defaults::path.py-10.1-py36_0
defaults::pcre-8.39-1
defaults::pexpect-4.2.1-py36_0
defaults::pickleshare-0.7.4-py36_0
defaults::pip-9.0.1-py36_1
defaults::pixman-0.34.0-0
defaults::prompt_toolkit-1.0.9-py36_0
defaults::ptyprocess-0.5.1-py36_0
defaults::pygments-2.1.3-py36_0
defaults::python-3.6.0-0
defaults::pyzmq-16.0.2-py36_0
defaults::r-assertthat-0.1-r3.3.2_4
defaults::r-backports-1.0.4-r3.3.2_0
defaults::r-base-3.3.2-1
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-broom-0.4.1-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-r3.3.2_2
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-1.5.2-r3.3.2_0
defaults::r-evaluate-0.10-r3.3.2_0
defaults::r-forcats-0.1.1-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-haven-1.0.0-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-hms-0.3-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-lubridate-1.6.0-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-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-mnormt-1.5_5-r3.3.2_0
defaults::r-modelmetrics-1.1.0-r3.3.2_0
defaults::r-modelr-0.1.0-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-psych-1.6.9-r3.3.2_0
defaults::r-purrr-0.2.2-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-r3.3.2_3
defaults::r-rcpp-0.12.8-r3.3.2_0
defaults::r-rcppeigen-0.3.2.9.0-r3.3.2_0
defaults::r-readr-1.0.0-r3.3.2_0
defaults::r-readxl-0.1.1-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-reshape2-1.4.2-r3.3.2_0
defaults::r-rmarkdown-1.3-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-rvest-0.3.2-r3.3.2_0
defaults::r-scales-0.4.1-r3.3.2_0
defaults::r-selectr-0.3_0-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-tidyverse-1.0.0-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-xml2-1.0.0-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::setuptools-27.2.0-py36_0
defaults::simplegeneric-0.8.1-py36_1
defaults::six-1.10.0-py36_0
defaults::sqlite-3.13.0-0
defaults::terminado-0.6-py36_0
defaults::testpath-0.3-py36_0
defaults::tk-8.5.18-0
defaults::tornado-4.4.2-py36_0
defaults::traitlets-4.3.1-py36_0
defaults::wcwidth-0.1.7-py36_0
defaults::wheel-0.29.0-py36_0
defaults::xz-5.2.2-1
defaults::zeromq-4.1.3-0
defaults::zlib-1.2.8-3

$ conda info -a
Current conda install:

               platform : osx-64
          conda version : 4.3.11
       conda is private : False
      conda-env version : 4.3.11
    conda-build version : not installed
         python version : 3.6.0.final.0
       requests version : 2.12.4
       root environment : /tmp/jupyter  (writable)
    default environment : /tmp/jupyter/envs/dspyr
       envs directories : /tmp/jupyter/envs
                          /Users/ijstokes/.conda/envs
          package cache : /tmp/jupyter/pkgs
                          /Users/ijstokes/.conda/pkgs
           channel URLs : https://conda.anaconda.org/anaconda-fusion/osx-64
                          https://conda.anaconda.org/anaconda-fusion/noarch
                          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 : /Users/ijstokes/.condarc
           offline mode : False
             user-agent : conda/4.3.11 requests/2.12.4 CPython/3.6.0 Darwin/16.4.0 OSX/10.12.3
                UID:GID : 502:20

# conda environments:
#
dspyr                 *  /tmp/jupyter/envs/dspyr
root                     /tmp/jupyter

sys.version: 3.6.0 |Continuum Analytics, Inc.| (defau...
sys.prefix: /tmp/jupyter
sys.executable: /tmp/jupyter/bin/python
conda location: /tmp/jupyter/lib/python3.6/site-packages/conda
conda-build: /Users/ijstokes/anaconda/bin/conda-build
conda-env: /tmp/jupyter/bin/conda-env
user site dirs: 

CIO_TEST: <not set>
CONDA_DEFAULT_ENV: dspyr
CONDA_ENVS_PATH: <not set>
DYLD_LIBRARY_PATH: <not set>
PATH: /tmp/jupyter/envs/dspyr/bin:/Users/ijstokes/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
PYTHONHOME: <not set>
PYTHONPATH: <not set>

WARNING: could not import _license.show_info
# try:
# $ conda install -n root _license

[mingwandroid]

As @msarahan mentioned in https://github.com/ContinuumIO/anaconda-issues/issues/1391#issuecomment-276976072, all the representations are 'printed' so you will always get that HTML Widgets warning. The important bit is that you also get the html representation, which you do:

$ text/html : chr "<!DOCTYPE html>\n<html>\n<head>\n<meta charset=\"utf-8\" />\n<script src=\"data:application/x-javascript;base64,KGZ1bmN0aW9uKCk"| __truncated__
$ text/plain: chr "HTML widgets cannot be represented in plain text (need html)"

[mingwandroid]

The mystery continues! Can I see the output from: lsof -p $(ps aux | grep "exec/R" | sort | head -1 | tr -s " " | cut -f2 -d' ') | grep "\.so\|.dylib" | tr -s " " | cut -f9 -d' ' | sort | xargs md5 | sed -E 's|(MD5 \()([0-9a-zA-Z/.+\_-]*)\) = ([0-9a-f]*)|\3 \2|g' | sort

Here I'm sorting by md5 since your macOS seems to be finding things in a folder different order to my macOS! Mine is:

01017fbde6945d925e51ffb52f4fde99 /private/tmp/jupyter/pkgs/r-pbdzmq-0.2_4-r3.3.2_0/lib/R/library/pbdZMQ/libs/pbdZMQ.so
05cddf1d2988e1366263f0080accde44 /usr/lib/system/libsystem_sandbox.dylib
0e4f7abe6cdb331c446e1a939808d55b /private/tmp/jupyter/pkgs/r-digest-0.6.10-r3.3.2_0/lib/R/library/digest/libs/digest.so
11de18e98c5b0327880d06fdf50e3262 /private/tmp/jupyter/envs/dspyr/lib/R/library/grid/libs/grid.so
162883974c1fb07f21bc892d283fe6c1 /private/tmp/jupyter/envs/dspyr/lib/R/library/maps/libs/maps.so
18a3affdc57f95c1f06b0ab31278f5ca /private/tmp/jupyter/envs/dspyr/lib/libstdc++.6.dylib
1c00c63f6ac2402ae4722e44c07db6cf /private/tmp/jupyter/pkgs/zeromq-4.1.3-0/lib/libzmq.5.dylib
1f7aa928ec398d59fe286cfc801bf425 /private/tmp/jupyter/envs/dspyr/lib/R/library/plyr/libs/plyr.so
24ef24669e10025ec0575d7d2b7f9b91 /private/tmp/jupyter/pkgs/libgcc-4.8.5-1/lib/libgfortran.3.dylib
252a84f70c6bef9b38f8b4b6699bce88 /private/tmp/jupyter/envs/dspyr/lib/R/library/yaml/libs/yaml.so
30d7575eb80fd878bd7125be7130426d /private/tmp/jupyter/envs/dspyr/lib/R/library/tibble/libs/tibble.so
346c3820cf02cc12a7e56af07bc1e153 /usr/lib/system/libsystem_kernel.dylib
36331432dd74e886e8aef01549318fdf /private/tmp/jupyter/pkgs/r-base-3.3.2-1/lib/R/library/graphics/libs/graphics.so
38a514e9bbb2c69fbe7ac0f050c62aa9 /private/tmp/jupyter/pkgs/icu-54.1-0/lib/libicuuc.54.1.dylib
3e302c3d7a55d68f3d563af09096808e /usr/lib/libSystem.B.dylib
4563da71ed233de27b9e21fc899c0b46 /private/tmp/jupyter/envs/dspyr/lib/R/library/colorspace/libs/colorspace.so
474984941ea1d1d1fc40e2aaa2f26f7f /private/tmp/jupyter/envs/dspyr/lib/R/library/htmltools/libs/htmltools.so
50360bb91fc7f160e2f07423d4a0ae77 /usr/lib/system/libsystem_networkextension.dylib
58dedf3c5ee743de351c171a643c601b /private/tmp/jupyter/pkgs/r-base-3.3.2-1/lib/R/library/stats/libs/stats.so
6379990a2a31c0b0706a53b884ba7da8 /private/tmp/jupyter/envs/dspyr/lib/R/library/scales/libs/scales.so
63e3310c6abfd83a20c0cd07951ff6bd /private/tmp/jupyter/pkgs/r-uuid-0.1_2-r3.3.2_0/lib/R/library/uuid/libs/uuid.so
6ccbcfaf77560186e636561e795e7dde /usr/lib/system/libsystem_symptoms.dylib
7ffb65a84922076bf9f9703927069d06 /private/tmp/jupyter/pkgs/r-base-3.3.2-1/lib/R/library/grDevices/libs/grDevices.so
876e5ca126d78f8f70d66aa59553068d /private/tmp/jupyter/envs/dspyr/lib/libiconv.2.dylib
8a8de9d4269d8c4fed23bdaabd2ec74e /private/tmp/jupyter/pkgs/r-stringi-1.1.2-r3.3.2_0/lib/R/library/stringi/libs/stringi.so
8ce46eed21723109e0995261078caf2b /private/tmp/jupyter/envs/dspyr/lib/R/lib/libR.dylib
97519c675246d521c9ae89c86d1dd4c0 /private/tmp/jupyter/envs/dspyr/lib/R/library/Rcpp/libs/Rcpp.so
9efd5b78a5bbbd12226ab8c5ec7e1621 /private/tmp/jupyter/envs/dspyr/lib/libintl.9.dylib
9f6554c2e50b81266928953ebeb70ab7 /private/tmp/jupyter/envs/dspyr/lib/R/library/hexbin/libs/hexbin.so
b046bd07a9730dc2cc56e289530f98bc /private/tmp/jupyter/pkgs/libgcc-4.8.5-1/lib/libgcc_s.1.dylib
b107ff96a11a867e0ff2368e9e061d9d /private/tmp/jupyter/envs/dspyr/lib/R/library/lazyeval/libs/lazyeval.so
b5dc76ed53bf2edacc34b39f4edccbbe /private/tmp/jupyter/envs/dspyr/lib/R/library/dplyr/libs/dplyr.so
bcac4111a08ef28530c77660640ed2d9 /private/tmp/jupyter/pkgs/xz-5.2.2-1/lib/liblzma.5.dylib
bce1dd21f4f13012d25aa1531ff60cbf /private/tmp/jupyter/pkgs/r-base-3.3.2-1/lib/R/library/methods/libs/methods.so
be8dc101791da5da7204099fce61e330 /usr/lib/system/libkxld.dylib
c764f398a33330c9721185d6fefcc69f /usr/lib/system/libsystem_coretls.dylib
c7ca60c64ec4f7e6031e08df717e9a75 /private/tmp/jupyter/envs/dspyr/lib/libquadmath.0.dylib
cb72876dac6edc330e0d2de9daa7e3fe /private/tmp/jupyter/envs/dspyr/lib/R/library/lattice/libs/lattice.so
cedf912a8744ed8350dd1b7de219101e /private/tmp/jupyter/pkgs/r-jsonlite-1.1-r3.3.2_0/lib/R/library/jsonlite/libs/jsonlite.so
d159af09c65333f9bbb424a0eee4078d /private/tmp/jupyter/pkgs/icu-54.1-0/lib/libicudata.54.1.dylib
d7cb98b69b34b681e604cf90041afad0 /private/tmp/jupyter/pkgs/r-base-3.3.2-1/lib/R/library/utils/libs/utils.so
dcfc8bb9b615176679aa9097f5b8acb5 /private/tmp/jupyter/pkgs/readline-6.2-2/lib/libreadline.6.2.dylib
de9ddda018993f0d4a1031bfc93b47b8 /usr/lib/system/libsystem_trace.dylib
e581f6eaa56d5cc5a73871954fa27858 /private/tmp/jupyter/pkgs/icu-54.1-0/lib/libicui18n.54.1.dylib
e933057789e60406502f57c28ba7dcb8 /private/tmp/jupyter/envs/dspyr/lib/libz.1.2.8.dylib
ecfe2aef1bd19212b429444d66974689 /private/tmp/jupyter/pkgs/pcre-8.39-1/lib/libpcre.1.dylib
f6098ab2aef1adebce43c6a4236b3699 /usr/lib/system/libdyld.dylib
fc3cf7e368f4b233cc69ac3b540981d5 /private/tmp/jupyter/pkgs/r-base-3.3.2-1/lib/R/library/tools/libs/tools.so
ffd1b91b7ef5cf9df274e090c38d57e3 /private/tmp/jupyter/envs/dspyr/lib/R/library/pryr/libs/pryr.so

[mingwandroid]

Here are yours:

01017fbde6945d925e51ffb52f4fde99 /private/tmp/jupyter/envs/dspyr/lib/R/library/pbdZMQ/libs/pbdZMQ.so
05cddf1d2988e1366263f0080accde44 /usr/lib/system/libsystem_sandbox.dylib
0e4f7abe6cdb331c446e1a939808d55b /private/tmp/jupyter/envs/dspyr/lib/R/library/digest/libs/digest.so
11de18e98c5b0327880d06fdf50e3262 /private/tmp/jupyter/envs/dspyr/lib/R/library/grid/libs/grid.so
162883974c1fb07f21bc892d283fe6c1 /private/tmp/jupyter/envs/dspyr/lib/R/library/maps/libs/maps.so
18a3affdc57f95c1f06b0ab31278f5ca /private/tmp/jupyter/envs/dspyr/lib/libstdc++.6.dylib
1c00c63f6ac2402ae4722e44c07db6cf /private/tmp/jupyter/envs/dspyr/lib/libzmq.5.dylib
1f7aa928ec398d59fe286cfc801bf425 /private/tmp/jupyter/envs/dspyr/lib/R/library/plyr/libs/plyr.so
24ef24669e10025ec0575d7d2b7f9b91 /private/tmp/jupyter/envs/dspyr/lib/libgfortran.3.dylib
252a84f70c6bef9b38f8b4b6699bce88 /private/tmp/jupyter/envs/dspyr/lib/R/library/yaml/libs/yaml.so
30d7575eb80fd878bd7125be7130426d /private/tmp/jupyter/envs/dspyr/lib/R/library/tibble/libs/tibble.so
346c3820cf02cc12a7e56af07bc1e153 /usr/lib/system/libsystem_kernel.dylib
36331432dd74e886e8aef01549318fdf /private/tmp/jupyter/envs/dspyr/lib/R/library/graphics/libs/graphics.so
38a514e9bbb2c69fbe7ac0f050c62aa9 /private/tmp/jupyter/envs/dspyr/lib/libicuuc.54.1.dylib
3e302c3d7a55d68f3d563af09096808e /usr/lib/libSystem.B.dylib
4563da71ed233de27b9e21fc899c0b46 /private/tmp/jupyter/envs/dspyr/lib/R/library/colorspace/libs/colorspace.so
474984941ea1d1d1fc40e2aaa2f26f7f /private/tmp/jupyter/envs/dspyr/lib/R/library/htmltools/libs/htmltools.so
50360bb91fc7f160e2f07423d4a0ae77 /usr/lib/system/libsystem_networkextension.dylib
58dedf3c5ee743de351c171a643c601b /private/tmp/jupyter/envs/dspyr/lib/R/library/stats/libs/stats.so
6379990a2a31c0b0706a53b884ba7da8 /private/tmp/jupyter/envs/dspyr/lib/R/library/scales/libs/scales.so
63e3310c6abfd83a20c0cd07951ff6bd /private/tmp/jupyter/envs/dspyr/lib/R/library/uuid/libs/uuid.so
6ccbcfaf77560186e636561e795e7dde /usr/lib/system/libsystem_symptoms.dylib
7ffb65a84922076bf9f9703927069d06 /private/tmp/jupyter/envs/dspyr/lib/R/library/grDevices/libs/grDevices.so
876e5ca126d78f8f70d66aa59553068d /private/tmp/jupyter/envs/dspyr/lib/libiconv.2.dylib
8a8de9d4269d8c4fed23bdaabd2ec74e /private/tmp/jupyter/envs/dspyr/lib/R/library/stringi/libs/stringi.so
8ce46eed21723109e0995261078caf2b /private/tmp/jupyter/envs/dspyr/lib/R/lib/libR.dylib
97519c675246d521c9ae89c86d1dd4c0 /private/tmp/jupyter/envs/dspyr/lib/R/library/Rcpp/libs/Rcpp.so
9efd5b78a5bbbd12226ab8c5ec7e1621 /private/tmp/jupyter/envs/dspyr/lib/libintl.9.dylib
9f6554c2e50b81266928953ebeb70ab7 /private/tmp/jupyter/envs/dspyr/lib/R/library/hexbin/libs/hexbin.so
b046bd07a9730dc2cc56e289530f98bc /private/tmp/jupyter/envs/dspyr/lib/libgcc_s.1.dylib
b107ff96a11a867e0ff2368e9e061d9d /private/tmp/jupyter/envs/dspyr/lib/R/library/lazyeval/libs/lazyeval.so
b5dc76ed53bf2edacc34b39f4edccbbe /private/tmp/jupyter/envs/dspyr/lib/R/library/dplyr/libs/dplyr.so
bcac4111a08ef28530c77660640ed2d9 /private/tmp/jupyter/envs/dspyr/lib/liblzma.5.dylib
bce1dd21f4f13012d25aa1531ff60cbf /private/tmp/jupyter/envs/dspyr/lib/R/library/methods/libs/methods.so
be8dc101791da5da7204099fce61e330 /usr/lib/system/libkxld.dylib
c764f398a33330c9721185d6fefcc69f /usr/lib/system/libsystem_coretls.dylib
c7ca60c64ec4f7e6031e08df717e9a75 /private/tmp/jupyter/envs/dspyr/lib/libquadmath.0.dylib
cb72876dac6edc330e0d2de9daa7e3fe /private/tmp/jupyter/envs/dspyr/lib/R/library/lattice/libs/lattice.so
cedf912a8744ed8350dd1b7de219101e /private/tmp/jupyter/envs/dspyr/lib/R/library/jsonlite/libs/jsonlite.so
d159af09c65333f9bbb424a0eee4078d /private/tmp/jupyter/envs/dspyr/lib/libicudata.54.1.dylib
d7cb98b69b34b681e604cf90041afad0 /private/tmp/jupyter/envs/dspyr/lib/R/library/utils/libs/utils.so
dcfc8bb9b615176679aa9097f5b8acb5 /private/tmp/jupyter/envs/dspyr/lib/libreadline.6.2.dylib
de9ddda018993f0d4a1031bfc93b47b8 /usr/lib/system/libsystem_trace.dylib
e581f6eaa56d5cc5a73871954fa27858 /private/tmp/jupyter/envs/dspyr/lib/libicui18n.54.1.dylib
e933057789e60406502f57c28ba7dcb8 /private/tmp/jupyter/envs/dspyr/lib/libz.1.2.8.dylib
ecfe2aef1bd19212b429444d66974689 /private/tmp/jupyter/envs/dspyr/lib/libpcre.1.dylib
f6098ab2aef1adebce43c6a4236b3699 /usr/lib/system/libdyld.dylib
fc3cf7e368f4b233cc69ac3b540981d5 /private/tmp/jupyter/envs/dspyr/lib/R/library/tools/libs/tools.so
ffd1b91b7ef5cf9df274e090c38d57e3 /private/tmp/jupyter/envs/dspyr/lib/R/library/pryr/libs/pryr.so

[mingwandroid]

Can you show me:

1. The output from ps aux | grep "exec/R" | sort | head -1
2. Your ~/.condarc?

It seems my R has loaded its shared libraries from the package cache while yours have been loaded from the environment itself. I'm wondering if you've set yours to copy instead of using hardlinks?

[mingwandroid]

@msarahan's (exactly the same as yours but different from mine, this works for Mike too):

01017fbde6945d925e51ffb52f4fde99 /private/tmp/jupyter/envs/dspyr/lib/R/library/pbdZMQ/libs/pbdZMQ.so
05cddf1d2988e1366263f0080accde44 /usr/lib/system/libsystem_sandbox.dylib
0e4f7abe6cdb331c446e1a939808d55b /private/tmp/jupyter/envs/dspyr/lib/R/library/digest/libs/digest.so
11de18e98c5b0327880d06fdf50e3262 /private/tmp/jupyter/envs/dspyr/lib/R/library/grid/libs/grid.so
162883974c1fb07f21bc892d283fe6c1 /private/tmp/jupyter/envs/dspyr/lib/R/library/maps/libs/maps.so
18a3affdc57f95c1f06b0ab31278f5ca /private/tmp/jupyter/envs/dspyr/lib/libstdc++.6.dylib
1c00c63f6ac2402ae4722e44c07db6cf /private/tmp/jupyter/envs/dspyr/lib/libzmq.5.dylib
1f7aa928ec398d59fe286cfc801bf425 /private/tmp/jupyter/envs/dspyr/lib/R/library/plyr/libs/plyr.so
24ef24669e10025ec0575d7d2b7f9b91 /private/tmp/jupyter/envs/dspyr/lib/libgfortran.3.dylib
252a84f70c6bef9b38f8b4b6699bce88 /private/tmp/jupyter/envs/dspyr/lib/R/library/yaml/libs/yaml.so
30d7575eb80fd878bd7125be7130426d /private/tmp/jupyter/envs/dspyr/lib/R/library/tibble/libs/tibble.so
346c3820cf02cc12a7e56af07bc1e153 /usr/lib/system/libsystem_kernel.dylib
36331432dd74e886e8aef01549318fdf /private/tmp/jupyter/envs/dspyr/lib/R/library/graphics/libs/graphics.so
38a514e9bbb2c69fbe7ac0f050c62aa9 /private/tmp/jupyter/envs/dspyr/lib/libicuuc.54.1.dylib
3e302c3d7a55d68f3d563af09096808e /usr/lib/libSystem.B.dylib
4563da71ed233de27b9e21fc899c0b46 /private/tmp/jupyter/envs/dspyr/lib/R/library/colorspace/libs/colorspace.so
474984941ea1d1d1fc40e2aaa2f26f7f /private/tmp/jupyter/envs/dspyr/lib/R/library/htmltools/libs/htmltools.so
50360bb91fc7f160e2f07423d4a0ae77 /usr/lib/system/libsystem_networkextension.dylib
58dedf3c5ee743de351c171a643c601b /private/tmp/jupyter/envs/dspyr/lib/R/library/stats/libs/stats.so
6379990a2a31c0b0706a53b884ba7da8 /private/tmp/jupyter/envs/dspyr/lib/R/library/scales/libs/scales.so
63e3310c6abfd83a20c0cd07951ff6bd /private/tmp/jupyter/envs/dspyr/lib/R/library/uuid/libs/uuid.so
6ccbcfaf77560186e636561e795e7dde /usr/lib/system/libsystem_symptoms.dylib
7ffb65a84922076bf9f9703927069d06 /private/tmp/jupyter/envs/dspyr/lib/R/library/grDevices/libs/grDevices.so
876e5ca126d78f8f70d66aa59553068d /private/tmp/jupyter/envs/dspyr/lib/libiconv.2.dylib
8a8de9d4269d8c4fed23bdaabd2ec74e /private/tmp/jupyter/envs/dspyr/lib/R/library/stringi/libs/stringi.so
8ce46eed21723109e0995261078caf2b /private/tmp/jupyter/envs/dspyr/lib/R/lib/libR.dylib
97519c675246d521c9ae89c86d1dd4c0 /private/tmp/jupyter/envs/dspyr/lib/R/library/Rcpp/libs/Rcpp.so
9efd5b78a5bbbd12226ab8c5ec7e1621 /private/tmp/jupyter/envs/dspyr/lib/libintl.9.dylib
9f6554c2e50b81266928953ebeb70ab7 /private/tmp/jupyter/envs/dspyr/lib/R/library/hexbin/libs/hexbin.so
b046bd07a9730dc2cc56e289530f98bc /private/tmp/jupyter/envs/dspyr/lib/libgcc_s.1.dylib
b107ff96a11a867e0ff2368e9e061d9d /private/tmp/jupyter/envs/dspyr/lib/R/library/lazyeval/libs/lazyeval.so
b5dc76ed53bf2edacc34b39f4edccbbe /private/tmp/jupyter/envs/dspyr/lib/R/library/dplyr/libs/dplyr.so
bcac4111a08ef28530c77660640ed2d9 /private/tmp/jupyter/envs/dspyr/lib/liblzma.5.dylib
bce1dd21f4f13012d25aa1531ff60cbf /private/tmp/jupyter/envs/dspyr/lib/R/library/methods/libs/methods.so
be8dc101791da5da7204099fce61e330 /usr/lib/system/libkxld.dylib
c764f398a33330c9721185d6fefcc69f /usr/lib/system/libsystem_coretls.dylib
c7ca60c64ec4f7e6031e08df717e9a75 /private/tmp/jupyter/envs/dspyr/lib/libquadmath.0.dylib
cb72876dac6edc330e0d2de9daa7e3fe /private/tmp/jupyter/envs/dspyr/lib/R/library/lattice/libs/lattice.so
cedf912a8744ed8350dd1b7de219101e /private/tmp/jupyter/envs/dspyr/lib/R/library/jsonlite/libs/jsonlite.so
d159af09c65333f9bbb424a0eee4078d /private/tmp/jupyter/envs/dspyr/lib/libicudata.54.1.dylib
d7cb98b69b34b681e604cf90041afad0 /private/tmp/jupyter/envs/dspyr/lib/R/library/utils/libs/utils.so
dcfc8bb9b615176679aa9097f5b8acb5 /private/tmp/jupyter/envs/dspyr/lib/libreadline.6.2.dylib
de9ddda018993f0d4a1031bfc93b47b8 /usr/lib/system/libsystem_trace.dylib
e581f6eaa56d5cc5a73871954fa27858 /private/tmp/jupyter/envs/dspyr/lib/libicui18n.54.1.dylib
e933057789e60406502f57c28ba7dcb8 /private/tmp/jupyter/envs/dspyr/lib/libz.1.2.8.dylib
ecfe2aef1bd19212b429444d66974689 /private/tmp/jupyter/envs/dspyr/lib/libpcre.1.dylib
f6098ab2aef1adebce43c6a4236b3699 /usr/lib/system/libdyld.dylib
fc3cf7e368f4b233cc69ac3b540981d5 /private/tmp/jupyter/envs/dspyr/lib/R/library/tools/libs/tools.so
ffd1b91b7ef5cf9df274e090c38d57e3 /private/tmp/jupyter/envs/dspyr/lib/R/library/pryr/libs/pryr.so

[mingwandroid]

@ijstokes are you using Firefox here?

[ijstokes]

FF was the final hurdle. With Chrome it works!

Any guesses as to why Python Bokeh inside Jupyter with FF works, but rbokeh inside Jupyter with FF fails?

In case you care about the other bits you asked about:

$ ps aux | grep "exec/R" | sort | head -1
ijstokes         48641   0.2  0.4  2569312  66200   ??  Ss    9:49AM   0:00.60 /tmp/jupyter/envs/dspyr/lib/R/bin/exec/R --slave -e IRkernel::main() --args /Users/ijstokes/Library/Jupyter/runtime/kernel-917ef1ba-e774-40c1-b239-d969237dde99.json

$ cat ~/.condarc
cat: /Users/ijstokes/.condarc: No such file or directory

$ conda info | grep "config file"
            config file : None

(I removed it to make sure it wasn't the problem)

[mingwandroid]

Any guesses as to why Python Bokeh inside Jupyter with FF works, but rbokeh inside Jupyter with FF fails?

No idea, I'm so far out of my comfort zone when it comes to JS and browsers. For me, it works on Chrome and Safari, but not Firefox.

Could you file a bug against the rbokeh project for this? You can see some warnings from both Firefox:

TypeError: body is null[Learn More]  main.min.js:20309:17
    OutputArea.prototype.create_output_subarea/< http://localhost:8888/static/notebook/js/main.min.js:20309:17
    x.event.dispatch http://localhost:8888/static/notebook/js/main.min.js:88:9954
    x.event.add/y.handle

.. and Chrome:

Uncaught TypeError: Cannot read property 'clientHeight' of null
    at e.get_width_height (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:12)
    at e.render (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:12)
    at e.<anonymous> (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:11)
    at y (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:22)
    at g (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:22)
    at p (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:22)
    at t.h.trigger (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:22)
    at t._resize (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:3)
    at t.resize (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:3)
    at o (data:application/x-javascript;base64,d2luZG93LkJva2VoPUJva2VoPWZ1bmN0aW9uKCl7dmFyIHQ9dm9pZCAwO3JldH…:54)

My guess is Chrome is just more tolerant!

[mingwandroid]

In main.min.js I see:

    OutputArea.prototype.create_output_subarea = function(md, classes, mime) {
        var subarea = $('<div/>').addClass('output_subarea').addClass(classes);
        if (_get_metadata_key(md, 'isolated', mime)) {
            // Create an iframe to isolate the subarea from the rest of the
            // document
            var iframe = $('<iframe/>').addClass('box-flex1');
            iframe.css({'height':1, 'width':'100%', 'display':'block'});
            iframe.attr('frameborder', 0);
            iframe.attr('scrolling', 'auto');

            // Once the iframe is loaded, the subarea is dynamically inserted
            iframe.on('load', function() {
                // Workaround needed by Firefox, to properly render svg inside
                // iframes, see http://stackoverflow.com/questions/10177190/
                // svg-dynamically-added-to-iframe-does-not-render-correctly
                this.contentDocument.open();

                // Insert the subarea into the iframe
                // We must directly write the html. When using Jquery's append
                // method, javascript is evaluated in the parent document and
                // not in the iframe document.  At this point, subarea doesn't
                // contain any user content.
                this.contentDocument.write(subarea.html());

                this.contentDocument.close();

                var body = this.contentDocument.body;
                // Adjust the iframe height automatically
                iframe.height(body.scrollHeight + 'px');
            });

            // Elements should be appended to the inner subarea and not to the
            // iframe
            iframe.append = function(that) {
                subarea.append(that);
            };

            return iframe;
        } else {
            return subarea;
        }
    };

Here:

                var body = this.contentDocument.body;
                // Adjust the iframe height automatically
                iframe.height(body.scrollHeight + 'px');

body (and this.contentDocument.body) is null.

.. if that's any use to anyone?

[mingwandroid]

A screen-grab of the Firefox debugger:

[mingwandroid]

@ijstokes, I think we should either close this or rename it, what's your preference?

[ijstokes]

@mingwandroid it felt like we got to the point where you updated enough pieces that this would work reliably in Chrome and Safari, but the outstanding issues are out of our control, correct? If that is the case I'd say this issue should be closed and possibly another issue opened, but in all likelihood the https://github.com/bokeh/rbokeh/issues/200 issue is sufficient.

[mingwandroid]

I hope the rbokeh issue is enough, even if the bug is mostly likely in htmlwidgets. I'd say let's leave it at rbokeh for now and if there's no progress in a few days then we can add a comment there asking if we should move it to htmlwidgets instead?

[damianavila]

Interesting research work... thank you both @mingwandroid and @ijstokes for fighting on this one.

[mingwandroid]

It was a fun deep dive. Shame it's not fixed yet though, the htmlwidgets bug has been quiet for a month now.

[steverweber]

i have this issue with chromium and firefox.

python code can render html

import ipywidgets as widgets
widgets.HTML(
    value="widgets test <b>hello World</b>"
)

however with R:

library(ggplot2)
library(plotly)
set.seed(100)
data(diamonds)
d <- diamonds[sample(nrow(diamonds), 1000), ]
attach(d)
plot_ly(d, x=~carat, y=~price, text=~paste("Clarity: ", clarity),
        type="scatter", mode="markers", color=~carat, size=~carat)

returns:

HTML widgets cannot be represented in plain text (need html)

i'm not using conda. but my install looks like

# ubuntu 16.04
apt-get install python3
python3 -m pip install notebook
python3 -m pip install --upgrade notebook
python3 -m pip install ipywidgets
python3 -m pip install widgetsnbextension
python3 -m pip install --upgrade widgetsnbextension
python3 -m pip install --upgrade ipywidgets
jupyter nbextension enable --py --sys-prefix widgetsnbextension

## install all r packages...
apt-get -y install $(apt-cache search '^r-.*' | cut -f1 -d' ' | sort | sed /geki3/d | sed /-rtree/d | sed /r-cran-r2jags/d | sed /r-other-bio3d/d | tr '\n' ' ')

#### R stuff
install.packages(c('curl'), repos='http://cran.utstat.utoronto.ca/')
install.packages(c('devtools'), repos='http://cran.utstat.utoronto.ca/')
install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'uuid', 'digest'), repos='http://cran.utstat.utoronto.ca/')
devtools::install_github(c('IRkernel/IRkernel'), force=TRUE)
IRkernel::installspec(user=FALSE)
install.packages(c('dplyr', 'tidyr', 'shiny', 'rmarkdown', 'forecast', 'nycflights13'), repos='http://cran.utstat.utoronto.ca/')
devtools::install_github('rstudio/leaflet')
install.packages(c('plotly'), repos='http://cran.utstat.utoronto.ca/')
install.packages(c('mlbench', 'PerformanceAnalytics', 'mosaic'), repos='http://cran.utstat.utoronto.ca/')
install.packages(c('formatR', 'jsonlite'), repos='http://cran.utstat.utoronto.ca/')
install.packages(c('formatR', 'jsonlite'), repos='http://cran.utstat.utoronto.ca/')
install.packages(c('rbokeh', 'd3heatmap'), repos='http://cran.utstat.utoronto.ca/')
install.packages(c('ggplot2'), repos='http://cran.utstat.utoronto.ca/')

[steverweber]

getOption("jupyter.display_mimetypes")
'text/plain' 'text/html' 'text/markdown' 'text/latex' 'application/json' 'application/javascript' 'application/pdf' 'image/png' 'image/jpeg' 'image/svg+xml'

[mingwandroid]

i'm not using conda

@steverweber, this is for reporting bugs against conda packages provided as part of the Anaconda Distribution. Please file your issue with Canonical, PyPA or The R Foundation.

Likely you are missing pandoc though.

[steverweber]

debug view.

options(jupyter.log_level=10)
library(ggplot2)
library(plotly)
set.seed(100)
data(diamonds)
d <- diamonds[sample(nrow(diamonds), 1000), ]
attach(d)
plot_ly(d, x=~carat, y=~price, text=~paste("Clarity: ", clarity),
        type="scatter", mode="markers", color=~carat, size=~carat)

DEBUG: main loop: after poll
DEBUG: main loop: shell
DEBUG: Sending msg status
[D 13:04:13.821 NotebookApp] activity on 31cbe78d-923b-4928-af85-ded6df7d5a18: status
DEBUG: Sending msg execute_input
[D 13:04:13.823 NotebookApp] activity on 31cbe78d-923b-4928-af85-ded6df7d5a18: execute_input
DEBUG: Executing code: options(jupyter.log_level=10)
library(ggplot2)
library(plotly)
set.seed(100)
data(diamonds)
d <- diamonds[sample(nrow(diamonds), 1000), ]
attach(d)
plot_ly(d, x=~carat, y=~price, text=~paste("Clarity: ", clarity),
        type="scatter", mode="markers", color=~carat, size=~carat)

DEBUG: Value output...
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Message output: simpleMessage in message(.maskedMsg(sort(same), pkg, by = i < db.pos), domain = NA): The following object is masked _by_ .GlobalEnv:

    z

DEBUG: Stream output: The following object is masked _by_ .GlobalEnv:

    z

DEBUG: Sending msg stream
DEBUG: Message output: simpleMessage in message(.maskedMsg(sort(same), pkg, by = i < db.pos), domain = NA): The following objects are masked from d (pos = 3):

    carat, clarity, color, cut, depth, price, table, x, y, z

DEBUG: Stream output: The following objects are masked from d (pos = 3):

    carat, clarity, color, cut, depth, price, table, x, y, z

[D 13:04:14.063 NotebookApp] activity on 31cbe78d-923b-4928-af85-ded6df7d5a18: stream
DEBUG: Sending msg stream
[D 13:04:14.065 NotebookApp] activity on 31cbe78d-923b-4928-af85-ded6df7d5a18: stream
DEBUG: Value output...
DEBUG: Value output...
DEBUG: Sending display_data: List of 1
 $ text/plain: chr "HTML widgets cannot be represented in plain text (need html)"
DEBUG: Sending msg display_data
[D 13:04:15.985 NotebookApp] activity on 31cbe78d-923b-4928-af85-ded6df7d5a18: display_data
DEBUG: Sending msg execute_reply
DEBUG: Sending msg status
[D 13:04:15.989 NotebookApp] activity on 31cbe78d-923b-4928-af85-ded6df7d5a18: status

[steverweber]

pandoc is installed anyways thought my feedback might be helpful if someone else ends up here.