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Installation of rstanarm under anaconda breaks r kernel for jupyter notebook #308

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MaxHoefl opened this issue Jul 26, 2018 · 0 comments
Open

Installation of rstanarm under anaconda breaks r kernel for jupyter notebook #308

MaxHoefl opened this issue Jul 26, 2018 · 0 comments

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@MaxHoefl
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Summary:

installation of rstanarm via anaconda breaks R kernel in jupyter notebook

Description:

Under anaconda 4.5.8, I created a clean conda environment
conda create -n r-environment r-essentials r-base
on linux redhat 6.6 (Santiago). I could start jupyter notebook, create an R 3.4.3 notebook and run commands (such as library(ggplot2)) successfully.

At this point conda list gave. I want to stress that at that point I am not using R MRO (microsoft R client) but r-base:

_r-mutex                  1.0.0               anacondar_1
appdirs                   1.4.3            py36h28b3542_0
asn1crypto                0.24.0                   py36_0
attrs                     18.1.0                   py36_0
automat                   0.7.0                    py36_0
backcall                  0.1.0                    py36_0
binutils_impl_linux-64    2.28.1               had2808c_3
binutils_linux-64         7.2.0               had2808c_27
bleach                    2.1.3                    py36_0
bwidget                   1.9.11                        0
bzip2                     1.0.6                h14c3975_5
ca-certificates           2018.03.07                    0
cairo                     1.14.12              h8948797_3
certifi                   2018.4.16                py36_0
cffi                      1.11.5           py36h9745a5d_0
constantly                15.1.0           py36h28b3542_0
cryptography              2.2.2            py36h14c3975_0
curl                      7.61.0               h84994c4_0
decorator                 4.3.0                    py36_0
entrypoints               0.2.3                    py36_2
fontconfig                2.13.0               h9420a91_0
freetype                  2.9.1                h8a8886c_0
fribidi                   1.0.4                h14c3975_0
gcc_impl_linux-64         7.2.0                habb00fd_3
gcc_linux-64              7.2.0               h550dcbe_27
gfortran_impl_linux-64    7.2.0                hdf63c60_3
gfortran_linux-64         7.2.0               h550dcbe_27
glib                      2.56.1               h000015b_0
gmp                       6.1.2                h6c8ec71_1
graphite2                 1.3.11               h16798f4_2
gsl                       2.4                  h14c3975_4
gxx_impl_linux-64         7.2.0                hdf63c60_3
gxx_linux-64              7.2.0               h550dcbe_27
harfbuzz                  1.8.4                hec2c2bc_0
html5lib                  1.0.1                    py36_0
hyperlink                 18.0.0                   py36_0
icu                       58.2                 h9c2bf20_1
idna                      2.7                      py36_0
incremental               17.5.0                   py36_0
ipykernel                 4.8.2                    py36_0
ipython                   6.4.0                    py36_1
ipython_genutils          0.2.0                    py36_0
jedi                      0.12.1                   py36_0
jinja2                    2.10                     py36_0
jpeg                      9b                   h024ee3a_2
jsonschema                2.6.0                    py36_0
jupyter_client            5.2.3                    py36_0
jupyter_core              4.4.0                    py36_0
krb5                      1.14.2               hcdc1b81_6
libcurl                   7.61.0               h1ad7b7a_0
libedit                   3.1                  heed3624_0
libffi                    3.2.1                hd88cf55_4
libgcc-ng                 7.2.0                hdf63c60_3
libgfortran-ng            7.2.0                hdf63c60_3
libopenblas               0.2.20               h9ac9557_7
libpng                    1.6.34               hb9fc6fc_0
libsodium                 1.0.16               h1bed415_0
libssh2                   1.8.0                h9cfc8f7_4
libstdcxx-ng              7.2.0                hdf63c60_3
libtiff                   4.0.9                he85c1e1_1
libuuid                   1.0.3                h1bed415_2
libxcb                    1.13                 h1bed415_1
libxml2                   2.9.8                h26e45fe_1
markupsafe                1.0              py36h14c3975_1
mistune                   0.8.3            py36h14c3975_1
nbconvert                 5.3.1                    py36_0
nbformat                  4.4.0                    py36_0
ncurses                   6.0                  h9df7e31_2
notebook                  5.6.0                    py36_0
openssl                   1.0.2o               h20670df_0
pandoc                    2.2.1                h629c226_0
pandocfilters             1.4.2                    py36_1
pango                     1.42.1               h8589676_0
parso                     0.3.1                    py36_0
pcre                      8.42                 h439df22_0
pexpect                   4.6.0                    py36_0
pickleshare               0.7.4                    py36_0
pip                       10.0.1                   py36_0
pixman                    0.34.0               hceecf20_3
prometheus_client         0.3.0                    py36_0
prompt_toolkit            1.0.15                   py36_0
ptyprocess                0.6.0                    py36_0
pyasn1                    0.4.3                    py36_0
pyasn1-modules            0.2.2                    py36_0
pycparser                 2.18                     py36_1
pygments                  2.2.0                    py36_0
pyopenssl                 18.0.0                   py36_0
python                    3.6.5                hc3d631a_2
python-dateutil           2.7.3                    py36_0
pyzmq                     17.0.0           py36h14c3975_3
r-assertthat              0.2.0            r343h889e2dd_0
r-backports               1.1.2            r343h086d26f_0
r-base                    3.4.3                h290ecf8_1
r-base64enc               0.1_3            r343h086d26f_4
r-bh                      1.65.0_1         r343h889e2dd_0
r-bindr                   0.1              r343h889e2dd_0
r-bindrcpp                0.2              r343h599a50d_0
r-boot                    1.3_20           r343h889e2dd_0
r-broom                   0.4.3            r343h889e2dd_0
r-callr                   1.0.0            r343h889e2dd_0
r-caret                   6.0_78           r343h086d26f_0
r-cellranger              1.1.0            r343h889e2dd_0
r-class                   7.3_14           r343h086d26f_4
r-cli                     1.0.0            r343h889e2dd_0
r-clipr                   0.4.0            r343h889e2dd_0
r-cluster                 2.0.6            r343h4829c52_0
r-codetools               0.2_15           r343h889e2dd_0
r-colorspace              1.3_2            r343h086d26f_0
r-crayon                  1.3.4            r343h889e2dd_0
r-curl                    3.1              r343h086d26f_0
r-cvst                    0.2_1            r343h889e2dd_0
r-data.table              1.10.4_3         r343h086d26f_0
r-dbi                     0.7              r343h889e2dd_0
r-dbplyr                  1.1.0            r343h889e2dd_0
r-ddalpha                 1.3.1            r343h44b0c2a_0
r-deoptimr                1.0_8            r343h889e2dd_0
r-dichromat               2.0_0            r343h889e2dd_4
r-digest                  0.6.13           r343h086d26f_0
r-dimred                  0.1.0            r343h889e2dd_0
r-dplyr                   0.7.4            r343h599a50d_0
r-drr                     0.0.2            r343h889e2dd_0
r-essentials              3.4.3                    r343_0
r-evaluate                0.10.1           r343h889e2dd_0
r-forcats                 0.2.0            r343h889e2dd_0
r-foreach                 1.4.4            r343h889e2dd_0
r-foreign                 0.8_69           r343h086d26f_0
r-formatr                 1.5              r343h889e2dd_0
r-ggplot2                 2.2.1            r343h889e2dd_0
r-glmnet                  2.0_13           r343h4829c52_0
r-glue                    1.2.0            r343h086d26f_0
r-gower                   0.1.2            r343h086d26f_0
r-gtable                  0.2.0            r343h889e2dd_0
r-haven                   1.1.0            r343h599a50d_0
r-hexbin                  1.27.1           r343h4829c52_4
r-highr                   0.6              r343h889e2dd_0
r-hms                     0.4.0            r343h889e2dd_0
r-htmltools               0.3.6            r343h599a50d_0
r-htmlwidgets             0.9              r343h889e2dd_0
r-httpuv                  1.3.5            r343h599a50d_0
r-httr                    1.3.1            r343h889e2dd_0
r-ipred                   0.9_6            r343h086d26f_0
r-irdisplay               0.4.4            r343h889e2dd_0
r-irkernel                0.8.11                   r343_0
r-iterators               1.0.9            r343h889e2dd_0
r-jsonlite                1.5              r343h086d26f_0
r-kernlab                 0.9_25           r343h44b0c2a_0
r-kernsmooth              2.23_15          r343h4829c52_4
r-knitr                   1.18             r343h889e2dd_0
r-labeling                0.3              r343h889e2dd_4
r-lattice                 0.20_35          r343h086d26f_0
r-lava                    1.5.1            r343h889e2dd_0
r-lazyeval                0.2.1            r343h086d26f_0
r-lubridate               1.7.1            r343h599a50d_0
r-magrittr                1.5              r343h889e2dd_4
r-maps                    3.2.0            r343h086d26f_0
r-markdown                0.8              r343h086d26f_0
r-mass                    7.3_48           r343h086d26f_0
r-matrix                  1.2_12           r343h086d26f_0
r-mgcv                    1.8_22           r343h086d26f_0
r-mime                    0.5              r343h086d26f_0
r-mnormt                  1.5_5            r343h4829c52_0
r-modelmetrics            1.1.0            r343h599a50d_0
r-modelr                  0.1.1            r343h889e2dd_0
r-munsell                 0.4.3            r343h889e2dd_0
r-nlme                    3.1_131          r343h4829c52_0
r-nnet                    7.3_12           r343h086d26f_0
r-numderiv                2016.8_1         r343h889e2dd_0
r-openssl                 0.9.9            r343h086d26f_0
r-pbdzmq                  0.3_0            r343hf484d3e_1
r-pillar                  1.0.1            r343h889e2dd_0
r-pkgconfig               2.0.1            r343h889e2dd_0
r-plogr                   0.1_1            r343h889e2dd_0
r-plyr                    1.8.4            r343h599a50d_0
r-prodlim                 1.6.1            r343h599a50d_0
r-psych                   1.7.8            r343h889e2dd_0
r-purrr                   0.2.4            r343h086d26f_0
r-quantmod                0.4_12           r343h889e2dd_0
r-r6                      2.2.2            r343h889e2dd_0
r-randomforest            4.6_12           r343h4829c52_4
r-rbokeh                  0.6.3                    r343_0
r-rcolorbrewer            1.1_2            r343h889e2dd_0
r-rcpp                    0.12.14          r343h599a50d_0
r-rcpproll                0.2.2            r343h599a50d_0
r-readr                   1.1.1            r343h599a50d_0
r-readxl                  1.0.0            r343h599a50d_0
r-recipes                 0.1.1            r343h889e2dd_0
r-recommended             3.4.3                    r343_0
r-rematch                 1.0.1            r343h889e2dd_0
r-repr                    0.12.0           r343h889e2dd_0
r-reprex                  0.1.1            r343h889e2dd_0
r-reshape2                1.4.3            r343h599a50d_0
r-rlang                   0.1.6            r343h086d26f_0
r-rmarkdown               1.8              r343h889e2dd_0
r-robustbase              0.92_8           r343h4829c52_0
r-rpart                   4.1_11           r343h086d26f_0
r-rprojroot               1.3_1            r343h889e2dd_0
r-rstudioapi              0.7              r343h889e2dd_0
r-rvest                   0.3.2            r343h889e2dd_0
r-scales                  0.5.0            r343h599a50d_0
r-selectr                 0.3_1            r343h889e2dd_0
r-sfsmisc                 1.1_1            r343h889e2dd_0
r-shiny                   1.0.5            r343h889e2dd_0
r-sourcetools             0.1.6            r343h599a50d_0
r-spatial                 7.3_11           r343h086d26f_4
r-stringi                 1.1.6            r343h599a50d_0
r-stringr                 1.2.0            r343h889e2dd_0
r-survival                2.41_3           r343h086d26f_0
r-tibble                  1.4.1            r343h086d26f_0
r-tidyr                   0.7.2            r343h599a50d_0
r-tidyselect              0.2.3            r343h599a50d_0
r-tidyverse               1.2.1            r343h889e2dd_0
r-timedate                3042.101         r343h889e2dd_0
r-ttr                     0.23_2           r343h4829c52_0
r-utf8                    1.1.2            r343h086d26f_0
r-uuid                    0.1_2            r343h086d26f_4
r-viridislite             0.2.0            r343h889e2dd_0
r-whisker                 0.3_2            r343h889e2dd_4
r-withr                   2.1.1            r343h889e2dd_0
r-xml2                    1.1.1            r343h599a50d_0
r-xtable                  1.8_2            r343h889e2dd_0
r-xts                     0.10_1           r343h4829c52_0
r-yaml                    2.1.16           r343h086d26f_0
r-zoo                     1.8_0            r343h086d26f_0
readline                  7.0                  ha6073c6_4
send2trash                1.5.0                    py36_0
service_identity          17.0.0           py36h28b3542_0
setuptools                39.2.0                   py36_0
simplegeneric             0.8.1                    py36_2
six                       1.11.0                   py36_1
sqlite                    3.23.1               he433501_0
terminado                 0.8.1                    py36_1
testpath                  0.3.1                    py36_0
tk                        8.6.7                hc745277_3
tktable                   2.10                 h14c3975_0
tornado                   5.0.2            py36h14c3975_0
traitlets                 4.3.2                    py36_0
twisted                   18.4.0           py36h14c3975_0
wcwidth                   0.1.7                    py36_0
webencodings              0.5.1                    py36_1
wheel                     0.31.1                   py36_0
xz                        5.2.4                h14c3975_4
zeromq                    4.2.5                hf484d3e_0
zlib                      1.2.11               ha838bed_2
zope                      1.0                      py36_0
zope.interface            4.5.0            py36h14c3975_0

Next, I installed rstanarm 2.17.4-r341_0 by typing
conda install --name r-environment -c conda-forge -r-rstanarm.

This prompted me with the following details


The following NEW packages will be INSTALLED:

    libgcc:           7.2.0-h69d50b8_2
    libgfortran:      3.0.0-1
    mro-base:         3.4.3-h1c2f66e_1
    r-abind:          1.4_5-r3.4.1_0           conda-forge
    r-bayesplot:      1.5.0-r3.4.1_0           conda-forge
    r-bitops:         1.0_6-r3.4.1_0           conda-forge
    r-colourpicker:   1.0-r3.4.1_0             conda-forge
    r-crosstalk:      1.0.0-r3.4.1_0           conda-forge
    r-debugme:        1.1.0-r3.4.1_0           conda-forge
    r-dt:             0.4-r3.4.1_0             conda-forge
    r-dygraphs:       1.1.1.6-r341_0           conda-forge
    r-geometry:       0.3_6-r3.4.1_0           conda-forge
    r-ggridges:       0.5.0-r3.4.1_0           conda-forge
    r-gistr:          0.4.2-r341_0             conda-forge
    r-gridextra:      2.3-r3.4.1_0             conda-forge
    r-gtools:         3.8.1-r341_0             conda-forge
    r-inline:         0.3.14-r3.4.1_0          conda-forge
    r-lme4:           1.1_13-r3.4.1_0          conda-forge
    r-loo:            2.0.0-r3.4.1_0           conda-forge
    r-magic:          1.5_6-r3.4.1_0           conda-forge
    r-matrixstats:    0.53.1-r341_0            conda-forge
    r-miniui:         0.1.1-r3.4.1_0           conda-forge
    r-minqa:          1.2.4-r3.4.1_0           conda-forge
    r-nloptr:         1.0.4-r3.4.1_1           conda-forge
    r-packrat:        0.4.9-r3.4.1_0           conda-forge
    r-pki:            0.1_3-r3.4.1_0           conda-forge
    r-pls:            2.6_0-r3.4.1_0           conda-forge
    r-praise:         1.0.0-r3.4.1_0           conda-forge
    r-pryr:           0.1.4-r3.4.1_0           conda-forge
    r-rcppeigen:      0.3.3.4.0-r3.4.1_0       conda-forge
    r-rcurl:          1.95_4.11-r341ha4d7672_0 conda-forge
    r-rjsonio:        1.3_0-r3.4.1_0           conda-forge
    r-rsconnect:      0.8.5-r3.4.1_0           conda-forge
    r-rstan:          2.17.3-r3.4.1_0          conda-forge
    r-rstanarm:       2.17.4-r341_0            conda-forge
    r-rstantools:     1.5.0-r3.4.1_0           conda-forge
    r-shinyjs:        0.9-r3.4.1_0             conda-forge
    r-shinystan:      2.5.0-r341_0             conda-forge
    r-shinythemes:    1.1.1-r3.4.1_0           conda-forge
    r-squarem:        2017.10_1-r3.4.1_0       conda-forge
    r-stanheaders:    2.17.2-r3.4.1_0          conda-forge
    r-testthat:       2.0.0-r3.4.1_1           conda-forge
    r-threejs:        0.2.2-r3.4.1_0           conda-forge
    r-tinytex:        0.5-r341h6115d3f_0       conda-forge
    xorg-kbproto:     1.0.7-h470a237_2         conda-forge
    xorg-libice:      1.0.9-h470a237_4         conda-forge
    xorg-libsm:       1.2.2-h470a237_4         conda-forge
    xorg-libx11:      1.6.5-h470a237_2         conda-forge
    xorg-libxext:     1.3.3-h470a237_4         conda-forge
    xorg-libxrender:  0.9.10-h470a237_2        conda-forge
    xorg-renderproto: 0.11.1-h470a237_2        conda-forge
    xorg-xextproto:   7.3.0-h470a237_2         conda-forge
    xorg-xproto:      7.0.31-h470a237_7        conda-forge

The following packages will be UPDATED:

    _r-mutex:         1.0.0-anacondar_1                    --> 1.0.0-mro_2
    ca-certificates:  2018.03.07-0                         --> 2018.4.16-0             conda-forge
    certifi:          2018.4.16-py36_0                     --> 2018.4.16-py36_0        conda-forge
    jpeg:             9b-h024ee3a_2                        --> 9c-h470a237_0           conda-forge
    libedit:          3.1-heed3624_0                       --> 3.1.20170329-haf1bffa_0 conda-forge
    ncurses:          6.0-h9df7e31_2                       --> 6.1-hfc679d8_1          conda-forge
    openssl:          1.0.2o-h20670df_0                    --> 1.0.2o-0                conda-forge
    r-assertthat:     0.2.0-r343h889e2dd_0                 --> 0.2.0-r3.4.1_0          conda-forge
    r-backports:      1.1.2-r343h086d26f_0                 --> 1.1.2-r3.4.1_0          conda-forge
    r-bh:             1.65.0_1-r343h889e2dd_0              --> 1.66.0_1-r3.4.1_0       conda-forge
    r-bindr:          0.1-r343h889e2dd_0                   --> 0.1.1-r3.4.1_0          conda-forge
    r-bindrcpp:       0.2-r343h599a50d_0                   --> 0.2.2-r341h9d2a408_0    conda-forge
    r-boot:           1.3_20-r343h889e2dd_0                --> 1.3_20-r3.4.1_0         conda-forge
    r-broom:          0.4.3-r343h889e2dd_0                 --> 0.5.0-r341_0            conda-forge
    r-callr:          1.0.0-r343h889e2dd_0                 --> 2.0.2-r3.4.1_0          conda-forge
    r-caret:          6.0_78-r343h086d26f_0                --> 6.0_80-r341hc070d10_0   conda-forge
    r-cellranger:     1.1.0-r343h889e2dd_0                 --> 1.1.0-r3.4.1_0          conda-forge
    r-cli:            1.0.0-r343h889e2dd_0                 --> 1.0.0-r3.4.1_0          conda-forge
    r-clipr:          0.4.0-r343h889e2dd_0                 --> 0.4.0-mro343h889e2dd_0
    r-cluster:        2.0.6-r343h4829c52_0                 --> 2.0.6-r3.4.1_0          conda-forge
    r-codetools:      0.2_15-r343h889e2dd_0                --> 0.2_15-r3.4.1_0         conda-forge
    r-colorspace:     1.3_2-r343h086d26f_0                 --> 1.3_2-r3.4.1_0          conda-forge
    r-crayon:         1.3.4-r343h889e2dd_0                 --> 1.3.4-r3.4.1_0          conda-forge
    r-curl:           3.1-r343h086d26f_0                   --> 3.2-r3.4.1_0            conda-forge
    r-cvst:           0.2_1-r343h889e2dd_0                 --> 0.2_1-r3.4.1_0          conda-forge
    r-data.table:     1.10.4_3-r343h086d26f_0              --> 1.11.4-r341hc070d10_0   conda-forge
    r-dbi:            0.7-r343h889e2dd_0                   --> 1.0.0-r341_0            conda-forge
    r-dbplyr:         1.1.0-r343h889e2dd_0                 --> 1.2.2-r341_0            conda-forge
    r-ddalpha:        1.3.1-r343h44b0c2a_0                 --> 1.3.4-r341_0            conda-forge
    r-deoptimr:       1.0_8-r343h889e2dd_0                 --> 1.0_8-r3.4.1_0          conda-forge
    r-digest:         0.6.13-r343h086d26f_0                --> 0.6.15-r3.4.1_0         conda-forge
    r-dimred:         0.1.0-r343h889e2dd_0                 --> 0.1.0-r3.4.1_0          conda-forge
    r-dplyr:          0.7.4-r343h599a50d_0                 --> 0.7.6-r341h9d2a408_0    conda-forge
    r-drr:            0.0.2-r343h889e2dd_0                 --> 0.0.3-r3.4.1_0          conda-forge
    r-evaluate:       0.10.1-r343h889e2dd_0                --> 0.10.1-r3.4.1_0         conda-forge
    r-forcats:        0.2.0-r343h889e2dd_0                 --> 0.3.0-r3.4.1_0          conda-forge
    r-foreach:        1.4.4-r343h889e2dd_0                 --> 1.4.4-r3.4.1_0          conda-forge
    r-formatr:        1.5-r343h889e2dd_0                   --> 1.5-r3.4.1_0            conda-forge
    r-ggplot2:        2.2.1-r343h889e2dd_0                 --> 3.0.0-r341h6115d3f_0    conda-forge
    r-glue:           1.2.0-r343h086d26f_0                 --> 1.3.0-r341_0            conda-forge
    r-gower:          0.1.2-r343h086d26f_0                 --> 0.1.2-r3.4.1_0          conda-forge
    r-gtable:         0.2.0-r343h889e2dd_0                 --> 0.2.0-r3.4.1_0          conda-forge
    r-haven:          1.1.0-r343h599a50d_0                 --> 1.1.2-r341_0            conda-forge
    r-hexbin:         1.27.1-r343h4829c52_4                --> 1.27.2-r3.4.1_0         conda-forge
    r-highr:          0.6-r343h889e2dd_0                   --> 0.7-r341_0              conda-forge
    r-htmltools:      0.3.6-r343h599a50d_0                 --> 0.3.6-r3.4.1_0          conda-forge
    r-htmlwidgets:    0.9-r343h889e2dd_0                   --> 1.0-r3.4.1_0            conda-forge
    r-httpuv:         1.3.5-r343h599a50d_0                 --> 1.3.6.2-r3.4.1_0        conda-forge
    r-httr:           1.3.1-r343h889e2dd_0                 --> 1.3.1-r3.4.1_0          conda-forge
    r-ipred:          0.9_6-r343h086d26f_0                 --> 0.9_6-r3.4.1_0          conda-forge
    r-irdisplay:      0.4.4-r343h889e2dd_0                 --> 0.4.4-r3.4.1_0          conda-forge
    r-irkernel:       0.8.11-r343_0                        --> 0.8.12-r341_0           conda-forge
    r-iterators:      1.0.9-r343h889e2dd_0                 --> 1.0.10-r341_0           conda-forge
    r-jsonlite:       1.5-r343h086d26f_0                   --> 1.5-r3.4.1_0            conda-forge
    r-kernlab:        0.9_25-r343h44b0c2a_0                --> 0.9_25-r3.4.1_0         conda-forge
    r-knitr:          1.18-r343h889e2dd_0                  --> 1.20-r3.4.1_0           conda-forge
    r-lava:           1.5.1-r343h889e2dd_0                 --> 1.6.2-r341_0            conda-forge
    r-lazyeval:       0.2.1-r343h086d26f_0                 --> 0.2.1-r3.4.1_0          conda-forge
    r-lubridate:      1.7.1-r343h599a50d_0                 --> 1.7.4-r3.4.1_0          conda-forge
    r-maps:           3.2.0-r343h086d26f_0                 --> 3.3.0-r3.4.1_0          conda-forge
    r-markdown:       0.8-r343h086d26f_0                   --> 0.8-r3.4.1_1            conda-forge
    r-mass:           7.3_48-r343h086d26f_0                --> 7.3_50-r341hc070d10_1   conda-forge
    r-matrix:         1.2_12-r343h086d26f_0                --> 1.2_14-r3.4.1_0         conda-forge
    r-mgcv:           1.8_22-r343h086d26f_0                --> 1.8_24-r341_0           conda-forge
    r-mime:           0.5-r343h086d26f_0                   --> 0.5-r3.4.1_0            conda-forge
    r-mnormt:         1.5_5-r343h4829c52_0                 --> 1.5_5-r3.4.1_0          conda-forge
    r-modelmetrics:   1.1.0-r343h599a50d_0                 --> 1.1.0-r3.4.1_0          conda-forge
    r-modelr:         0.1.1-r343h889e2dd_0                 --> 0.1.2-r341_0            conda-forge
    r-munsell:        0.4.3-r343h889e2dd_0                 --> 0.5.0-r341_0            conda-forge
    r-nlme:           3.1_131-r343h4829c52_0               --> 3.1_131-r3.4.1_0        conda-forge
    r-nnet:           7.3_12-r343h086d26f_0                --> 7.3_12-r3.4.1_0         conda-forge
    r-numderiv:       2016.8_1-r343h889e2dd_0              --> 2016.8_1-r3.4.1_0       conda-forge
    r-openssl:        0.9.9-r343h086d26f_0                 --> 1.0.1-r3.4.1_0          conda-forge
    r-pbdzmq:         0.3_0-r343hf484d3e_1                 --> 0.3_2-r3.4.1_0          conda-forge
    r-pillar:         1.0.1-r343h889e2dd_0                 --> 1.2.2-r341h6115d3f_1    conda-forge
    r-pkgconfig:      2.0.1-r343h889e2dd_0                 --> 2.0.1-r3.4.1_0          conda-forge
    r-plogr:          0.1_1-r343h889e2dd_0                 --> 0.2.0-r341h6115d3f_0    conda-forge
    r-plyr:           1.8.4-r343h599a50d_0                 --> 1.8.4-r3.4.1_0          conda-forge
    r-prodlim:        1.6.1-r343h599a50d_0                 --> 2018.04.18-r3.4.1_0     conda-forge
    r-psych:          1.7.8-r343h889e2dd_0                 --> 1.8.4-r341_0            conda-forge
    r-purrr:          0.2.4-r343h086d26f_0                 --> 0.2.4-r3.4.1_0          conda-forge
    r-r6:             2.2.2-r343h889e2dd_0                 --> 2.2.2-r3.4.1_0          conda-forge
    r-rcolorbrewer:   1.1_2-r343h889e2dd_0                 --> 1.1_2-r3.4.1_0          conda-forge
    r-rcpp:           0.12.14-r343h599a50d_0               --> 0.12.17-r341h9d2a408_0  conda-forge
    r-rcpproll:       0.2.2-r343h599a50d_0                 --> 0.2.2-r3.4.1_0          conda-forge
    r-readr:          1.1.1-r343h599a50d_0                 --> 1.1.1-r3.4.1_0          conda-forge
    r-readxl:         1.0.0-r343h599a50d_0                 --> 1.1.0-r341_0            conda-forge
    r-recipes:        0.1.1-r343h889e2dd_0                 --> 0.1.3-r341_0            conda-forge
    r-rematch:        1.0.1-r343h889e2dd_0                 --> 1.0.1-r3.4.1_0          conda-forge
    r-repr:           0.12.0-r343h889e2dd_0                --> 0.15-r341_0             conda-forge
    r-reprex:         0.1.1-r343h889e2dd_0                 --> 0.1.1-mro343h889e2dd_0
    r-reshape2:       1.4.3-r343h599a50d_0                 --> 1.4.3-r3.4.1_0          conda-forge
    r-rlang:          0.1.6-r343h086d26f_0                 --> 0.2.1-r341_0            conda-forge
    r-rmarkdown:      1.8-r343h889e2dd_0                   --> 1.10-r341h6115d3f_0     conda-forge
    r-rpart:          4.1_11-r343h086d26f_0                --> 4.1_13-r3.4.1_0         conda-forge
    r-rprojroot:      1.3_1-r343h889e2dd_0                 --> 1.3_2-r3.4.1_0          conda-forge
    r-rstudioapi:     0.7-r343h889e2dd_0                   --> 0.7-r3.4.1_0            conda-forge
    r-rvest:          0.3.2-r343h889e2dd_0                 --> 0.3.2-r3.4.1_0          conda-forge
    r-scales:         0.5.0-r343h599a50d_0                 --> 0.5.0-r3.4.1_0          conda-forge
    r-selectr:        0.3_1-r343h889e2dd_0                 --> 0.3_1-r3.4.1_0          conda-forge
    r-sfsmisc:        1.1_1-r343h889e2dd_0                 --> 1.1_1-r3.4.1_0          conda-forge
    r-shiny:          1.0.5-r343h889e2dd_0                 --> 1.0.5-r3.4.1_0          conda-forge
    r-sourcetools:    0.1.6-r343h599a50d_0                 --> 0.1.6-r3.4.1_0          conda-forge
    r-stringi:        1.1.6-r343h599a50d_0                 --> 1.2.3-r341_0            conda-forge
    r-stringr:        1.2.0-r343h889e2dd_0                 --> 1.3.1-r341_0            conda-forge
    r-survival:       2.41_3-r343h086d26f_0                --> 2.42_6-r341_0           conda-forge
    r-tibble:         1.4.1-r343h086d26f_0                 --> 1.4.2-r3.4.1_0          conda-forge
    r-tidyr:          0.7.2-r343h599a50d_0                 --> 0.8.1-r341_0            conda-forge
    r-tidyselect:     0.2.3-r343h599a50d_0                 --> 0.2.4-r3.4.1_0          conda-forge
    r-utf8:           1.1.2-r343h086d26f_0                 --> 1.1.3-r3.4.1_0          conda-forge
    r-viridislite:    0.2.0-r343h889e2dd_0                 --> 0.3.0-r3.4.1_0          conda-forge
    r-withr:          2.1.1-r343h889e2dd_0                 --> 2.1.1-r3.4.1_0          conda-forge
    r-xml2:           1.1.1-r343h599a50d_0                 --> 1.2.0-r341_0            conda-forge
    r-xtable:         1.8_2-r343h889e2dd_0                 --> 1.8_2-r3.4.1_0          conda-forge
    r-xts:            0.10_1-r343h4829c52_0                --> 0.10_2-r341h364d78e_0   conda-forge
    r-yaml:           2.1.16-r343h086d26f_0                --> 2.1.19-r341_0           conda-forge
    r-zoo:            1.8_0-r343h086d26f_0                 --> 1.8_2-r341hc070d10_0    conda-forge

The following packages will be DOWNGRADED:

    r-base:           3.4.3-h290ecf8_1                     --> 3.4.1-hff14c37_6        conda-forge
    r-base64enc:      0.1_3-r343h086d26f_4                 --> 0.1_3-r3.4.1_0          conda-forge
    r-class:          7.3_14-r343h086d26f_4                --> 7.3_14-r3.4.1_0         conda-forge
    r-dichromat:      2.0_0-r343h889e2dd_4                 --> 2.0_0-r3.4.1_0          conda-forge
    r-essentials:     3.4.3-r343_0                         --> 3.4.1-r3.4.1_0          conda-forge
    r-foreign:        0.8_69-r343h086d26f_0                --> 0.8_67-r3.4.1_0         conda-forge
    r-glmnet:         2.0_13-r343h4829c52_0                --> 2.0_5-r3.4.1_0          conda-forge
    r-hms:            0.4.0-r343h889e2dd_0                 --> 0.3-r3.4.1_0            conda-forge
    r-kernsmooth:     2.23_15-r343h4829c52_4               --> 2.23_15-r3.4.1_0        conda-forge
    r-labeling:       0.3-r343h889e2dd_4                   --> 0.3-r3.4.1_0            conda-forge
    r-lattice:        0.20_35-r343h086d26f_0               --> 0.20_34-r3.4.1_0        conda-forge
    r-magrittr:       1.5-r343h889e2dd_4                   --> 1.5-r3.4.1_0            conda-forge
    r-quantmod:       0.4_12-r343h889e2dd_0                --> 0.4_8-r3.4.1_0          conda-forge
    r-randomforest:   4.6_12-r343h4829c52_4                --> 4.6_12-r3.4.1_0         conda-forge
    r-rbokeh:         0.6.3-r343_0                         --> 0.5.0-r3.4.1_0          conda-forge
    r-recommended:    3.4.3-r343_0                         --> 3.4.1-r3.4.1_0          conda-forge
    r-robustbase:     0.92_8-r343h4829c52_0                --> 0.92_7-r3.4.1_0         conda-forge
    r-spatial:        7.3_11-r343h086d26f_4                --> 7.3_11-r3.4.1_0         conda-forge
    r-tidyverse:      1.2.1-r343h889e2dd_0                 --> 1.1.1-r3.4.1_0          conda-forge
    r-timedate:       3042.101-r343h889e2dd_0              --> 3012.100-r3.4.1_0       conda-forge
    r-ttr:            0.23_2-r343h4829c52_0                --> 0.23_1-r3.4.1_0         conda-forge
    r-uuid:           0.1_2-r343h086d26f_4                 --> 0.1_2-r3.4.1_0          conda-forge
    r-whisker:        0.3_2-r343h889e2dd_4                 --> 0.3_2-r3.4.1_0          conda-forge
    twisted:          18.4.0-py36h14c3975_0                --> 17.5.0-py36_0

Here I want to point out that r-base is downgraded from 3.4.3 to 3.4.1 and _r-mutex changes to some mro version.

Now when I start the jupyter notebook and create a new R notebook, the kernel dies and I get

During startup - Warning message:
package 'RevoUtils' was built under R version 3.4.3
[I 17:36:27.016 NotebookApp] Adapting to protocol v5.0 for kernel f24c7eae-e945-4371-b1c1-b31c9ccfad70
Error in .External2(C_X11, paste0("png::", filename), g$width, g$height,  :
  unable to start device PNG
Calls: <Anonymous> ... evaluate -> dev.new -> do.call -> <Anonymous> -> ok_device
In addition: Warning message:
In ok_device(filename, ...) : no png support in this version of R
Execution halted

I can still start R (which R gives ~/anaconda3/envs/r-environment/bin/R). When I import the library ggplot2 in the R session it prints the same warning

During startup - Warning message:
package 'RevoUtils' was built under R version 3.4.3

but doesnt halt the r session.

Reproducible Steps:

see description

RStanARM Version:

rstanarm 2.17.4-r341_0

R Version:

R 3.4.3 (anaconda)

Operating System:

linux redhat 6.6 (Santiago)

Thanks for the help
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