Installation of rstanarm under anaconda breaks r kernel for jupyter notebook
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Description
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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Research direction
Start by reproducing the reported clean r-environment setup with conda create -n r-environment r-essentials r-base, then install rstanarm and launch jupyter notebook as described. Confirm whether the R kernel fails only after installing rstanarm; the issue is resolved when the kernel remains usable with the package installed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- anaconda, jupyter-notebook, r
- Domain
- developer-experience, tooling
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100