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R kernel in Jupyter keeps dying #1268

Closed dthboyd closed 7 years ago

dthboyd commented 7 years ago

Creating new notebook in [I 15:35:49.247 NotebookApp] Kernel started: ebfa1f01-cb7b-432e-a109-8f87c2253f49 dyld: Library not loaded: @rpath/libicuuc.54.dylib Referenced from: /Users/davidboyd/anaconda/lib/R/bin/exec/../../..//R/lib/libR.dylib Reason: image not found

Please Help

mingwandroid commented 7 years ago

From Terminal run: /Users/davidboyd/anaconda/bin/activate root

Then show the output of conda info and the output from conda list --show-channel-urls

dthboyd commented 7 years ago

Error: activate must be sourced. Run 'source activate envname' instead of 'activate envname'. david-boyds-iMac:pkgs davidboyd$ conda info Current conda install:

           platform : osx-64
      conda version : 4.2.13
   conda is private : False
  conda-env version : 4.2.13
conda-build version : 1.21.3
     python version : 3.5.2.final.0
   requests version : 2.10.0
   root environment : /Users/davidboyd/anaconda  (writable)
default environment : /Users/davidboyd/anaconda
   envs directories : /Users/davidboyd/anaconda/envs
      package cache : /Users/davidboyd/anaconda/pkgs
       channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                      https://conda.anaconda.org/conda-forge/noarch
                      https://repo.continuum.io/pkgs/free/osx-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/pro/osx-64
                      https://repo.continuum.io/pkgs/pro/noarch
        config file : /Users/davidboyd/.condarc
       offline mode : False

packages in environment at /Users/davidboyd/anaconda: # _nb_ext_conf 0.2.0 py35_0 defaults alabaster 0.7.8 py35_0 defaults anaconda custom py35_0 defaults anaconda-client 1.4.0 py35_0 defaults anaconda-navigator 1.2.1 py35_0 defaults aplus 0.11.0 py35_0 conda-forge appnope 0.1.0 py35_0 defaults appscript 1.0.1 py35_0 defaults argcomplete 1.0.0 py35_1 defaults astropy 1.2.1 np111py35_0 defaults babel 2.3.3 py35_0 defaults backports 1.0 py35_0 defaults backports.shutil_get_terminal_size 1.0.0 py35_0 conda-forge beautifulsoup4 4.4.1 py35_0 defaults bitarray 0.8.1 py35_0 defaults blas 1.1 openblas conda-forge blaze 0.10.1 py35_0 defaults bokeh 0.12.0 py35_0 defaults boto 2.40.0 py35_0 defaults bottlechest 0.7.1 py35_0 defaults bottleneck 1.1.0 np111py35_0 defaults cachetools 2.0.0 py35_0 conda-forge cffi 1.6.0 py35_0 defaults chardet 2.3.0 py35_0 defaults chest 0.2.3 py35_0 defaults click 6.6 py35_0 defaults cloudpickle 0.2.1 py35_0 defaults clyent 1.2.2 py35_0 defaults colorama 0.3.7 py35_0 defaults conda 4.2.13 py35_0 conda-forge conda-build 1.21.3 py35_0 defaults conda-env 2.6.0 0 conda-forge configobj 5.0.6 py35_0 defaults contextlib2 0.5.3 py35_0 defaults cryptography 1.4 py35_0 defaults curl 7.49.0 0 defaults cycler 0.10.0 py35_0 defaults cython 0.24 py35_0 defaults cytoolz 0.8.0 py35_0 defaults dask 0.10.0 py35_0 defaults datashape 0.5.2 py35_0 defaults decorator 4.0.10 py35_0 defaults dill 0.2.5 py35_0 defaults docutils 0.12 py35_2 defaults dynd-python 0.7.2 py35_0 defaults entrypoints 0.2.2 py35_0 defaults et_xmlfile 1.0.1 py35_0 defaults fastcache 1.0.2 py35_1 defaults findspark 1.1.0 flask 0.11.1 py35_0 defaults flask-cors 2.1.2 py35_0 defaults freetype 2.5.5 1 defaults future 0.15.2 py35_0 conda-forge futures 3.0.3 py35_0 defaults get_terminal_size 1.0.0 py35_0 defaults gevent 1.1.1 py35_0 defaults glueviz 0.8.2 py35_0 defaults greenlet 0.4.10 py35_0 defaults gsl 1.16 2 r h5py 2.6.0 np111py35_1 defaults hdf5 1.8.16 0 defaults heapdict 1.0.0 py35_1 defaults icu 56.1 4 conda-forge idna 2.1 py35_0 defaults imagesize 0.7.1 py35_0 defaults ipykernel 4.3.1 py35_0 defaults ipyparallel 5.2.0 ipython 4.2.0 py35_1 defaults ipython-notebook 4.0.4 py35_0 defaults ipython_genutils 0.1.0 py35_0 defaults ipywidgets 4.1.1 py35_0 defaults itsdangerous 0.24 py35_0 defaults jbig 2.1 0 defaults jdcal 1.2 py35_1 defaults jedi 0.9.0 py35_1 defaults jinja2 2.8 py35_1 defaults joblib 0.9.4 py35_0 defaults jpeg 8d 1 defaults jsonschema 2.5.1 py35_0 defaults jupyter 1.0.0 py35_3 defaults jupyter_client 4.3.0 py35_0 defaults jupyter_console 4.1.1 py35_0 defaults jupyter_core 4.1.0 py35_0 defaults libdynd 0.7.2 0 defaults libgcc 4.8.5 1 r libgfortran 3.0.0 0 conda-forge libpng 1.6.22 0 defaults libsodium 1.0.10 0 conda-forge libtiff 4.0.6 2 defaults libxml2 2.9.2 0 defaults libxslt 1.1.28 2 defaults llvmlite 0.11.0 py35_0 defaults locket 0.2.0 py35_1 defaults lxml 3.6.0 py35_0 defaults markupsafe 0.23 py35_2 defaults matplotlib 1.5.1 np111py35_0 defaults mistune 0.7.2 py35_1 defaults mkl 11.3.3 0 defaults mkl-service 1.1.2 py35_2 defaults mock 2.0.0 py35_0 conda-forge mpmath 0.19 py35_1 defaults multipledispatch 0.4.8 py35_0 defaults nb_anacondacloud 1.1.0 py35_0 defaults nb_conda 1.1.0 py35_0 defaults nb_conda_kernels 1.0.3 py35_0 defaults nbconvert 4.2.0 py35_0 defaults nbformat 4.0.1 py35_0 defaults nbpresent 3.0.2 py35_0 defaults ncurses 5.9 8 r networkx 1.11 py35_0 defaults nltk 3.2.1 py35_0 defaults nose 1.3.7 py35_1 defaults notebook 4.2.1 py35_0 defaults numba 0.26.0 np111py35_0 defaults numexpr 2.6.0 np111py35_0 defaults numpy 1.11.2 py35_blas_openblas_201 [blas_openblas] conda-forge odo 0.5.0 py35_1 defaults openblas 0.2.18 6 conda-forge openpyxl 2.3.2 py35_0 defaults openssl 1.0.2h 1 defaults orange-app 1.0.1 py35_0 defaults orange3 3.3.6 py35_0 defaults pandas 0.18.1 np111py35_0 defaults pandas-datareader 0.2.1 py35_0 anaconda partd 0.3.4 py35_0 defaults path.py 8.2.1 py35_0 defaults pathlib2 2.1.0 py35_0 defaults patsy 0.4.1 py35_0 defaults pbr 1.10.0 py35_0 conda-forge pcre 8.38 1 conda-forge pep8 1.7.0 py35_0 defaults pexpect 4.0.1 py35_0 defaults pickleshare 0.7.2 py35_0 defaults pillow 3.2.0 py35_1 defaults pip 8.1.2 py35_0 defaults pip 9.0.1 ply 3.8 py35_0 defaults progressbar2 3.10.1 py35_0 conda-forge prompt_toolkit 1.0.4 py35_0 conda-forge protobuf 3.0.0b2 py35_0 conda-forge psutil 4.3.0 py35_0 defaults ptyprocess 0.5.1 py35_0 defaults py 1.4.31 py35_0 defaults pyasn1 0.1.9 py35_0 defaults pycosat 0.6.1 py35_1 defaults pycparser 2.14 py35_1 defaults pycrypto 2.6.1 py35_4 defaults pycurl 7.43.0 py35_0 defaults pyflakes 1.2.3 py35_0 defaults pygments 2.1.3 py35_0 defaults pyopengl 3.1.0 py35_0 conda-forge pyopenssl 0.16.0 py35_0 defaults pyparsing 2.1.4 py35_0 defaults pyqt 4.11.4 py35_3 defaults pyqtgraph 0.9.10 py35_1 defaults pytables 3.2.2 np111py35_4 defaults pytest 2.9.2 py35_0 defaults pytest-runner 2.9 py35_0 conda-forge python 3.5.2 0 defaults python-dateutil 2.5.3 py35_0 defaults python-utils 2.0.0 py35_0 conda-forge python.app 1.2 py35_4 defaults pytz 2016.4 py35_0 defaults pyyaml 3.11 py35_4 defaults pyzmq 15.2.0 py35_1 defaults qt 4.8.7 3 defaults qtconsole 4.2.1 py35_0 defaults qtpy 1.0.2 py35_0 defaults r 3.3.1 r3.3.1_0 r r-assertthat 0.1 r3.3.1_4 r r-base 3.3.1 0 r r-base64enc 0.1_3 r3.3.1_0 r r-bh 1.60.0_2 r3.3.1_0 r r-bitops 1.0_6 r3.3.1_2 r r-boot 1.3_18 r3.3.1_0 r r-car 2.1_2 r3.3.1_0 r r-caret 6.0_70 r3.3.1_0 r r-catools 1.17.1 r3.3.1_2 r r-chron 2.3_47 r3.3.1_0 r r-class 7.3_14 r3.3.1_0 r r-cluster 2.0.4 r3.3.1_0 r r-codetools 0.2_14 r3.3.1_0 r r-colorspace 1.2_6 r3.3.1_0 r r-crayon 1.3.1 r3.3.1_0 r r-curl 0.9.7 r3.3.1_0 r r-data.table 1.9.6 r3.3.1_0 r r-dbi 0.4_1 r3.3.1_0 r r-dichromat 2.0_0 r3.3.1_2 r r-digest 0.6.9 r3.3.1_0 r r-dplyr 0.4.3 r3.3.1_0 r r-essentials 1.4.3 r3.3.1_0 r r-evaluate 0.9 r3.3.1_0 r r-foreach 1.4.3 r3.3.1_0 r r-foreign 0.8_66 r3.3.1_0 r r-formatr 1.4 r3.3.1_0 r r-ggplot2 2.1.0 r3.3.1_0 r r-gistr 0.3.6 r3.3.1_0 r r-glmnet 2.0_5 r3.3.1_0 r r-gtable 0.2.0 r3.3.1_0 r r-hexbin 1.27.1 r3.3.1_0 r r-highr 0.6 r3.3.1_0 r r-htmltools 0.3.5 r3.3.1_0 r r-htmlwidgets 0.6 r3.3.1_0 r r-httpuv 1.3.3 r3.3.1_0 r r-httr 1.2.0 r3.3.1_0 r r-irdisplay 0.4.3 r3.3.1_2 r r-irkernel 0.7 r3.3.1_2 r r-iterators 1.0.8 r3.3.1_0 r r-jsonlite 0.9.22 r3.3.1_0 r r-kernsmooth 2.23_15 r3.3.1_0 r r-knitr 1.13 r3.3.1_0 r r-labeling 0.3 r3.3.1_2 r r-lattice 0.20_33 r3.3.1_0 r r-lazyeval 0.2.0 r3.3.1_0 r r-lme4 1.1_12 r3.3.1_0 r r-magrittr 1.5 r3.3.1_2 r r-maps 3.1.0 r3.3.1_0 r r-markdown 0.7.7 r3.3.1_2 r r-mass 7.3_45 r3.3.1_0 r r-matrix 1.2_6 r3.3.1_0 r r-matrixmodels 0.4_1 r3.3.1_0 r r-memoise 1.0.0 r3.3.1_0 r r-mgcv 1.8_12 r3.3.1_0 r r-mime 0.4 r3.3.1_0 r r-minqa 1.2.4 r3.3.1_2 r r-munsell 0.4.3 r3.3.1_0 r r-nlme 3.1_128 r3.3.1_0 r r-nloptr 1.0.4 r3.3.1_2 r r-nnet 7.3_12 r3.3.1_0 r r-openssl 0.9.4 r3.3.1_0 r r-pbdzmq 0.2_3 r3.3.1_0 r r-pbkrtest 0.4_6 r3.3.1_0 r r-plyr 1.8.4 r3.3.1_0 r r-pryr 0.1.2 r3.3.1_0 r r-quantmod 0.4_5 r3.3.1_2 r r-quantreg 5.26 r3.3.1_0 r r-r6 2.1.2 r3.3.1_0 r r-randomforest 4.6_12 r3.3.1_0 r r-rbokeh 0.4.2 r3.3.1_0 r r-rcolorbrewer 1.1_2 2a r r-rcpp 0.12.5 r3.3.1_0 r r-rcppeigen 0.3.2.8.1 r3.3.1_0 r r-recommended 3.3.1 r3.3.1_0 r r-repr 0.7 r3.3.1_0 r r-reshape2 1.4.1 1a r r-rmarkdown 0.9.6 r3.3.1_0 r r-rpart 4.1_10 r3.3.1_0 r r-scales 0.4.0 r3.3.1_0 r r-shiny 0.13.2 r3.3.1_0 r r-sparsem 1.7 r3.3.1_0 r r-spatial 7.3_11 r3.3.1_0 r r-stringi 1.1.1 r3.3.1_0 r r-stringr 1.0.0 r3.3.1_0 r r-survival 2.39_4 r3.3.1_0 r r-tibble 1.0 r3.3.1_0 r r-tidyr 0.5.1 r3.3.1_0 r r-ttr 0.23_1 r3.3.1_0 r r-uuid 0.1_2 r3.3.1_0 r r-xtable 1.8_2 r3.3.1_0 r r-xts 0.9_7 r3.3.1_2 r r-yaml 2.1.13 r3.3.1_2 r r-zoo 1.7_13 r3.3.1_0 r readline 6.2 0 conda-forge redis 3.2.0 0 defaults redis-py 2.10.5 py35_0 defaults requests 2.10.0 py35_0 defaults requests-file 1.4 py35_0 anaconda rope 0.9.4 py35_1 defaults rpy2 2.8.2 py35r3.3.1_1 r ruamel_yaml 0.11.14 py35_0 defaults scikit-image 0.12.3 np111py35_1 defaults scikit-learn 0.18 np111py35_blas_openblas_202 [blas_openblas] conda-forge scipy 0.18.1 np111py35_blas_openblas_200 [blas_openblas] conda-forge setproctitle 1.1.10 py35_0 conda-forge setuptools 23.0.0 py35_0 defaults simplegeneric 0.8.1 py35_1 defaults singledispatch 3.4.0.3 py35_0 defaults sip 4.16.9 py35_0 defaults six 1.10.0 py35_0 defaults six 1.10.0 snowballstemmer 1.2.1 py35_0 defaults sockjs-tornado 1.0.3 py35_0 defaults sphinx 1.4.1 py35_0 defaults sphinx_rtd_theme 0.1.9 py35_0 defaults spyder 2.3.9 py35_0 defaults sqlalchemy 1.0.13 py35_0 defaults sqlite 3.13.0 0 defaults statsmodels 0.6.1 np111py35_1 defaults sympy 1.0 py35_0 defaults tensorflow 0.10.0 py35_0 conda-forge terminado 0.6 py35_0 defaults Theano 0.8.2 tk 8.5.18 0 defaults toolz 0.8.0 py35_0 defaults tornado 4.3 py35_1 defaults traitlets 4.2.1 py35_0 defaults unicodecsv 0.14.1 py35_0 defaults Unidecode 0.4.19 vaex 1.0.0b3 py35_1 conda-forge wcwidth 0.1.7 py35_0 conda-forge werkzeug 0.11.10 py35_0 defaults wheel 0.29.0 py35_0 defaults xlrd 1.0.0 py35_0 defaults xlsxwriter 0.9.2 py35_0 defaults xlwings 0.7.2 py35_0 defaults xlwt 1.1.2 py35_0 defaults xonsh 0.4.4 py35_1 conda-forge xz 5.2.2 0 defaults yaml 0.1.6 0 defaults zeromq 4.1.3 0 defaults zlib 1.2.8 3 defaults david-boyds-iMac:pkgs davidboyd$

mingwandroid commented 7 years ago

The problem is that you have installed software from conda-forge and conda-forge and conda defaults are mutually incompatible. In this case, at least icu is problematic:

icu 56.1 4 conda-forge

Please force the installation of icu from conda defaults via:

conda install -c defaults icu

dthboyd commented 7 years ago

On 2016-11-29, at 4:01 PM, Ray Donnelly wrote:

conda install -c defaults icu

dyld: Library not loaded: @rpath/libncurses.5.dylib Referenced from: /Users/davidboyd/anaconda/lib/R/lib/../..//libreadline.6.2.dylib Reason: image not found

the new error after i do the above

mingwandroid commented 7 years ago

Right, so we continue:

Looking at your output we see:

readline 6.2 0 conda-forge

therefore:

conda install -c defaults readline

It may be better not to install anything from conda-forge, or to use separate environments for conda-forge software and conda defaults software.

dthboyd commented 7 years ago

thank you so much, R notebooks working now, i got the following message when i started up the notebook Warning: namespace ‘SparkR’ is not available and has been replaced by .GlobalEnv when processing object ‘predictions’, was wondering if this is a potential problem? Anyway, thanks again. On 2016-11-29, at 4:21 PM, Ray Donnelly wrote:

Right, so we continue:

Looking at your output we see:

readline 6.2 0 conda-forge

therefore:

conda install -c defaults readline

It may be better not to install anything from conda-forge, or to use separate environments for conda-forge software and conda defaults software.

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mingwandroid commented 7 years ago

You probably had an old R installation from elsewhere and it left some files in your %AppData% folder.

Warnings are warnings, I try not to get overly concerned with them esp. when I have errors to deal with.