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Anaconda issue tracking
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R not working Mac OS Mojave: dyld: Library not loaded: @rpath/libreadline.6.2.dylib #11184

Open gitfilla opened 5 years ago

gitfilla commented 5 years ago

Actual Behavior

(base) Josephs-MacBook-Pro:~ joef$ r dyld: Library not loaded: @rpath/libreadline.6.2.dylib Referenced from: /Users/joef/anaconda3/lib/R/lib/libR.dylib Reason: image not found Abort trap: 6

Expected Behavior

r would start

Steps to Reproduce

Anaconda or Miniconda version:

(base) Josephs-MacBook-Pro:~ joef$ conda --version conda 4.7.10

Operating System:
conda info
``` (base) Josephs-MacBook-Pro:~ joef$ conda info active environment : base active env location : /Users/joef/anaconda3 shell level : 1 user config file : /Users/joef/.condarc populated config files : /Users/joef/.condarc conda version : 4.7.10 conda-build version : 3.18.9 python version : 3.7.3.final.0 virtual packages : base environment : /Users/joef/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /Users/joef/anaconda3/pkgs /Users/joef/.conda/pkgs envs directories : /Users/joef/anaconda3/envs /Users/joef/.conda/envs platform : osx-64 user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Darwin/18.7.0 OSX/10.14.6 UID:GID : 501:20 netrc file : /Users/joef/.netrc offline mode : False ```
conda list --show-channel-urls
``` (base) Josephs-MacBook-Pro:~ joef$ conda list --show-channel-urls # packages in environment at /Users/joef/anaconda3: # # Name Version Build Channel _anaconda_depends 2019.03 py37_0 defaults _ipyw_jlab_nb_ext_conf 0.1.0 py37_0 defaults _r-mutex 1.0.0 anacondar_1 defaults alabaster 0.7.12 py37_0 defaults anaconda custom py37_1 defaults anaconda-client 1.7.2 py37_0 defaults anaconda-navigator 1.9.7 py37_0 defaults anaconda-project 0.8.3 py_0 defaults appnope 0.1.0 py37_0 defaults appscript 1.1.0 py37h1de35cc_0 defaults asn1crypto 0.24.0 py37_0 defaults astroid 2.2.5 py37_0 defaults astropy 3.2.1 py37h1de35cc_0 defaults atomicwrites 1.3.0 py37_1 defaults attrs 19.1.0 py37_1 defaults babel 2.7.0 py_0 defaults backcall 0.1.0 py37_0 defaults backports 1.0 py_2 defaults backports.functools_lru_cache 1.5 py_2 defaults backports.os 0.1.1 py37_0 defaults backports.shutil_get_terminal_size 1.0.0 py37_2 defaults backports.tempfile 1.0 py_1 defaults backports.weakref 1.0.post1 py_1 defaults beautifulsoup4 4.7.1 py37_1 defaults bitarray 0.9.3 py37h1de35cc_0 defaults bkcharts 0.2 py37_0 defaults blas 1.0 mkl defaults bleach 3.1.0 py37_0 defaults blosc 1.16.3 hd9629dc_0 defaults bokeh 1.3.2 py37_0 defaults boto 2.49.0 py37_0 defaults bottleneck 1.2.1 py37h1d22016_1 defaults bzip2 1.0.8 h1de35cc_0 defaults ca-certificates 2019.5.15 0 defaults certifi 2019.6.16 py37_1 defaults cffi 1.12.3 py37hb5b8e2f_0 defaults chardet 3.0.4 py37_1003 defaults click 7.0 py37_0 defaults cloudpickle 1.2.1 py_0 defaults clyent 1.2.2 py37_1 defaults colorama 0.4.1 py37_0 defaults conda 4.7.10 py37_0 defaults conda-build 3.18.9 py37_0 defaults conda-env 2.6.0 1 defaults conda-package-handling 1.3.11 py37_0 defaults conda-verify 3.4.2 py_1 defaults contextlib2 0.5.5 py37_0 defaults cryptography 2.7 py37ha12b0ac_0 defaults curl 7.65.2 ha441bb4_0 defaults cycler 0.10.0 py37_0 defaults cython 0.29.12 py37h0a44026_0 defaults cytoolz 0.10.0 py37h1de35cc_0 defaults dask 2.2.0 py_0 defaults dask-core 2.2.0 py_0 defaults dbus 1.13.6 h90a0687_0 defaults decorator 4.4.0 py37_1 defaults defusedxml 0.6.0 py_0 defaults distributed 2.2.0 py_1 defaults docutils 0.15.1 py37_0 defaults entrypoints 0.3 py37_0 defaults et_xmlfile 1.0.1 py37_0 defaults expat 2.2.6 h0a44026_0 defaults fastcache 1.1.0 py37h1de35cc_0 defaults filelock 3.0.12 py_0 defaults flask 1.1.1 py_0 defaults freetype 2.9.1 hb4e5f40_0 defaults fsspec 0.4.0 py_0 defaults future 0.17.1 py37_0 defaults get_terminal_size 1.0.0 h7520d66_0 defaults gettext 0.19.8.1 h15daf44_3 defaults gevent 1.4.0 py37h1de35cc_0 defaults glib 2.56.2 hd9629dc_0 defaults glob2 0.7 py_0 defaults gmp 6.1.2 hb37e062_1 defaults gmpy2 2.0.8 py37h6ef4df4_2 defaults greenlet 0.4.15 py37h1de35cc_0 defaults gsl 2.4 h1de35cc_4 defaults h5py 2.9.0 py37h3134771_0 defaults hdf5 1.10.4 hfa1e0ec_0 defaults heapdict 1.0.0 py37_2 defaults html5lib 1.0.1 py37_0 defaults icu 58.2 h4b95b61_1 defaults idna 2.8 py37_0 defaults imageio 2.5.0 py37_0 defaults imagesize 1.1.0 py37_0 defaults importlib_metadata 0.17 py37_1 defaults intel-openmp 2019.4 233 defaults ipykernel 5.1.1 py37h39e3cac_0 defaults ipython 7.7.0 py37h39e3cac_0 defaults ipython_genutils 0.2.0 py37_0 defaults ipywidgets 7.5.0 py_0 defaults isort 4.3.21 py37_0 defaults itsdangerous 1.1.0 py37_0 defaults jbig 2.1 h4d881f8_0 defaults jdcal 1.4.1 py_0 defaults jedi 0.13.3 py37_0 defaults jinja2 2.10.1 py37_0 defaults joblib 0.13.2 py37_0 defaults jpeg 9b he5867d9_2 defaults json5 0.8.4 py_0 defaults jsonschema 3.0.1 py37_0 defaults jupyter 1.0.0 py37_7 defaults jupyter_client 5.3.1 py_0 defaults jupyter_console 6.0.0 py37_0 defaults jupyter_core 4.5.0 py_0 defaults jupyterlab 1.0.2 py37hf63ae98_0 defaults jupyterlab_server 1.0.0 py_0 defaults keyring 18.0.0 py37_0 defaults kiwisolver 1.1.0 py37h0a44026_0 defaults krb5 1.16.1 hddcf347_7 defaults lazy-object-proxy 1.4.1 py37h1de35cc_0 defaults libarchive 3.3.3 h786848e_5 defaults libcurl 7.65.2 h051b688_0 defaults libcxx 4.0.1 hcfea43d_1 defaults libcxxabi 4.0.1 hcfea43d_1 defaults libedit 3.1.20181209 hb402a30_0 defaults libffi 3.2.1 h475c297_4 defaults libgcc 4.8.5 hdbeacc1_10 defaults libgfortran 3.0.1 h93005f0_2 defaults libiconv 1.15 hdd342a3_7 defaults liblief 0.9.0 h2a1bed3_2 defaults libpng 1.6.37 ha441bb4_0 defaults libsodium 1.0.16 h3efe00b_0 defaults libssh2 1.8.2 ha12b0ac_0 defaults libtiff 4.0.10 hcb84e12_2 defaults libxml2 2.9.9 hf6e021a_1 defaults libxslt 1.1.33 h33a18ac_0 defaults llvm-openmp 4.0.1 hcfea43d_1 defaults llvmlite 0.29.0 py37h98b8051_0 defaults locket 0.2.0 py37_1 defaults lxml 4.3.4 py37hef8c89e_0 defaults lz4-c 1.8.1.2 h1de35cc_0 defaults lzo 2.10 h362108e_2 defaults markupsafe 1.1.1 py37h1de35cc_0 defaults matplotlib 3.1.0 py37h54f8f79_0 defaults mccabe 0.6.1 py37_1 defaults mistune 0.8.4 py37h1de35cc_0 defaults mkl 2019.4 233 defaults mkl-service 2.0.2 py37h1de35cc_0 defaults mkl_fft 1.0.12 py37h5e564d8_0 defaults mkl_random 1.0.2 py37h27c97d8_0 defaults mock 3.0.5 py37_0 defaults more-itertools 7.2.0 py37_0 defaults mpc 1.1.0 h6ef4df4_1 defaults mpfr 4.0.1 h3018a27_3 defaults mpmath 1.1.0 py37_0 defaults msgpack-python 0.6.1 py37h04f5b5a_1 defaults multipledispatch 0.6.0 py37_0 defaults navigator-updater 0.2.1 py37_0 defaults nbconvert 5.5.0 py_0 defaults nbformat 4.4.0 py37_0 defaults ncurses 6.1 h0a44026_1 defaults networkx 2.3 py_0 defaults nltk 3.4.4 py37_0 defaults nose 1.3.7 py37_2 defaults notebook 6.0.0 py37_0 defaults numba 0.45.0 py37h6440ff4_0 defaults numexpr 2.6.9 py37h7413580_0 defaults numpy 1.16.4 py37hacdab7b_0 defaults numpy-base 1.16.4 py37h6575580_0 defaults numpydoc 0.9.1 py_0 defaults olefile 0.46 py37_0 defaults openpyxl 2.6.2 py_0 defaults openssl 1.1.1c h1de35cc_1 defaults packaging 19.0 py37_0 defaults pandas 0.25.0 py37h0a44026_0 defaults pandoc 2.2.3.2 0 defaults pandocfilters 1.4.2 py37_1 defaults parso 0.5.0 py_0 defaults partd 1.0.0 py_0 defaults path.py 12.0.1 py_0 defaults pathlib2 2.3.4 py37_0 defaults patsy 0.5.1 py37_0 defaults pcre 8.43 h0a44026_0 defaults pep8 1.7.1 py37_0 defaults pexpect 4.7.0 py37_0 defaults pickleshare 0.7.5 py37_0 defaults pillow 6.1.0 py37hb68e598_0 defaults pip 19.1.1 py37_0 defaults pkginfo 1.5.0.1 py37_0 defaults pluggy 0.12.0 py_0 defaults ply 3.11 py37_0 defaults prometheus_client 0.7.1 py_0 defaults prompt_toolkit 2.0.9 py37_0 defaults psutil 5.6.3 py37h1de35cc_0 defaults ptyprocess 0.6.0 py37_0 defaults py 1.8.0 py37_0 defaults py-lief 0.9.0 py37h1413db1_2 defaults pycodestyle 2.5.0 py37_0 defaults pycosat 0.6.3 py37h1de35cc_0 defaults pycparser 2.19 py37_0 defaults pycrypto 2.6.1 py37h1de35cc_9 defaults pycurl 7.43.0.3 py37ha12b0ac_0 defaults pyflakes 2.1.1 py37_0 defaults pygments 2.4.2 py_0 defaults pylint 2.3.1 py37_0 defaults pyodbc 4.0.26 py37h0a44026_0 defaults pyopenssl 19.0.0 py37_0 defaults pyparsing 2.4.0 py_0 defaults pyqt 5.9.2 py37h655552a_2 defaults pyrsistent 0.14.11 py37h1de35cc_0 defaults pysocks 1.7.0 py37_0 defaults pytables 3.5.2 py37h5bccee9_1 defaults pytest 5.0.1 py37_0 defaults pytest-arraydiff 0.3 py37h39e3cac_0 defaults pytest-astropy 0.5.0 py37_0 defaults pytest-doctestplus 0.3.0 py37_0 defaults pytest-openfiles 0.3.2 py37_0 defaults pytest-remotedata 0.3.2 py37_0 defaults python 3.7.3 h359304d_0 defaults python-dateutil 2.8.0 py37_0 defaults python-libarchive-c 2.8 py37_13 defaults python.app 2 py37_9 defaults pytz 2019.1 py_0 defaults pywavelets 1.0.3 py37h1d22016_1 defaults pyyaml 5.1.1 py37h1de35cc_0 defaults pyzmq 18.0.0 py37h0a44026_0 defaults qt 5.9.7 h468cd18_1 defaults qtawesome 0.5.7 py37_1 defaults qtconsole 4.5.2 py_0 defaults qtpy 1.8.0 py_0 defaults r-assertthat 0.1 r3.3.1_4 defaults r-base 3.3.1 0 defaults r-base64enc 0.1_3 r3.3.1_0 defaults r-bh 1.60.0_2 r3.3.1_0 defaults r-bitops 1.0_6 r3.3.1_2 defaults r-boot 1.3_18 r3.3.1_0 defaults r-car 2.1_2 r3.3.1_0 defaults r-caret 6.0_70 r3.3.1_0 defaults r-catools 1.17.1 r3.3.1_2 defaults r-chron 2.3_47 r3.3.1_0 defaults r-class 7.3_14 r3.3.1_0 defaults r-cluster 2.0.4 r3.3.1_0 defaults r-codetools 0.2_14 r3.3.1_0 defaults r-colorspace 1.2_6 r3.3.1_0 defaults r-crayon 1.3.1 r3.3.1_0 defaults r-curl 0.9.7 r3.3.1_0 defaults r-data.table 1.9.6 r3.3.1_0 defaults r-dbi 0.4_1 r3.3.1_0 defaults r-dichromat 2.0_0 r3.3.1_2 defaults r-digest 0.6.9 r3.3.1_0 defaults r-dplyr 0.4.3 r3.3.1_0 defaults r-essentials 1.4.3 r3.3.1_0 defaults r-evaluate 0.9 r3.3.1_0 defaults r-foreach 1.4.3 r3.3.1_0 defaults r-foreign 0.8_66 r3.3.1_0 defaults r-formatr 1.4 r3.3.1_0 defaults r-ggplot2 2.1.0 r3.3.1_0 defaults r-gistr 0.3.6 r3.3.1_0 defaults r-glmnet 2.0_5 r3.3.1_0 defaults r-gtable 0.2.0 r3.3.1_0 defaults r-hexbin 1.27.1 r3.3.1_0 defaults r-highr 0.6 r3.3.1_0 defaults r-htmltools 0.3.5 r3.3.1_0 defaults r-htmlwidgets 0.6 r3.3.1_0 defaults r-httpuv 1.3.3 r3.3.1_0 defaults r-httr 1.2.0 r3.3.1_0 defaults r-irdisplay 0.4.3 r3.3.1_2 defaults r-irkernel 0.7 r3.3.1_2 defaults r-iterators 1.0.8 r3.3.1_0 defaults r-jsonlite 0.9.22 r3.3.1_0 defaults r-kernsmooth 2.23_15 r3.3.1_0 defaults r-knitr 1.13 r3.3.1_0 defaults r-labeling 0.3 r3.3.1_2 defaults r-lattice 0.20_33 r3.3.1_0 defaults r-lazyeval 0.2.0 r3.3.1_0 defaults r-lme4 1.1_12 r3.3.1_0 defaults r-magrittr 1.5 r3.3.1_2 defaults r-maps 3.1.0 r3.3.1_0 defaults r-markdown 0.7.7 r3.3.1_2 defaults r-mass 7.3_45 r3.3.1_0 defaults r-matrix 1.2_6 r3.3.1_0 defaults r-matrixmodels 0.4_1 r3.3.1_0 defaults r-memoise 1.0.0 r3.3.1_0 defaults r-mgcv 1.8_12 r3.3.1_0 defaults r-mime 0.4 r3.3.1_0 defaults r-minqa 1.2.4 r3.3.1_2 defaults r-munsell 0.4.3 r3.3.1_0 defaults r-nlme 3.1_128 r3.3.1_0 defaults r-nloptr 1.0.4 r3.3.1_2 defaults r-nnet 7.3_12 r3.3.1_0 defaults r-openssl 0.9.4 r3.3.1_0 defaults r-pbdzmq 0.2_3 r3.3.1_0 defaults r-pbkrtest 0.4_6 r3.3.1_0 defaults r-plyr 1.8.4 r3.3.1_0 defaults r-pryr 0.1.2 r3.3.1_0 defaults r-quantmod 0.4_5 r3.3.1_2 defaults r-quantreg 5.26 r3.3.1_0 defaults r-r6 2.1.2 r3.3.1_0 defaults r-randomforest 4.6_12 r3.3.1_0 defaults r-rbokeh 0.4.2 r3.3.1_0 defaults r-rcolorbrewer 1.1_2 r3.3.1_3 defaults r-rcpp 0.12.5 r3.3.1_0 defaults r-rcppeigen 0.3.2.8.1 r3.3.1_0 defaults r-recommended 3.3.1 r3.3.1_0 defaults r-repr 0.7 r3.3.1_0 defaults r-reshape2 1.4.1 r3.3.1_2 defaults r-rmarkdown 0.9.6 r3.3.1_0 defaults r-rpart 4.1_10 r3.3.1_0 defaults r-scales 0.4.0 r3.3.1_0 defaults r-shiny 0.13.2 r3.3.1_0 defaults r-sparsem 1.7 r3.3.1_0 defaults r-spatial 7.3_11 r3.3.1_0 defaults r-stringi 1.1.1 r3.3.1_0 defaults r-stringr 1.0.0 r3.3.1_0 defaults r-survival 2.39_4 r3.3.1_0 defaults r-tibble 1.0 r3.3.1_0 defaults r-tidyr 0.5.1 r3.3.1_0 defaults r-ttr 0.23_1 r3.3.1_0 defaults r-uuid 0.1_2 r3.3.1_0 defaults r-xtable 1.8_2 r3.3.1_0 defaults r-xts 0.9_7 r3.3.1_2 defaults r-yaml 2.1.13 r3.3.1_2 defaults r-zoo 1.7_13 r3.3.1_0 defaults readline 7.0 h1de35cc_5 defaults requests 2.22.0 py37_0 defaults rope 0.14.0 py_0 defaults rstudio 1.0.44 0 defaults ruamel_yaml 0.15.46 py37h1de35cc_0 defaults scikit-image 0.15.0 py37h0a44026_0 defaults scikit-learn 0.21.2 py37h27c97d8_0 defaults scipy 1.3.0 py37h1410ff5_0 defaults seaborn 0.9.0 py37_0 defaults send2trash 1.5.0 py37_0 defaults setuptools 41.0.1 py37_0 defaults simplegeneric 0.8.1 py37_2 defaults singledispatch 3.4.0.3 py37_0 defaults sip 4.19.8 py37h0a44026_0 defaults six 1.12.0 py37_0 defaults snappy 1.1.7 he62c110_3 defaults snowballstemmer 1.9.0 py_0 defaults sortedcollections 1.1.2 py37_0 defaults sortedcontainers 2.1.0 py37_0 defaults soupsieve 1.9.2 py37_0 defaults sphinx 2.1.2 py_0 defaults sphinxcontrib 1.0 py37_1 defaults sphinxcontrib-applehelp 1.0.1 py_0 defaults sphinxcontrib-devhelp 1.0.1 py_0 defaults sphinxcontrib-htmlhelp 1.0.2 py_0 defaults sphinxcontrib-jsmath 1.0.1 py_0 defaults sphinxcontrib-qthelp 1.0.2 py_0 defaults sphinxcontrib-serializinghtml 1.1.3 py_0 defaults sphinxcontrib-websupport 1.1.2 py_0 defaults spyder 3.3.6 py37_0 defaults spyder-kernels 0.5.1 py37_0 defaults sqlalchemy 1.3.5 py37h1de35cc_0 defaults sqlite 3.29.0 ha441bb4_0 defaults statsmodels 0.10.1 py37h1d22016_0 defaults sympy 1.4 py37_0 defaults tblib 1.4.0 py_0 defaults terminado 0.8.2 py37_0 defaults testpath 0.4.2 py37_0 defaults tk 8.6.8 ha441bb4_0 defaults toolz 0.10.0 py_0 defaults tornado 6.0.3 py37h1de35cc_0 defaults tqdm 4.32.1 py_0 defaults traitlets 4.3.2 py37_0 defaults unicodecsv 0.14.1 py37_0 defaults unixodbc 2.3.7 h1de35cc_0 defaults urllib3 1.24.2 py37_0 defaults wcwidth 0.1.7 py37_0 defaults webencodings 0.5.1 py37_1 defaults werkzeug 0.15.4 py_0 defaults wheel 0.33.4 py37_0 defaults widgetsnbextension 3.5.0 py37_0 defaults wrapt 1.11.2 py37h1de35cc_0 defaults wurlitzer 1.0.3 py37_0 defaults xlrd 1.2.0 py37_0 defaults xlsxwriter 1.1.8 py_0 defaults xlwings 0.15.8 py37_0 defaults xlwt 1.3.0 py37_0 defaults xz 5.2.4 h1de35cc_4 defaults yaml 0.1.7 hc338f04_2 defaults zeromq 4.3.1 h0a44026_3 defaults zict 1.0.0 py_0 defaults zipp 0.5.2 py_0 defaults zlib 1.2.11 h1de35cc_3 defaults zstd 1.3.7 h5bba6e5_0 defaults ```
hansenaw commented 5 years ago

I'm having the same exact error when attempting to start R, but with macOS High Sierra (v10.13.6).

Recently ran conda update conda followed by conda install r-essentials, both of which executed without throwing any errors.

conda info

Details

``` active environment : base active env location : /Users/awhansen/anaconda3 shell level : 1 user config file : /Users/awhansen/.condarc populated config files : /Users/awhansen/.condarc conda version : 4.7.11 conda-build version : 3.18.8 python version : 3.7.3.final.0 virtual packages : base environment : /Users/awhansen/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /Users/awhansen/anaconda3/pkgs /Users/awhansen/.conda/pkgs envs directories : /Users/awhansen/anaconda3/envs /Users/awhansen/.conda/envs platform : osx-64 user-agent : conda/4.7.11 requests/2.22.0 CPython/3.7.3 Darwin/17.7.0 OSX/10.13.6 UID:GID : 502:20 netrc file : None offline mode : False ```

conda list --show-channel-urls

Details

``` (base) adamsmacbookpro:~ awhansen$ conda list --show-channel-urls # packages in environment at /Users/awhansen/anaconda3: # # Name Version Build Channel _anaconda_depends 2019.03 py37_0 defaults _ipyw_jlab_nb_ext_conf 0.1.0 py37_0 defaults _r-mutex 1.0.0 anacondar_1 defaults alabaster 0.7.12 py37_0 defaults anaconda 2019.07 py37_0 defaults anaconda-client 1.7.2 py37_0 defaults anaconda-navigator 1.9.7 py37_0 defaults anaconda-project 0.8.3 py_0 defaults appnope 0.1.0 py37_0 defaults appscript 1.1.0 py37h1de35cc_0 defaults asn1crypto 0.24.0 py37_0 defaults astroid 2.2.5 py37_0 defaults astropy 3.2.1 py37h1de35cc_0 defaults atomicwrites 1.3.0 py37_1 defaults attrs 19.1.0 py37_1 defaults babel 2.7.0 py_0 defaults backcall 0.1.0 py37_0 defaults backports 1.0 py_2 defaults backports.functools_lru_cache 1.5 py_2 defaults backports.os 0.1.1 py37_0 defaults backports.shutil_get_terminal_size 1.0.0 py37_2 defaults backports.tempfile 1.0 py_1 defaults backports.weakref 1.0.post1 py_1 defaults beautifulsoup4 4.7.1 py37_1 defaults bitarray 0.9.3 py37h1de35cc_0 defaults bkcharts 0.2 py37_0 defaults blas 1.0 mkl defaults bleach 3.1.0 py37_0 defaults blosc 1.16.3 hd9629dc_0 defaults bokeh 1.2.0 py37_0 defaults boto 2.49.0 py37_0 defaults bottleneck 1.2.1 py37h1d22016_1 defaults bzip2 1.0.8 h1de35cc_0 defaults ca-certificates 2019.5.15 0 defaults certifi 2019.6.16 py37_0 defaults cffi 1.12.3 py37hb5b8e2f_0 defaults chardet 3.0.4 py37_1 defaults click 7.0 py37_0 defaults cloudpickle 1.2.1 py_0 defaults clyent 1.2.2 py37_1 defaults colorama 0.4.1 py37_0 defaults conda 4.7.11 py37_0 conda-forge conda-build 3.18.8 py37_0 defaults conda-env 2.6.0 1 defaults conda-package-handling 1.3.11 py37_0 defaults conda-verify 3.4.2 py_1 defaults contextlib2 0.5.5 py37_0 defaults cryptography 2.7 py37ha12b0ac_0 defaults curl 7.65.2 ha441bb4_0 defaults cycler 0.10.0 py37_0 defaults cython 0.29.12 py37h0a44026_0 defaults cytoolz 0.10.0 py37h1de35cc_0 defaults dask 2.1.0 py_0 defaults dask-core 2.1.0 py_0 defaults dbus 1.13.6 h90a0687_0 defaults decorator 4.4.0 py37_1 defaults defusedxml 0.6.0 py_0 defaults distributed 2.1.0 py_0 defaults docutils 0.14 py37_0 defaults entrypoints 0.3 py37_0 defaults et_xmlfile 1.0.1 py37_0 defaults expat 2.2.6 h0a44026_0 defaults fastcache 1.1.0 py37h1de35cc_0 defaults filelock 3.0.12 py_0 defaults flask 1.1.1 py_0 defaults freetype 2.9.1 hb4e5f40_0 defaults fsspec 0.4.0 py_0 defaults future 0.17.1 py37_0 defaults get_terminal_size 1.0.0 h7520d66_0 defaults gettext 0.19.8.1 h15daf44_3 defaults gevent 1.4.0 py37h1de35cc_0 defaults glib 2.56.2 hd9629dc_0 defaults glob2 0.7 py_0 defaults gmp 6.1.2 hb37e062_1 defaults gmpy2 2.0.8 py37h6ef4df4_2 defaults greenlet 0.4.15 py37h1de35cc_0 defaults gsl 2.4 h1de35cc_4 defaults h5py 2.9.0 py37h3134771_0 defaults hdf5 1.10.4 hfa1e0ec_0 defaults heapdict 1.0.0 py37_2 defaults html5lib 1.0.1 py37_0 defaults icu 58.2 h4b95b61_1 defaults idna 2.8 py37_0 defaults imageio 2.5.0 py37_0 defaults 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defaults more-itertools 7.0.0 py37_0 defaults mpc 1.1.0 h6ef4df4_1 defaults mpfr 4.0.1 h3018a27_3 defaults mpmath 1.1.0 py37_0 defaults msgpack-python 0.6.1 py37h04f5b5a_1 defaults multipledispatch 0.6.0 py37_0 defaults navigator-updater 0.2.1 py37_0 defaults nbconvert 5.5.0 py_0 defaults nbformat 4.4.0 py37_0 defaults ncurses 6.1 h0a44026_1 defaults networkx 2.3 py_0 defaults nltk 3.4.4 py37_0 defaults nose 1.3.7 py37_2 defaults notebook 6.0.0 py37_0 defaults numba 0.44.1 py37h6440ff4_0 defaults numexpr 2.6.9 py37h7413580_0 defaults numpy 1.16.4 py37hacdab7b_0 defaults numpy-base 1.16.4 py37h6575580_0 defaults numpydoc 0.9.1 py_0 defaults olefile 0.46 py37_0 defaults openpyxl 2.6.2 py_0 defaults openssl 1.1.1c h1de35cc_1 defaults packaging 19.0 py37_0 defaults pandas 0.24.2 py37h0a44026_0 defaults pandoc 2.2.3.2 0 defaults pandocfilters 1.4.2 py37_1 defaults parso 0.5.0 py_0 defaults partd 1.0.0 py_0 defaults path.py 12.0.1 py_0 defaults pathlib2 2.3.4 py37_0 defaults patsy 0.5.1 py37_0 defaults pcre 8.43 h0a44026_0 defaults pep8 1.7.1 py37_0 defaults pexpect 4.7.0 py37_0 defaults pickleshare 0.7.5 py37_0 defaults pillow 6.1.0 py37hb68e598_0 defaults pip 19.1.1 py37_0 defaults pkginfo 1.5.0.1 py37_0 defaults pluggy 0.12.0 py_0 defaults ply 3.11 py37_0 defaults prometheus_client 0.7.1 py_0 defaults prompt_toolkit 2.0.9 py37_0 defaults psutil 5.6.3 py37h1de35cc_0 defaults ptyprocess 0.6.0 py37_0 defaults py 1.8.0 py37_0 defaults py-lief 0.9.0 py37h1413db1_2 defaults pycodestyle 2.5.0 py37_0 defaults pycosat 0.6.3 py37h1de35cc_0 defaults pycparser 2.19 py37_0 defaults pycrypto 2.6.1 py37h1de35cc_9 defaults pycurl 7.43.0.3 py37ha12b0ac_0 defaults pyflakes 2.1.1 py37_0 defaults pygments 2.4.2 py_0 defaults pylint 2.3.1 py37_0 defaults pyodbc 4.0.26 py37h0a44026_0 defaults pyopenssl 19.0.0 py37_0 defaults pyparsing 2.4.0 py_0 defaults pyqt 5.9.2 py37h655552a_2 defaults pyrsistent 0.14.11 py37h1de35cc_0 defaults pysocks 1.7.0 py37_0 defaults pytables 3.5.2 py37h5bccee9_1 defaults pytest 5.0.1 py37_0 defaults pytest-arraydiff 0.3 py37h39e3cac_0 defaults pytest-astropy 0.5.0 py37_0 defaults pytest-doctestplus 0.3.0 py37_0 defaults pytest-openfiles 0.3.2 py37_0 defaults pytest-remotedata 0.3.1 py37_0 defaults python 3.7.3 h359304d_0 defaults python-dateutil 2.8.0 py37_0 defaults python-libarchive-c 2.8 py37_11 defaults python.app 2 py37_9 defaults pytz 2019.1 py_0 defaults pywavelets 1.0.3 py37h1d22016_1 defaults pyyaml 5.1.1 py37h1de35cc_0 defaults pyzmq 18.0.0 py37h0a44026_0 defaults qt 5.9.7 h468cd18_1 defaults qtawesome 0.5.7 py37_1 defaults qtconsole 4.5.1 py_0 defaults qtpy 1.8.0 py_0 defaults r-assertthat 0.1 r3.3.1_4 defaults r-base 3.3.1 0 defaults r-base64enc 0.1_3 r3.3.1_0 defaults r-bh 1.60.0_2 r3.3.1_0 defaults r-bitops 1.0_6 r3.3.1_2 defaults r-boot 1.3_18 r3.3.1_0 defaults r-car 2.1_2 r3.3.1_0 defaults r-caret 6.0_70 r3.3.1_0 defaults r-catools 1.17.1 r3.3.1_2 defaults r-chron 2.3_47 r3.3.1_0 defaults r-class 7.3_14 r3.3.1_0 defaults r-cluster 2.0.4 r3.3.1_0 defaults r-codetools 0.2_14 r3.3.1_0 defaults r-colorspace 1.2_6 r3.3.1_0 defaults r-crayon 1.3.1 r3.3.1_0 defaults r-curl 0.9.7 r3.3.1_0 defaults r-data.table 1.9.6 r3.3.1_0 defaults r-dbi 0.4_1 r3.3.1_0 defaults r-dichromat 2.0_0 r3.3.1_2 defaults r-digest 0.6.9 r3.3.1_0 defaults r-dplyr 0.4.3 r3.3.1_0 defaults r-essentials 1.4.3 r3.3.1_0 defaults r-evaluate 0.9 r3.3.1_0 defaults r-foreach 1.4.3 r3.3.1_0 defaults r-foreign 0.8_66 r3.3.1_0 defaults r-formatr 1.4 r3.3.1_0 defaults r-ggplot2 2.1.0 r3.3.1_0 defaults r-gistr 0.3.6 r3.3.1_0 defaults r-glmnet 2.0_5 r3.3.1_0 defaults r-gtable 0.2.0 r3.3.1_0 defaults r-hexbin 1.27.1 r3.3.1_0 defaults r-highr 0.6 r3.3.1_0 defaults r-htmltools 0.3.5 r3.3.1_0 defaults r-htmlwidgets 0.6 r3.3.1_0 defaults r-httpuv 1.3.3 r3.3.1_0 defaults r-httr 1.2.0 r3.3.1_0 defaults r-irdisplay 0.4.3 r3.3.1_2 defaults r-irkernel 0.7 r3.3.1_2 defaults r-iterators 1.0.8 r3.3.1_0 defaults r-jsonlite 0.9.22 r3.3.1_0 defaults r-kernsmooth 2.23_15 r3.3.1_0 defaults r-knitr 1.13 r3.3.1_0 defaults r-labeling 0.3 r3.3.1_2 defaults r-lattice 0.20_33 r3.3.1_0 defaults r-lazyeval 0.2.0 r3.3.1_0 defaults r-lme4 1.1_12 r3.3.1_0 defaults r-magrittr 1.5 r3.3.1_2 defaults r-maps 3.1.0 r3.3.1_0 defaults r-markdown 0.7.7 r3.3.1_2 defaults r-mass 7.3_45 r3.3.1_0 defaults r-matrix 1.2_6 r3.3.1_0 defaults r-matrixmodels 0.4_1 r3.3.1_0 defaults r-memoise 1.0.0 r3.3.1_0 defaults r-mgcv 1.8_12 r3.3.1_0 defaults r-mime 0.4 r3.3.1_0 defaults r-minqa 1.2.4 r3.3.1_2 defaults r-munsell 0.4.3 r3.3.1_0 defaults r-nlme 3.1_128 r3.3.1_0 defaults r-nloptr 1.0.4 r3.3.1_2 defaults r-nnet 7.3_12 r3.3.1_0 defaults r-openssl 0.9.4 r3.3.1_0 defaults r-pbdzmq 0.2_3 r3.3.1_0 defaults r-pbkrtest 0.4_6 r3.3.1_0 defaults r-plyr 1.8.4 r3.3.1_0 defaults r-pryr 0.1.2 r3.3.1_0 defaults r-quantmod 0.4_5 r3.3.1_2 defaults r-quantreg 5.26 r3.3.1_0 defaults r-r6 2.1.2 r3.3.1_0 defaults r-randomforest 4.6_12 r3.3.1_0 defaults r-rbokeh 0.4.2 r3.3.1_0 defaults r-rcolorbrewer 1.1_2 r3.3.1_3 defaults r-rcpp 0.12.5 r3.3.1_0 defaults r-rcppeigen 0.3.2.8.1 r3.3.1_0 defaults r-recommended 3.3.1 r3.3.1_0 defaults r-repr 0.7 r3.3.1_0 defaults r-reshape2 1.4.1 r3.3.1_2 defaults r-rmarkdown 0.9.6 r3.3.1_0 defaults r-rpart 4.1_10 r3.3.1_0 defaults r-scales 0.4.0 r3.3.1_0 defaults r-shiny 0.13.2 r3.3.1_0 defaults r-sparsem 1.7 r3.3.1_0 defaults r-spatial 7.3_11 r3.3.1_0 defaults r-stringi 1.1.1 r3.3.1_0 defaults r-stringr 1.0.0 r3.3.1_0 defaults r-survival 2.39_4 r3.3.1_0 defaults r-tibble 1.0 r3.3.1_0 defaults r-tidyr 0.5.1 r3.3.1_0 defaults r-ttr 0.23_1 r3.3.1_0 defaults r-uuid 0.1_2 r3.3.1_0 defaults r-xtable 1.8_2 r3.3.1_0 defaults r-xts 0.9_7 r3.3.1_2 defaults r-yaml 2.1.13 r3.3.1_2 defaults r-zoo 1.7_13 r3.3.1_0 defaults readline 7.0 h1de35cc_5 defaults requests 2.22.0 py37_0 defaults rope 0.14.0 py_0 defaults ruamel_yaml 0.15.46 py37h1de35cc_0 defaults scikit-image 0.15.0 py37h0a44026_0 defaults scikit-learn 0.21.2 py37h27c97d8_0 defaults scipy 1.3.0 py37h1410ff5_0 defaults seaborn 0.9.0 py37_0 defaults send2trash 1.5.0 py37_0 defaults setuptools 41.0.1 py37_0 defaults simplegeneric 0.8.1 py37_2 defaults singledispatch 3.4.0.3 py37_0 defaults sip 4.19.8 py37h0a44026_0 defaults six 1.12.0 py37_0 defaults snappy 1.1.7 he62c110_3 defaults snowballstemmer 1.9.0 py_0 defaults sortedcollections 1.1.2 py37_0 defaults sortedcontainers 2.1.0 py37_0 defaults soupsieve 1.8 py37_0 defaults sphinx 2.1.2 py_0 defaults sphinxcontrib 1.0 py37_1 defaults sphinxcontrib-applehelp 1.0.1 py_0 defaults sphinxcontrib-devhelp 1.0.1 py_0 defaults sphinxcontrib-htmlhelp 1.0.2 py_0 defaults sphinxcontrib-jsmath 1.0.1 py_0 defaults sphinxcontrib-qthelp 1.0.2 py_0 defaults sphinxcontrib-serializinghtml 1.1.3 py_0 defaults sphinxcontrib-websupport 1.1.2 py_0 defaults spyder 3.3.6 py37_0 defaults spyder-kernels 0.5.1 py37_0 defaults sqlalchemy 1.3.5 py37h1de35cc_0 defaults sqlite 3.29.0 ha441bb4_0 defaults statsmodels 0.10.0 py37h1d22016_0 defaults sympy 1.4 py37_0 defaults tbb 2019.4 h04f5b5a_0 defaults tblib 1.4.0 py_0 defaults terminado 0.8.2 py37_0 defaults testpath 0.4.2 py37_0 defaults tk 8.6.8 ha441bb4_0 defaults toolz 0.10.0 py_0 defaults tornado 6.0.3 py37h1de35cc_0 defaults tqdm 4.32.1 py_0 defaults traitlets 4.3.2 py37_0 defaults unicodecsv 0.14.1 py37_0 defaults unixodbc 2.3.7 h1de35cc_0 defaults urllib3 1.24.2 py37_0 defaults wcwidth 0.1.7 py37_0 defaults webencodings 0.5.1 py37_1 defaults werkzeug 0.15.4 py_0 defaults wheel 0.33.4 py37_0 defaults widgetsnbextension 3.5.0 py37_0 defaults wordcloud 1.5.0 py37h1de35cc_1000 conda-forge wrapt 1.11.2 py37h1de35cc_0 defaults wurlitzer 1.0.2 py37_0 defaults xlrd 1.2.0 py37_0 defaults xlsxwriter 1.1.8 py_0 defaults xlwings 0.15.8 py37_0 defaults xlwt 1.3.0 py37_0 defaults xz 5.2.4 h1de35cc_4 defaults yaml 0.1.7 hc338f04_2 defaults zeromq 4.3.1 h0a44026_3 defaults zict 1.0.0 py_0 defaults zipp 0.5.1 py_0 defaults zlib 1.2.11 h1de35cc_3 defaults zstd 1.3.7 h5bba6e5_0 defaults ```

gitfilla commented 5 years ago

I reran 'conda update conda' and 'conda install r-essentials'

Still getting the error: (base) Josephs-MacBook-Pro:~ joef$ r dyld: Library not loaded: @rpath/libreadline.6.2.dylib Referenced from: /Users/joef/anaconda3/lib/R/lib/libR.dylib Reason: image not found Abort trap: 6

I did some searching and this is the same error that was occurring in 2017. Don't know if it ever was fixed, or if something new has popped up (again).

fonnesbeck commented 5 years ago

Can confirm this on OS X 10.14.6.

mingwandroid commented 5 years ago

This is a dependency issue in a very old R release (3.3.1). While we should try to fix it, I suspect you would not want that old version of R now-a-days.

The issue is, AFAICT because you've got anaconda=2019.07 installed in this env and you then try to install r-essentials too. The mutual the requirements of those specifications leads to only being able to use a very old R (3.3.1).

You have two/three options, in order of my own preference:

  1. Create a new env. for R, conda create -n r r-essentials (this should install R 3.6)
  2. Start from Miniconda instead of Anaconda. It has far less packages and no metapackage enforcing such pinnings.
  3. Install the 'custom' version of the anaconda package (which has no pinnings) instead of the current one. To do this at the same time as installing r-essentials you can use conda install anaconda=custom r-essentials

Please let me know if this works for you. The anaconda metapackage is quite problematic, I must say.

maggiex commented 4 years ago

On OS Catalina, running into the same problem when trying to launch Jupyter notebook R.

CommonClimate commented 4 years ago

I have the exact same issue, after installing R via conda in a miniconda environment.

maggiex commented 4 years ago

If you are on Catalina, install 3.6.3 directly from R website and remove the R in conda (3.6.1). Hope it helps.

CommonClimate commented 4 years ago

That's what I ended up doing, and it does work. Still, it's a bug that needs to be addressed at some point.

vijayvd commented 4 years ago

I am having the same issue. I uninstalled the R in conda environment. I also have an R from website installed outside the conda environment. How to make the conda environment aware of the outside installation? My goal is to be able to use R from jupyter book.

dsbrown commented 4 years ago

I am having the same issue with 10.14, and have the same goal as vijayvd, use R in jupyter notebook. I am now trying to uninstall r-essentials from Anaconda, it wants to remove crazy amounts of stuff like gcc, but heck, i will try it, maybe I can then roll forward. That didn't work. At this time I will uninstall Anaconda and go all command line. Its too bad, Anaconda is supposed to make things easy; but the proper lack of support for R, has cost me hours and will make me not use them until they get this fixed.

ljchang commented 4 years ago

I'm running MacOS 10.15.5 and also experiencing the same issue.

(base) lukechang@x86_64-apple-darwin13 Github % which R
/Users/lukechang/anaconda3/bin/R
(base) lukechang@x86_64-apple-darwin13 Github % R
dyld: Library not loaded: @rpath/libreadline.6.2.dylib
  Referenced from: /Users/lukechang/anaconda3/lib/R/lib/libR.dylib
  Reason: image not found
zsh: abort      R
wusunlab commented 4 years ago

I'm having the same issue with Anaconda 2020.7 on macOS Catalina 10.15.6. Due to mysterious package conflicts, I was not allowed to install any R version except the outdated version 3.3.1, which was unable to run due to the said dyld error.

In the end I gave up and happily settled on a stand-alone R 4.0.2 installation outside of the conda environment (brew install R). I also installed Jupyter R kernel following the instructions here: https://irkernel.github.io/installation/. It works.

I still don't understand why having Python 3.8 would restrict R to 3.3.1. It's kinda frustrating for people who use both languages interactively. In previous versions, I quite enjoyed the convenience of managing both languages with conda. I hope that the bug will be fixed.

scottkall commented 4 years ago

Running macOS Catalina, 10.15.5. conda base env has r=3.3.1, python 3.8.3. This is the error I get upon trying to load R. Incidentally, I'm also having trouble opening RStudio -- errors there as well. R 4.0.3 is working in another conda env, and R is also working via Homebrew. Shell is zsh (ohmy.zsh configuration).

(base) ➜  R
dyld: Library not loaded: @rpath/libreadline.6.2.dylib
  Referenced from: /Users/<name redacted>/opt/anaconda3/lib/R/lib/libR.dylib
  Reason: image not found
[1]    74122 abort      R
yfarjoun commented 3 years ago

same problem. weird thing is that rstudio manages to run, but not r...

natemella commented 3 years ago

I'm getting the same error:

dyld: Library not loaded: @rpath/libreadline.6.2.dylib Referenced from: /Users/nathanmella/opt/anaconda3/lib/R/lib/libR.dylib Reason: image not found zsh: abort R

jaamarks commented 3 years ago

I was having the same issue. This GitHub comment resolved it for me.