Conda: R not loading after installing essentials. `dyld: Library not loaded: @rpath/libpcre.1.dylib`
$ which R
/Users/jespinoz/anaconda/bin/R
$ R
dyld: Library not loaded: @rpath/libpcre.1.dylib
Referenced from: /Users/jespinoz/anaconda/lib/R/lib/libR.dylib
Reason: image not found
Trace/BPT trap: 5
Is it the linking that is going wrong? How can I fix this error? I installed my R through anaconda. It was working a little bit ago but when I started installing the libraries it got messed up.
jolespin
All 49 comments
Please show the output of conda info.
mingwandroid
on 20 Jul 2016
I ended up deleting my anaconda directory and reinstalled everything from scratch to get things working again.
jolespin
on 20 Jul 2016
Since I'm having the exact same problem, here you go:
Warning: could not import binstar_client ('args' object has no attribute 'site')An unexpected error has occurred, please consider sending the
following traceback to the conda GitHub issue tracker at:
https://github.com/conda/conda/issues
Include the output of the command 'conda info' in your report.
Traceback (most recent call last):
File "/Users/marlie/anaconda/bin/conda", line 6, in
sys.exit(main())
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 120, in main
exit_code = args_func(args, p)
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 130, in args_func
exit_code = args.func(args, p)
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/cli/main_info.py", line 158, in execute
init_binstar(True)
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/config.py", line 244, in init_binstar
binstar_domain = binstar_client.domain.replace("api", "conda").rstrip('/') + '/'
AttributeError: 'NoneType' object has no attribute 'domain'
twistingstar
on 20 Jul 2016
Which is only slightly different from the error I get if I try to revert to an earlier version:
conda install --revision 4
Fetching package metadata .......
.
Package plan for installation in environment /Users/marlie/anaconda:
The following packages will be downloaded:
An unexpected error has occurred, please consider sending the
following traceback to the conda GitHub issue tracker at:
https://github.com/conda/conda/issues
Include the output of the command 'conda info' in your report.
Traceback (most recent call last):
File "/Users/marlie/anaconda/bin/conda", line 6, in
sys.exit(main())
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 120, in main
exit_code = args_func(args, p)
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 130, in args_func
exit_code = args.func(args, p)
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/cli/main_install.py", line 78, in execute
install(args, parser, 'install')
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/cli/install.py", line 394, in install
display_actions(actions, index, show_channel_urls=args.show_channel_urls)
File "/Users/marlie/anaconda/lib/python2.7/site-packages/conda/plan.py", line 73, in display_actions
info = index[dist + '.tar.bz2']
KeyError: 'r-mgcv-1.8_9-r3.2.2_0a.tar.bz2'
twistingstar
on 20 Jul 2016
@twistingstar Please show the output of conda info
mingwandroid
on 20 Jul 2016
Ah, sorry to be unclear - the first is the current output of conda info when I attempt to use it. I meant to show that conda info seems to be erring as well.
twistingstar
on 20 Jul 2016
Can you show the contents of your pkgs directory please? Your conda seems to be broken somehow, @kalefranz any ideas about this one?
mingwandroid
on 20 Jul 2016
The strange thing is I can still run conda update and install. I started noticing issues after I attempted to install R-essentials. That seemed to break my R installation instead.
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gsl-1.16-2.tar.bz2 r-assertthat-0.1-r3.3.1_2 scikit-learn-0.17.1-np110py27_0
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h5py-2.5.0-np19py27_3 r-base-3.2.2-0.tar.bz2 scipy-0.15.1-np19py27_0.tar.bz2
h5py-2.5.0-np19py27_3.tar.bz2 r-base-3.3.1-0 scipy-0.17.0-np110py27_0
hdf5-1.8.15.1-1 r-base-3.3.1-0.tar.bz2 scipy-0.17.0-np19py27_0
hdf5-1.8.15.1-1.tar.bz2 r-base64enc-0.1_3-r3.3.1_0 scipy-0.17.0-np19py27_0.tar.bz2
hdf5-1.8.15.1-2 r-base64enc-0.1_3-r3.3.1_0.tar.bz2 seaborn-0.7.0-py27_0
heapdict-1.0.0-py27_0 r-bh-1.60.0_2-r3.3.1_0 seaborn-0.7.0-py27_0.tar.bz2
husl-4.0.0-py27_0.tar.bz2 r-bh-1.60.0_2-r3.3.1_0.tar.bz2 setuptools-17.1.1-py27_0
icu-54.1-0 r-bitops-1.0_6-r3.3.1_2 setuptools-17.1.1-py27_0.tar.bz2
icu-54.1-0.tar.bz2 r-bitops-1.0_6-r3.3.1_2.tar.bz2 setuptools-20.3-py27_0
idna-2.0-py27_0 r-boot-1.3_17-r3.2.2_0a.tar.bz2 simplegeneric-0.8.1-py27_0
ipaddress-1.0.14-py27_0 r-boot-1.3_18-r3.3.1_0 singledispatch-3.4.0.3-py27_0
ipaddress-1.0.7-py27_0 r-boot-1.3_18-r3.3.1_0.tar.bz2 sip-4.16.5-py27_0
ipaddress-1.0.7-py27_0.tar.bz2 r-car-2.1_2-r3.3.1_0 sip-4.16.5-py27_0.tar.bz2
ipykernel-4.0.3-py27_0 r-car-2.1_2-r3.3.1_0.tar.bz2 sip-4.16.9-py27_0
ipykernel-4.0.3-py27_0.tar.bz2 r-caret-6.0_70-r3.3.1_0 six-1.10.0-py27_0
ipykernel-4.3.1-py27_0 r-caret-6.0_70-r3.3.1_0.tar.bz2 six-1.9.0-py27_0
ipython-3.2.0-py27_0 r-catools-1.17.1-1a six-1.9.0-py27_0.tar.bz2
ipython-3.2.0-py27_0.tar.bz2 r-catools-1.17.1-1a.tar.bz2 snowballstemmer-1.2.0-py27_0
ipython-4.1.2-py27_1 r-chron-2.3_47-r3.3.1_0 snowballstemmer-1.2.0-py27_0.tar.bz2
ipython-notebook-3.2.0-py27_0 r-chron-2.3_47-r3.3.1_0.tar.bz2 snowballstemmer-1.2.1-py27_0
ipython-notebook-3.2.0-py27_0.tar.bz2 r-class-7.3_14-r3.2.2_0a.tar.bz2 sockjs-tornado-1.0.1-py27_0
ipython-qtconsole-3.2.0-py27_0 r-class-7.3_14-r3.3.1_0 sphinx-1.3.1-py27_0
ipython-qtconsole-3.2.0-py27_0.tar.bz2 r-class-7.3_14-r3.3.1_0.tar.bz2 sphinx-1.3.1-py27_0.tar.bz2
ipython_genutils-0.1.0-py27_0 r-cluster-2.0.3-r3.2.2_0a.tar.bz2 sphinx-1.3.5-py27_0
ipywidgets-4.1.1-py27_0 r-cluster-2.0.4-r3.3.1_0 sphinx_rtd_theme-0.1.7-py27_0
itsdangerous-0.24-py27_0 r-cluster-2.0.4-r3.3.1_0.tar.bz2 sphinx_rtd_theme-0.1.7-py27_0.tar.bz2
jbig-2.1-0 r-codetools-0.2_14-r3.2.2_0a.tar.bz2 sphinx_rtd_theme-0.1.9-py27_0
jdcal-1.0-py27_0 r-codetools-0.2_14-r3.3.1_0 spyder-2.3.5.2-py27_0
jdcal-1.0-py27_0.tar.bz2 r-codetools-0.2_14-r3.3.1_0.tar.bz2 spyder-2.3.5.2-py27_0.tar.bz2
jdcal-1.2-py27_0 r-colorspace-1.2_6-r3.3.1_0 spyder-2.3.8-py27_1
jedi-0.8.1-py27_0 r-colorspace-1.2_6-r3.3.1_0.tar.bz2 spyder-app-2.3.5.2-py27_0
jedi-0.8.1-py27_0.tar.bz2 r-curl-0.9.7-r3.3.1_0 spyder-app-2.3.5.2-py27_0.tar.bz2
jedi-0.9.0-py27_0 r-curl-0.9.7-r3.3.1_0.tar.bz2 sqlalchemy-1.0.12-py27_0
jinja2-2.7.3-py27_1 r-data.table-1.9.6-r3.3.1_0 sqlalchemy-1.0.5-py27_0
jinja2-2.7.3-py27_1.tar.bz2 r-data.table-1.9.6-r3.3.1_0.tar.bz2 sqlalchemy-1.0.5-py27_0.tar.bz2
jinja2-2.8-py27_0 r-dbi-0.4_1-r3.3.1_0 sqlite-3.13.0-0
jpeg-8d-1 r-dbi-0.4_1-r3.3.1_0.tar.bz2 sqlite-3.13.0-0.tar.bz2
jsonschema-2.4.0-py27_0 r-dichromat-2.0_0-r3.3.1_2 sqlite-3.8.4.1-1
jupyter-1.0.0-py27_2 r-dichromat-2.0_0-r3.3.1_2.tar.bz2 sqlite-3.8.4.1-1.tar.bz2
jupyter_client-4.2.2-py27_0 r-digest-0.6.9-r3.3.1_0 sqlite-3.9.2-0
jupyter_console-4.1.1-py27_0 r-digest-0.6.9-r3.3.1_0.tar.bz2 ssl_match_hostname-3.4.0.2-py27_0
jupyter_core-4.1.0-py27_0 r-dplyr-0.4.3-r3.3.1_0 statsmodels-0.6.1-np110py27_0
launcher-1.0.0-3 r-dplyr-0.4.3-r3.3.1_0.tar.bz2 statsmodels-0.6.1-np19py27_0
launcher-1.0.0-3.tar.bz2 r-essentials-1.4-0 statsmodels-0.6.1-np19py27_0.tar.bz2
libdynd-0.6.5-0 r-essentials-1.4-0.tar.bz2 sympy-0.7.6-py27_0
libdynd-0.6.5-0.tar.bz2 r-evaluate-0.9-r3.3.1_0 sympy-0.7.6-py27_0.tar.bz2
libdynd-0.7.2-0 r-evaluate-0.9-r3.3.1_0.tar.bz2 sympy-1.0-py27_0
libgcc-4.8.5-1.tar.bz2 r-foreach-1.4.3-r3.3.1_0 terminado-0.5-py27_0
libpng-1.6.17-0 r-foreach-1.4.3-r3.3.1_0.tar.bz2 terminado-0.5-py27_0.tar.bz2
libsodium-0.4.5-0 r-foreign-0.8_66-r3.2.2_0a.tar.bz2 terminado-0.5-py27_1
libsodium-0.4.5-0.tar.bz2 r-foreign-0.8_66-r3.3.1_0 tk-8.5.18-0
libtiff-4.0.2-1 r-foreign-0.8_66-r3.3.1_0.tar.bz2 toolz-0.7.2-py27_0
libtiff-4.0.2-1.tar.bz2 r-formatr-1.4-r3.3.1_0 toolz-0.7.2-py27_0.tar.bz2
libtiff-4.0.6-1 r-formatr-1.4-r3.3.1_0.tar.bz2 toolz-0.7.4-py27_0
libtiff-4.0.6-2 r-ggplot2-2.1.0-r3.3.1_0 tornado-4.2-py27_0
libtiff-4.0.6-2.tar.bz2 r-ggplot2-2.1.0-r3.3.1_0.tar.bz2 tornado-4.2-py27_0.tar.bz2
libxml2-2.9.2-0 r-gistr-0.3.6-r3.3.1_0 tornado-4.3-py27_0
libxslt-1.1.28-2 r-gistr-0.3.6-r3.3.1_0.tar.bz2 traitlets-4.2.1-py27_0
llvmlite-0.5.0-py27_0 r-glmnet-2.0_5-r3.3.1_0 ujson-1.33-py27_0
llvmlite-0.5.0-py27_0.tar.bz2 r-glmnet-2.0_5-r3.3.1_0.tar.bz2 ujson-1.33-py27_0.tar.bz2
llvmlite-0.9.0-py27_0 r-gtable-0.2.0-r3.3.1_0 unicodecsv-0.14.1-py27_0
locket-0.2.0-py27_0 r-gtable-0.2.0-r3.3.1_0.tar.bz2 unicodecsv-0.9.4-py27_0
lxml-3.4.4-py27_0 r-hexbin-1.27.1-r3.3.1_0 unicodecsv-0.9.4-py27_0.tar.bz2
lxml-3.4.4-py27_0.tar.bz2 r-hexbin-1.27.1-r3.3.1_0.tar.bz2 urls.txt
lxml-3.6.0-py27_0 r-highr-0.6-r3.3.1_0 werkzeug-0.10.4-py27_0
markupsafe-0.23-py27_0 r-highr-0.6-r3.3.1_0.tar.bz2 werkzeug-0.10.4-py27_0.tar.bz2
matplotlib-1.4.3-np19py27_2 r-htmltools-0.3.5-r3.3.1_0 werkzeug-0.11.4-py27_0
matplotlib-1.4.3-np19py27_2.tar.bz2 r-htmltools-0.3.5-r3.3.1_0.tar.bz2 wheel-0.29.0-py27_0
matplotlib-1.4.3-np19py27_3 r-htmlwidgets-0.6-r3.3.1_0 xlrd-0.9.3-py27_0
matplotlib-1.4.3-np19py27_3.tar.bz2 r-htmlwidgets-0.6-r3.3.1_0.tar.bz2 xlrd-0.9.3-py27_0.tar.bz2
matplotlib-1.5.1-np110py27_0 r-httpuv-1.3.3-r3.3.1_0 xlrd-0.9.4-py27_0
mistune-0.5.1-py27_1 r-httpuv-1.3.3-r3.3.1_0.tar.bz2 xlsxwriter-0.7.3-py27_0
mistune-0.5.1-py27_1.tar.bz2 r-httr-1.2.0-r3.3.1_0 xlsxwriter-0.7.3-py27_0.tar.bz2
mistune-0.7.2-py27_1 r-httr-1.2.0-r3.3.1_0.tar.bz2 xlsxwriter-0.8.4-py27_0
mkl-11.3.1-0 r-irdisplay-0.3-r3.3.1_2 xlwings-0.3.5-py27_0
mkl-service-1.1.2-py27_0 r-irdisplay-0.3-r3.3.1_2.tar.bz2 xlwings-0.3.5-py27_0.tar.bz2
mock-1.0.1-py27_0 r-irkernel-0.6.1-r3.3.1_0 xlwings-0.7.0-py27_0
mock-1.0.1-py27_0.tar.bz2 r-irkernel-0.6.1-r3.3.1_0.tar.bz2 xlwt-1.0.0-py27_0
mpmath-0.19-py27_0 r-iterators-1.0.8-r3.3.1_0 xz-5.0.5-1
multipledispatch-0.4.7-py27_0 r-iterators-1.0.8-r3.3.1_0.tar.bz2 xz-5.2.2-0
multipledispatch-0.4.7-py27_0.tar.bz2 r-jsonlite-0.9.22-r3.3.1_0 xz-5.2.2-0.tar.bz2
multipledispatch-0.4.8-py27_0 r-jsonlite-0.9.22-r3.3.1_0.tar.bz2 yaml-0.1.6-0
nbconvert-4.1.0-py27_0 r-kernsmooth-2.23_15-r3.2.2_0a.tar.bz2 zeromq-4.0.5-0
nbformat-4.0.1-py27_0 r-kernsmooth-2.23_15-r3.3.1_0 zeromq-4.0.5-0.tar.bz2
ncurses-5.9-1.tar.bz2 r-kernsmooth-2.23_15-r3.3.1_0.tar.bz2 zeromq-4.1.3-0
networkx-1.11-py27_0 r-knitr-1.13-r3.3.1_0 zlib-1.2.8-0
twistingstar
on 20 Jul 2016
Any time conda updates packages it updates itself (unless you tell it not to). IMHO that's what caused conda to break itself, not anything to do with r-essentials.
mingwandroid
on 20 Jul 2016
In that case it is broken in a way I'm not sure how to work around. I attempted to return conda to version. 4.1.6 and reset the conda automatic update setting. I then uninstalled and r installed r to no effect,
However if I now attempt to call conda info it returns:
Current conda install:
platform : osx-64
conda version : 4.1.6
conda-env version : 2.5.2
conda-build version : 0+unknown
python version : 2.7.10.final.0
requests version : 2.7.0
root environment : /Users/marlie/anaconda (writable)
default environment : /Users/marlie/anaconda
envs directories : /Users/marlie/anaconda/envs
package cache : /Users/marlie/anaconda/pkgs
channel URLs : 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/marlie/.condarc
offline mode : False
is foreign system : False
twistingstar
on 20 Jul 2016
Looking through the errors and my revision log I noticed that an old version of pcre was added at some point in the process. Resetting pcre to 8.39 allows me to now launch r from the command line.
twistingstar
on 20 Jul 2016
I will pin the version number the next time I rebuild R for OS X.
mingwandroid
on 20 Jul 2016
Hi, same issue: R kernel not working in anaconda/jupyter.
Error:
[I 11:48:14.169 NotebookApp] Kernel started: d71a000d-1b10-40fb-a3ca-17b7ae39aae5
dyld: Library not loaded: @rpath/libicuuc.56.dylib
Referenced from: /Users/danofer/anaconda/lib/R/lib/libR.dylib
Reason: image not found
[I 11:48:17.172 NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING: ignoring environment value of R_HOME
dyld: Library not loaded: @rpath/libicuuc.56.dylib
Referenced from: /Users/danofer/anaconda/lib/R/lib/libR.dylib
Reason: image not found
conda info output:
Current conda install:
platform : osx-64
conda version : 4.2.13
conda is private : False
conda-env version : 4.2.13
conda-build version : 2.1.0
python version : 3.5.2.final.0
requests version : 2.12.4
root environment : /Users/danofer/anaconda (writable)
default environment : /Users/danofer/anaconda
envs directories : /Users/danofer/anaconda/envs
package cache : /Users/danofer/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/danofer/.condarc
offline mode : False
ddofer
on 11 Jan 2017
Please show the output from conda list --show-channel-urls
mingwandroid
on 11 Jan 2017
$ conda list --show-channel-urls
# packages in environment at /Users/danofer/anaconda:
#
_license 1.1 py35_1 defaults
_nb_ext_conf 0.3.0 py35_0 defaults
accelerate 2.3.0 np111py35_3 defaults
accelerate_cudalib 2.0 0 defaults
alabaster 0.7.9 py35_0 conda-forge
anaconda custom py35_0 defaults
anaconda-clean 1.1.0 py35_0 defaults
anaconda-client 1.5.1 py35_0 conda-forge
anaconda-navigator 1.3.2 py35_0 defaults
appnope 0.1.0 py35_0 defaults
appscript 1.0.1 py35_0 defaults
argcomplete 1.0.0 py35_1 defaults
astroid 1.4.8 py35_0 conda-forge
astropy 1.3 np111py35_0 defaults
babel 2.3.4 py35_0 conda-forge
backports 1.0 py35_0 defaults
backports.shutil_get_terminal_size 1.0.0 py35_1
conda-forge
beautifulsoup4 4.5.3 py35_0 defaults
biopython 1.68 np111py35_0 defaults
bitarray 0.8.1 py35_0 defaults
blas 1.1 openblas conda-forge
blaze 0.10.1 py35_0 defaults
bokeh 0.12.3 py35_0 defaults
boto 2.45.0 py35_0 defaults
bottleneck 1.2.0 np111py35_0 conda-forge
bz2file 0.98 py35_0 defaults
ca-certificates 2016.9.26 0 conda-forge
cairo 1.14.6 0 defaults
certifi 2016.9.26 py35_0 conda-forge
cffi 1.9.1 py35_0 defaults
chest 0.2.3 py35_0 defaults
click 6.6 py35_1 conda-forge
cloudpickle 0.2.2 py35_2 conda-forge
clyent 1.2.1 py35_0 conda-forge
colorama 0.3.7 py35_0 conda-forge
conda 4.2.13 py35_0 conda-forge
conda-build 2.1.0 py35_0 defaults
conda-env 2.6.0 0 conda-forge
conda-verify 2.0.0 py35_0 defaults
configobj 5.0.6 py35_0 defaults
contextlib2 0.5.4 py35_0 conda-forge
cryptography 1.7.1 py35_0 defaults
cudatoolkit 7.5 0 defaults
curl 7.49.1 2 conda-forge
cycler 0.10.0 py35_0 conda-forge
cymem 1.31.2 py35_0 defaults
cython 0.25.2 py35_0 conda-forge
cytoolz 0.8.2 py35_0 conda-forge
dask 0.13.0 py35_0 conda-forge
datashape 0.5.4 py35_0 defaults
decorator 4.0.10 py35_0 conda-forge
dill 0.2.5 py35_1 conda-forge
docutils 0.12 py35_0 conda-forge
dynd-python 0.7.2 py35_0 defaults
entrypoints 0.2.2 py35_0 conda-forge
et_xmlfile 1.0.1 py35_0 defaults
fastcache 1.0.2 py35_1 defaults
filelock 2.0.6 py35_0 conda-forge
flask 0.11.1 py35_0 conda-forge
flask-cors 3.0.2 py35_0 conda-forge
fontconfig 2.12.1 0 defaults
freetype 2.5.5 1 defaults
gensim 0.13.4 np111py35_0 defaults
get_terminal_size 1.0.0 py35_0 defaults
gettext 0.19.7 1 conda-forge
gevent 1.2.0 py35_0 defaults
glib 2.50.2 0 defaults
gmp 6.1.2 0 conda-forge
gmpy2 2.0.7 py35_1 conda-forge
greenlet 0.4.11 py35_0 defaults
gsl 2.2.1 1 conda-forge
h5py 2.6.0 np111py35_7 conda-forge
harfbuzz 0.9.39 1 defaults
hdf5 1.8.17 8 conda-forge
heapdict 1.0.0 py35_0 conda-forge
icu 54.1 0 defaults
idna 2.1 py35_0 conda-forge
imagesize 0.7.1 py35_0 conda-forge
ipykernel 4.5.2 py35_0 conda-forge
ipython 5.1.0 py35_1 conda-forge
ipython_genutils 0.1.0 py35_0 conda-forge
ipywidgets 5.2.2 py35_2 conda-forge
isort 4.2.5 py35_0 conda-forge
itsdangerous 0.24 py35_0 conda-forge
jbig 2.1 0 defaults
jdcal 1.3 py35_0 defaults
jedi 0.9.0 py35_0 conda-forge
jinja2 2.8 py35_1 conda-forge
jpeg 8d 2 defaults
jsonschema 2.5.1 py35_0 conda-forge
jupyter 1.0.0 py35_3 defaults
jupyter_client 4.4.0 py35_0 conda-forge
jupyter_console 5.0.0 py35_0 conda-forge
jupyter_core 4.2.1 py35_0 conda-forge
keras 1.0.7 py35_0 conda-forge
lazy-object-proxy 1.2.2 py35_0 conda-forge
libdynd 0.7.2 0 defaults
libffi 3.2.1 3 conda-forge
libgcc 4.8.5 1 defaults
libgfortran 3.0.0 0 conda-forge
libiconv 1.14 4 conda-forge
libpng 1.6.26 0 conda-forge
libsodium 1.0.10 0 conda-forge
libtiff 4.0.6 2 defaults
libxml2 2.9.4 0 defaults
libxslt 1.1.29 2 conda-forge
llvmlite 0.11.0 py35_0 defaults
locket 0.2.0 py35_1 conda-forge
lxml 3.7.1 py35_0 conda-forge
markupsafe 0.23 py35_1 conda-forge
matplotlib 1.5.3 np111py35_1 defaults
mccabe 0.5.3 py35_0 conda-forge
mistune 0.7.3 py35_0 conda-forge
mkl 11.3.3 0 defaults
mkl-service 1.1.2 py35_2 defaults
mock 2.0.0 py35_0 conda-forge
mpc 1.0.3 3 conda-forge
mpfr 3.1.5 0 conda-forge
mpmath 0.19 py35_1 conda-forge
multipledispatch 0.4.8 py35_0 conda-forge
murmurhash 0.26.4 py35_0 defaults
nb_anacondacloud 1.2.0 py35_0 conda-forge
nb_conda 2.0.0 py35_0 conda-forge
nb_conda_kernels 2.0.0 py35_0 conda-forge
nbconvert 4.2.0 py35_0 conda-forge
nbformat 4.2.0 py35_0 conda-forge
nbpresent 3.0.2 py35_1 conda-forge
ncurses 5.9 10 conda-forge
networkx 1.11 py35_0 conda-forge
nltk 3.2.1 py35_0 conda-forge
nose 1.3.7 py35_2 conda-forge
notebook 4.3.1 py35_0 conda-forge
numba 0.26.0 np111py35_0 defaults
numexpr 2.6.1 np111py35_1 conda-forge
numpy 1.11.3 py35_blas_openblas_200
[blas_openblas] conda-forge
odo 0.5.0 py35_1 defaults
openblas 0.2.19 0 conda-forge
openpyxl 2.4.0 py35_0 defaults
openssl 1.0.2h 3 conda-forge
pandas 0.19.2 np111py35_1 conda-forge
pango 1.40.3 0 defaults
partd 0.3.7 py35_0 conda-forge
path.py 8.2.1 py35_0 conda-forge
pathlib2 2.1.0 py35_0 conda-forge
patsy 0.4.1 py35_0 conda-forge
pbr 1.10.0 py35_0 conda-forge
pcre 8.39 1 defaults
pep8 1.7.0 py35_0 conda-forge
pexpect 4.2.1 py35_0 conda-forge
pickleshare 0.7.3 py35_0 conda-forge
pillow 3.2.0 py35_0 conda-forge
pip 9.0.1 py35_0 conda-forge
pixman 0.34.0 0 conda-forge
pkginfo 1.2.1 py35_0 conda-forge
plac 0.9.6 py35_0 defaults
ply 3.9 py35_0 conda-forge
preshed 0.46.4 py35_0 defaults
prompt_toolkit 1.0.9 py35_0 conda-forge
protobuf 3.0.0 py35_0 conda-forge
psutil 4.3.0 py35_0 conda-forge
ptyprocess 0.5.1 py35_0 conda-forge
py 1.4.31 py35_0 conda-forge
pyasn1 0.1.9 py35_0 conda-forge
pycosat 0.6.1 py35_0 conda-forge
pycparser 2.17 py35_0 conda-forge
pycrypto 2.6.1 py35_0 conda-forge
pycurl 7.43.0 py35_0 defaults
pyflakes 1.3.0 py35_0 conda-forge
pygments 2.1.3 py35_1 conda-forge
pylint 1.6.4 py35_0 conda-forge
pyopenssl 16.0.0 py35_0 conda-forge
pyparsing 2.1.10 py35_0 conda-forge
pyqt 5.6.0 py35_1 defaults
pytables 3.3.0 np111py35_0 conda-forge
pytest 3.0.5 py35_0 conda-forge
python 3.5.2 3 conda-forge
python-dateutil 2.6.0 py35_0 conda-forge
python.app 1.2 py35_4 defaults
pytz 2016.10 py35_0 conda-forge
pyyaml 3.11 py35_0 conda-forge
pyzmq 16.0.2 py35_0 conda-forge
qt 5.6.2 0 defaults
qtawesome 0.3.3 py35_0 conda-forge
qtconsole 4.2.1 py35_0 conda-forge
qtpy 1.1.1 py35_0 conda-forge
r-assertthat 0.1 r3.3.2_4 r
r-backports 1.0.4 r3.3.2_0 r
r-base 3.3.2 1 conda-forge
r-base64enc 0.1_3 r3.3.2_0 r
r-bh 1.62.0_1 r3.3.2_0 r
r-bitops 1.0_6 r3.3.2_2 r
r-boot 1.3_18 r3.3.2_0 r
r-broom 0.4.1 r3.3.2_0 r
r-car 2.1_4 r3.3.2_0 r
r-caret 6.0_73 r3.3.2_0 r
r-catools 1.17.1 r3.3.2_2 r
r-class 7.3_14 r3.3.2_0 r
r-cluster 2.0.5 r3.3.2_0 r
r-codetools 0.2_15 r3.3.2_0 r
r-colorspace 1.3_1 r3.3.2_0 r
r-crayon 1.3.2 r3.3.2_0 r
r-curl 2.3 r3.3.2_0 r
r-data.table 1.10.0 r3.3.2_0 r
r-dbi 0.5_1 r3.3.2_0 r
r-dichromat 2.0_0 r3.3.2_2 r
r-digest 0.6.10 r3.3.2_0 r
r-dplyr 0.5.0 r3.3.2_0 r
r-essentials 1.5.1 0 r
r-evaluate 0.10 r3.3.2_0 r
r-forcats 0.1.1 r3.3.2_0 r
r-foreach 1.4.3 r3.3.2_0 r
r-foreign 0.8_67 r3.3.2_0 r
r-formatr 1.4 r3.3.2_0 r
r-ggplot2 2.2.0 r3.3.2_0 r
r-gistr 0.3.6 r3.3.2_0 r
r-glmnet 2.0_5 r3.3.2_0 r
r-gtable 0.2.0 r3.3.2_0 r
r-haven 1.0.0 r3.3.2_0 r
r-hexbin 1.27.1 r3.3.2_0 r
r-highr 0.6 r3.3.2_0 r
r-hms 0.3 r3.3.2_0 r
r-htmltools 0.3.5 r3.3.2_0 r
r-htmlwidgets 0.8 r3.3.2_0 r
r-httpuv 1.3.3 r3.3.2_0 r
r-httr 1.2.1 r3.3.2_0 r
r-irdisplay 0.4.4 r3.3.2_0 r
r-irkernel 0.7.1 r3.3.2_0 r
r-iterators 1.0.8 r3.3.2_0 r
r-jsonlite 1.1 r3.3.2_0 r
r-kernsmooth 2.23_15 r3.3.2_0 r
r-knitr 1.15.1 r3.3.2_0 r
r-labeling 0.3 r3.3.2_2 r
r-lattice 0.20_34 r3.3.2_0 r
r-lazyeval 0.2.0 r3.3.2_0 r
r-lme4 1.1_12 r3.3.2_0 r
r-lubridate 1.6.0 r3.3.2_0 r
r-magrittr 1.5 r3.3.2_2 r
r-maps 3.1.1 r3.3.2_0 r
r-markdown 0.7.7 r3.3.2_2 r
r-mass 7.3_45 r3.3.2_0 r
r-matrix 1.2_7.1 r3.3.2_0 r
r-matrixmodels 0.4_1 r3.3.2_0 r
r-mgcv 1.8_16 r3.3.2_0 r
r-mime 0.5 r3.3.2_0 r
r-minqa 1.2.4 r3.3.2_2 r
r-mnormt 1.5_5 r3.3.2_0 r
r-modelmetrics 1.1.0 r3.3.2_0 r
r-modelr 0.1.0 r3.3.2_0 r
r-munsell 0.4.3 r3.3.2_0 r
r-nlme 3.1_128 r3.3.2_0 r
r-nloptr 1.0.4 r3.3.2_2 r
r-nnet 7.3_12 r3.3.2_0 r
r-openssl 0.9.5 r3.3.2_0 r
r-pbdzmq 0.2_4 r3.3.2_0 r
r-pbkrtest 0.4_6 r3.3.2_0 r
r-plyr 1.8.4 r3.3.2_0 r
r-pryr 0.1.2 r3.3.2_0 r
r-psych 1.6.9 r3.3.2_0 r
r-purrr 0.2.2 r3.3.2_0 r
r-quantmod 0.4_7 r3.3.2_0 r
r-quantreg 5.29 r3.3.2_0 r
r-r6 2.2.0 r3.3.2_0 r
r-randomforest 4.6_12 r3.3.2_0 r
r-rbokeh 0.5.0 r3.3.2_0 r
r-rcolorbrewer 1.1_2 r3.3.2_3 r
r-rcpp 0.12.8 r3.3.2_0 r
r-rcppeigen 0.3.2.9.0 r3.3.2_0 r
r-readr 1.0.0 r3.3.2_0 r
r-readxl 0.1.1 r3.3.2_0 r
r-recommended 3.3.2 r3.3.2_0 r
r-repr 0.10 r3.3.2_0 r
r-reshape2 1.4.2 r3.3.2_0 r
r-rmarkdown 1.2 r3.3.2_0 r
r-rpart 4.1_10 r3.3.2_0 r
r-rprojroot 1.1 r3.3.2_0 r
r-rvest 0.3.2 r3.3.2_0 r
r-scales 0.4.1 r3.3.2_0 r
r-selectr 0.3_0 r3.3.2_0 r
r-shiny 0.14.2 r3.3.2_0 r
r-sourcetools 0.1.5 r3.3.2_0 r
r-sparsem 1.74 r3.3.2_0 r
r-spatial 7.3_11 r3.3.2_0 r
r-stringi 1.1.2 r3.3.2_0 r
r-stringr 1.1.0 r3.3.2_0 r
r-survival 2.40_1 r3.3.2_0 r
r-tibble 1.2 r3.3.2_0 r
r-tidyr 0.6.0 r3.3.2_0 r
r-tidyverse 1.0.0 r3.3.2_0 r
r-ttr 0.23_1 r3.3.2_0 r
r-uuid 0.1_2 r3.3.2_0 r
r-xml2 1.0.0 r3.3.2_0 r
r-xtable 1.8_2 r3.3.2_0 r
r-xts 0.9_7 r3.3.2_2 r
r-yaml 2.1.14 r3.3.2_0 r
r-zoo 1.7_13 r3.3.2_0 r
readline 6.2 0 conda-forge
redis 3.2.0 0 defaults
redis-py 2.10.5 py35_0 conda-forge
requests 2.12.4 py35_0 conda-forge
rope 0.9.4 py35_1 defaults
ruamel_yaml 0.11.14 py35_0 defaults
scikit-image 0.12.3 np111py35_0 conda-forge
scikit-learn 0.18 np111py35_blas_openblas_203
[blas_openblas] conda-forge
scipy 0.18.1 np111py35_blas_openblas_201
[blas_openblas] conda-forge
seaborn 0.7.1 py35_0 conda-forge
semver 2.7.3 py35_0 defaults
setuptools 32.3.0 py35_0 conda-forge
simplegeneric 0.8.1 py35_0 conda-forge
singledispatch 3.4.0.3 py35_0 conda-forge
sip 4.18 py35_1 conda-forge
six 1.10.0 py35_1 conda-forge
smart_open 1.3.5 py35_0 conda-forge
snakeviz 0.4.1 py35_0 defaults
snowballstemmer 1.2.1 py35_0 conda-forge
sockjs-tornado 1.0.3 py35_0 defaults
spacy 0.101.0 py35_0 defaults
sphinx 1.5 py35_0 conda-forge
sputnik 0.9.3 py35_1 defaults
spyder 2.3.9 py35_1 conda-forge
sqlalchemy 1.1.4 py35_0 conda-forge
sqlite 3.13.0 1 conda-forge
statsmodels 0.6.1 np111py35_0 conda-forge
sympy 1.0 py35_0 conda-forge
tensorflow 0.11.0 py35_0 conda-forge
terminado 0.6 py35_0 conda-forge
theano 0.8.2 py35_0 conda-forge
thinc 5.0.8 py35_0 defaults
tk 8.5.19 1 conda-forge
toolz 0.8.2 py35_0 conda-forge
tornado 4.4.2 py35_0 conda-forge
traitlets 4.3.1 py35_0 conda-forge
ujson 1.35 py35_0 defaults
unicodecsv 0.14.1 py35_0 defaults
wcwidth 0.1.7 py35_0 conda-forge
werkzeug 0.11.10 py35_0 conda-forge
wheel 0.29.0 py35_0 conda-forge
widgetsnbextension 1.2.6 py35_3 conda-forge
wrapt 1.10.8 py35_0 conda-forge
xgboost 0.6a2 <pip>
xlrd 1.0.0 py35_0 defaults
xlsxwriter 0.9.6 py35_0 defaults
xlwings 0.10.1 py35_0 defaults
xlwt 1.1.2 py35_0 defaults
xz 5.2.2 0 conda-forge
yaml 0.1.6 0 conda-forge
zeromq 4.1.5 0 conda-forge
zlib 1.2.8 3 conda-forge
On Wed, Jan 11, 2017 at 12:53 PM, Ray Donnelly <[email protected]>
wrote:
> Please show the output from conda list --show-channel-urls
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/conda/conda/issues/3113#issuecomment-271838590>, or mute
> the thread
> <https://github.com/notifications/unsubscribe-auth/AE4hg3dtgK4L5tHsIL43uXZ2Wo1jOH1Iks5rRLSUgaJpZM4JQKaC>
> .
>
--
Dan Ofer - דן עופר
Publications http://scholar.google.co.il/citations?hl=en&user=uDx2ItYAAAAJ
Photography
http://picasaweb.google.com/ddofer
http://500px.com/DanOfer
ddofer
on 11 Jan 2017
You have installed r-base from conda-forge:
r-base 3.3.2 1 conda-forge
conda-forge and conda-defaults are not Binary Compatible.
I have no idea why conda-forge have released r-base as to the best of my knowledge conda-forge's R isn't ready @jakirkham any thoughts?
mingwandroid
on 11 Jan 2017
To remedy this you should remove conda-forge from your channels and update all of your packages.
mingwandroid
on 11 Jan 2017
How should this be done?
Clean install?
On Jan 11, 2017 4:50 PM, "Ray Donnelly" notifications@github.com wrote:
To remedy this you should remove conda-forge from your channels and
update all of your packages.—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
https://github.com/conda/conda/issues/3113#issuecomment-271887654, or mute
the thread
https://github.com/notifications/unsubscribe-auth/AE4hgz4m3SgE2-mftho5jSalq2sdQvNaks5rROwygaJpZM4JQKaC
.
ddofer
on 11 Jan 2017
That's probably the best approach yes. In future, I think conda will support per-env channels which would allow a small amount of happy co-existence.
mingwandroid
on 12 Jan 2017
Closing, mixing conda and conda-forge is out of scope.
mingwandroid
on 25 Feb 2017
As conda-forge grows in popularity it might be worth adding a warning to https://conda.io/docs/r-with-conda.html that conda-forge has to be removed from the channel list prior to installing.
pstjohn
on 4 Apr 2017
There are a few R packages in conda-forge and a community pretty interested in growing R support there. Maybe it would be worth requesting or PRing packages of interest to conda-forge if you are running into particular issues.
jakirkham
on 4 Apr 2017
My R experience is fairly minimal, but this issue pops up if you run
conda create -n my-r-env -c r r-essentials when conda-forge is listed in your channels.
Maybe the solution would be to add an r-essentials package to conda-forge? But it might be confusing if it doesn't install the same packages as the conda R channel's does.
pstjohn
on 4 Apr 2017
I think that will take a bit as that appears to be a massive metapackage, but yes I agree.
Maybe a more reasonable near term goal would be add the package(s) from that metapackage, which were having difficulties. So narrowing it down to the packages, which failed to load due to ABI issues for instance.
jakirkham
on 4 Apr 2017
I wasn't even at that stage of trying out packages to be honest, just googled 'conda R jupyter' and started following the instructions 😄 . After building the environment, the R cli fails with a dylib error.
It works when you remove conda-forge as a channel and re-build the environment.
pstjohn
on 4 Apr 2017
I am having a very similar issue when I try to run R from the command line:
$ R
dyld: Library not loaded: @rpath/libintl.9.dylib
Referenced from: /Users/christinebuckler/anaconda3/lib/R/lib/libR.dylib
Reason: image not found
Abort trap: 6
Originally I used $ brew install R
which allowed me to run R and Rscripts from the command line.
This week I installed a kernel for jupyter notebooks with $ conda install -c r r-essentials
and now I get the error above.
Is there a way to fix this so that I can use both from CMI and jupter notebook?
christinebuckler
on 17 Oct 2017
I have test releases of r 3.4.2 available on the rdonnellyr channel. Please try these if you have time.
mingwandroid
on 17 Oct 2017
@mingwandroid Do those releases address the issue I'm seeing?
christinebuckler
on 17 Oct 2017
For the reference above asking how to remove a channel, either edit your ~/.condarc file, or
conda config --remove channels conda-forge
kalefranz
on 17 Oct 2017
@kalefranz I tried this and got:
$ conda config --remove channels conda-forge
CondaKeyError: 'channels': 'conda-forge' is not in the 'channels' key of the config file
christinebuckler
on 17 Oct 2017
@christinebuckler I do not think you have added conda-forge, you are suffering a different problem here. But yes, the packages on rdonnellyr should get you going again, they fix that problem (among others).
mingwandroid
on 17 Oct 2017
@mingwandroid I am not familiar with channels. Where/How do I find this? And how do I install the package from there?
christinebuckler
on 17 Oct 2017
No problem.
When you entered conda install -c r r-essentials
.. here, -c r identified to get r-essentials from the r channel, so to change this to rdonnellyr you can do instead conda install -c rdonnellyr r-essentials.
mingwandroid
on 17 Oct 2017
@mingwandroid I tried installing as above and now I am getting a slightly different error when trying to run R from the command line:
$ R
dyld: Library not loaded: @rpath/libiconv.2.dylib
Referenced from: /Users/christinebuckler/anaconda3/lib/R/lib/libR.dylib
Reason: Incompatible library version: libR.dylib requires version 9.0.0 or later, but libiconv.2.dylib provides version 8.0.0
Abort trap: 6
christinebuckler
on 17 Oct 2017
OK, please do:
conda update conda
then:
conda update -c rdonnellyr --all
mingwandroid
on 17 Oct 2017
@mingwandroid Excellent! Everything is working now! Thank you so much!
christinebuckler
on 18 Oct 2017
Great, thanks for the feedback.
mingwandroid
on 18 Oct 2017
@mingwandroid after
conda update -c rdonnellyr --all
New error comes out:
‘/Users/***/anaconda3/lib/R/library/digest/libs/digest.so’：:
dlopen(/Users/***/anaconda3/lib/R/library/digest/libs/digest.so, 6): Library not loaded: @rpath/R/lib/libR.dylib
Referenced from: /Users/***/anaconda3/lib/R/library/digest/libs/digest.so
Reason: Incompatible library version: digest.so requires version 3.4.0 or later, but libR.dylib provides version 3.3.0
conda info:
platform : osx-64
conda version : 4.3.27
conda is private : False
conda-env version : 4.3.27
conda-build version : 3.0.19
python version : 3.6.2.final.0
requests version : 2.14.2
root environment : /Users/***/anaconda3 (writable)
default environment : /Users/***/anaconda3
envs directories : /Users/***/anaconda3/envs
/Users/***/.conda/envs
package cache : /Users/***/anaconda3/pkgs
/Users/***/.conda/pkgs
channel URLs : https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/osx-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/osx-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r/noarch
https://repo.continuum.io/pkgs/main/osx-64
https://repo.continuum.io/pkgs/main/noarch
https://repo.continuum.io/pkgs/free/osx-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/osx-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/osx-64
https://repo.continuum.io/pkgs/pro/noarch
config file : /Users/***/.condarc
netrc file : None
offline mode : False
user-agent : conda/4.3.27 requests/2.14.2 CPython/3.6.2 Darwin/17.0.0 OSX/10.13
UID:GID : 501:20
packages in environment at /Users/*/anaconda3:
#
_ipyw_jlab_nb_ext_conf 0.1.0 py36h2fc01ae_0 defaults
_license 1.1 py36_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
alabaster 0.7.10 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
anaconda custom py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
anaconda-client 1.6.3 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
anaconda-navigator 1.6.4 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
anaconda-project 0.6.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
appnope 0.1.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
appscript 1.0.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
asn1crypto 0.22.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
astroid 1.5.3 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
astropy 2.0.2 py36h4654939_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
babel 2.5.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
backports 1.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
backports.shutil_get_terminal_size 1.0.0 py36hd7a2ee4_2 defaults
beautifulsoup4 4.6.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bitarray 0.8.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bkcharts 0.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
blaze 0.10.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bleach 1.5.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bokeh 0.12.7 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
boto 2.48.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bottleneck 1.2.1 np113py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ca-certificates 2017.08.26 ha1e5d58_0 defaults
certifi 2016.2.28 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cffi 1.10.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
chardet 3.0.4 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
click 6.7 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cloudpickle 0.4.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
clyent 1.2.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
colorama 0.3.9 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
conda 4.3.27 py36hb556a21_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
conda-build 3.0.19 py36h997aa4c_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
conda-env 2.6.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
conda-verify 2.0.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
contextlib2 0.5.5 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cryptography 1.8.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
curl 7.52.1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cycler 0.10.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cython 0.26 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cytoolz 0.8.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
dask 0.15.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
dask-core 0.15.3 py36hc0be6b7_0 defaults
datashape 0.5.4 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
dbus 1.10.22 h50d9ad6_0 defaults
decorator 4.1.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
distributed 1.18.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
docutils 0.14 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
entrypoints 0.2.3 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
et_xmlfile 1.0.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
expat 2.1.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
fastcache 1.0.2 py36_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
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seaborn 0.8 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
setuptools 36.4.0 py36_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
simplegeneric 0.8.1 py36_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
singledispatch 3.4.0.3 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sip 4.18 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
six 1.10.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
snowballstemmer 1.2.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sortedcollections 0.5.3 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sortedcontainers 1.5.7 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sphinx 1.6.3 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sphinxcontrib 1.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sphinxcontrib-websupport 1.0.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
spyder 3.2.3 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sqlalchemy 1.1.13 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sqlite 3.13.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
statsmodels 0.8.0 np113py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sympy 1.1.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tblib 1.3.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
terminado 0.6 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
testpath 0.3.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tk 8.5.18 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
toolz 0.8.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tornado 4.5.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
traitlets 4.3.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
typing 3.6.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
unicodecsv 0.14.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
unixodbc 2.3.4 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
urllib3 1.21.1 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
wcwidth 0.1.7 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
webencodings 0.5.1 py36h3b9701d_1 defaults
werkzeug 0.12.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
wheel 0.29.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
widgetsnbextension 3.0.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
wrapt 1.10.11 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xlrd 1.1.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xlsxwriter 0.9.8 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xlwings 0.11.4 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xlwt 1.3.0 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xz 5.2.3 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
yaml 0.1.6 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
yapf 0.19.0
zeromq 4.1.3 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zict 0.1.2 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zlib 1.2.11 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
arthurire
on 20 Oct 2017
You are not using our servers here: https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
.. the free channel should not be getting used now (except for some legacy packages and nomkl ones).
If you switch to our official repository and update all this should fix it. The new channel is called main.
mingwandroid
on 20 Oct 2017
@mingwandroid In fact, this is the only mirror available in China now. Download speed from official repo is only ~5KB/s.
Maybe I should write to those who are running this mirror.
arthurire
on 20 Oct 2017
Maybe I cannot offer support regarding unofficial mirrors.
mingwandroid
on 20 Oct 2017
@mingwandroid I totally understand this. Thank you for your help and I'll try my best to switch to the official repo
arthurire
on 20 Oct 2017
@mingwandroid I'm not sure why but I am having the same issue again and the previous fix doesn't resolve it this time.
$ R
dyld: Library not loaded: @loader_path/../../libreadline.6.2.dylib
Referenced from: /Users/.../anaconda3/lib/R/lib/libR.dylib
Reason: image not found
Abort trap: 6
christinebuckler
on 23 Oct 2017
Is this issue fixed ? I still have this issue on conda 4.3.31
zjffdu
on 20 Dec 2017
@zjffdu This issue is fixed yes.
Please open a new issue here instead of adding to this one. In it please include the output from conda info and conda list --show-channel-urls.
mingwandroid
on 20 Dec 2017
I ran conda install -c r r-essentials
the issue is the same :
dyld: Library not loaded: @rpath/libintl.9.dylib
Referenced from: /Users/yuandet/miniconda3/lib/R/lib/libR.dylib
Reason: image not found
Trace/BPT trap: 5
after running conda update condo and conda update -c rdonnellyr --all
The issue is still not addressed:
dyld: Library not loaded: @rpath/libintl.9.dylib
Referenced from: /Users/yuandet/miniconda3/lib/R/lib/libR.dylib
Reason: image not found
Trace/BPT trap: 5
How to fix this issue? Before I ran conda install R, I simply deleted R in miniconda3/lib using rm -rf.
Yuande
on 27 Apr 2018
after running conda update condo and conda update -c rdonnellyr --all
rdonnellyr is where I sometimes put previews of forthcoming R releases. You should not use it unless you want a preview and have been told to do so by me, otherwise who knows how old the stuff there is or how compatible it is with anything else.
How to fix this issue? Before I ran conda install R, I simply deleted R in miniconda3/lib using rm -rf.
Why on earth did you do that? You cannot just delete random parts of an Anaconda Distribution installation and expect things to work.
I recommend you remove everything and reinstall from scratch. If you still have trouble please open a new issue.
mingwandroid
on 27 Apr 2018
Having the exact same issue. Everything was working fine till I did conda install. Now I can't use R at all.
jen0liu
on 13 Jul 2019
I answered your question on another issue.
mingwandroid
on 13 Jul 2019
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Most helpful comment
Looking through the errors and my revision log I noticed that an old version of pcre was added at some point in the process. Resetting pcre to 8.39 allows me to now launch r from the command line.