mingwandroid
commented
8 years ago please show the output from conda list --show-channel-urls
Closed AlloriMD closed 8 years ago
mingwandroid
commented
8 years ago please show the output from conda list --show-channel-urls
mingwandroid
commented
8 years ago Can you try the following and let me know if it works please?
conda install -c defaults zeromq
chdoig
commented
8 years ago Hi, @mingwandroid, if I understand currently, it should also be fixed now by just running the standard:
conda install -c r r-essentialsFrom the "I haven't installed anything perspective" yes conda install -c r r-essentials should work fine, but since I did some package removal and this is a rare occurrence, I'm not entirely sure how conda will react, so from the "I'm already in this broken state with zeromq installed from the wrong channel" state I'm hedging my bets by recommending forcing the installation of the package from the correct channel. I've tested that and it worked.
Since I've removed the old, broken package from my computer and also from the r channel, it's too late for me to test other strategies to fix things, mcg1969 or @kalefranz may know whether e.g. conda update zeromq would also fix things in this case!
AlloriMD
commented
8 years ago Okay, I have tested a few things:
conda install -c r r-essentials did not fix t he problem; nor did conda update r-essentials.conda install -c defaults zeromq did fix the problem -- I could successfully create a new Jupyter R notebook and execute the commands.Anaconda3-4.1.1-MacOSX-x86_64.pkg), updated via conda update conda and conda update anaconda, and then installed r-essentials via conda install -c r r-essentials. Now, running Jupyter notebooks, I can successfully create a new R notebook and execute commands.In summary, for my prior install, conda install -c defaults zeromq seemed to fix the problem. Additionally, a fresh install of Anaconda and the r-essentials packages seems to work well now.
So, could you please summarize what the problem was? Is it likely to recur with future updates?
mingwandroid
commented
8 years ago Thanks, that's really useful feedback.
My understand can be summarized as:
About a year ago, before I worked on the Anaconda Distribution, my predecessor added zeromq packages to the R channel. The old behavior of the conda solver (pre 4.0) meant that it didn't matter that those old zeromq packages were present because package versions were compared globally and the newer ones in defaults got selected.
Since conda 4.0 we have channel priorities which means that the old zeromq packages were found and given a higher priority when you use -c r (the rationale being that build numbers of packages from different channels cannot meaningfully be compared).
Due to this change, I need to be more vigilant that the R channel doesn't contain old software that doesn't belong there.
I'm happy that the issue will not reoccur but in general the maintainers of popular channels (including defaults!) need to be mindful of compatibility.
ijstokes
commented
8 years ago Root env kernel crashes, while (clean-room) rlatest env works fine. Hope that helps identify the differences.
What I notice (just a selection of the potentially interesting bits, where < is root, > is rlatest):
< anaconda-nb-extensions=0.1.4=py27_0
< anaconda-notebook=4.0=0
< gevent=1.1.1=py27_0
< ipykernel=4.3.1=py27_0
< ipyparallel=4.1.0=py27_0
< ipython-notebook=4.0.4=py27_0
< ipython-qtconsole=4.0.1=py27_0
< ipython=4.2.0=py27_1
---
> ipykernel=4.4.1=py27_0
> ipython=5.1.0=py27_0
105,106c22
< ipywidgets=4.1.1=py27_0
---
> ipywidgets=5.2.2=py27_0
115,119c29,30
< jupyter_console=4.1.1=py27_0
< jupyter_core=4.1.0=py27_0
---
> jupyter_console=5.0.0=py27_0
> jupyter_core=4.1.1=py27_0
< nb_anaconda_theme=0.1.1=py27_0
< nb_anacondacloud=1.1.0=py27_0
< nb_conda=1.1.0=py27_0
< nb_conda_kernels=1.0.3=py27_0
< nb_config_manager=0.1.2=py27_0
---
> nb_anacondacloud=1.2.0=py27_0
> nb_conda=2.0.0=py27_0
> nb_conda_kernels=2.0.0=py27_0
145c41
< nbformat=4.0.1=py27_0
---
> nbformat=4.1.0=py27_0
147,169c43,45
< nbsetuptools=0.1.5=py27_0
< notebook=4.2.1=py27_0
---
> notebook=4.2.2=py27_0
207,209c61,62
< pyzmq=15.2.0=py27_1
---
> pyzmq=15.4.0=py27_0
290d139
< r-rzmq=0.7.7=r3.3.1_2
308,320c157,158
< redis-py=2.10.5=py27_0
< redis=3.2.0=0
< requests=2.10.0=py27_0
---
> requests=2.11.1=py27_0
338,344c167,169
< tornado=4.3=py27_1
< traitlets=4.2.1=py27_0
< twisted=15.4.0=py27_0
< werkzeug=0.11.10=py27_0
---
> tornado=4.4.1=py27_0
> traitlets=4.2.2=py27_0
> widgetsnbextension=1.2.6=py27_0
352,354c174,175
< zeromq=4.0.5=0
< zlib=1.2.8=3
---
> zeromq=4.1.3=0
> zlib=1.2.8=1So figuring I had nothing to loose, I tried an update by doing:
$ conda update zeromq zlib tornado traitlets requests pyzmq notebook nbformat \
nb_conda_kernels nb_conda nb_anacondacloud jupyter \
jupyter_console ipywidgets ipython ipykernelAnd that left me with:
But still no luck with R kernels:
[W 12:42:39.891 NotebookApp] Timeout waiting for kernel_info reply from 879d2e3a-229e-4cb2-adee-b3b90997a4dc
[I 12:42:41.496 NotebookApp] KernelRestarter: restarting kernel (4/5)
WARNING:root:kernel 879d2e3a-229e-4cb2-adee-b3b90997a4dc restarted
dyld: Library not loaded: @rpath/libpcre.1.dylib
Referenced from: /Users/ijstokes/anaconda/lib/R/lib/libR.dylib
Reason: image not found
[W 12:42:43.985 NotebookApp] Replacing stale connection: 0caac471-b8b7-4544-90ed-481f18e29b70:610259020E7A4A87871908AF34F21BD5
[W 12:42:44.505 NotebookApp] KernelRestarter: restart failed
[W 12:42:44.505 NotebookApp] Kernel 879d2e3a-229e-4cb2-adee-b3b90997a4dc died, removing from map.
ERROR:root:kernel 879d2e3a-229e-4cb2-adee-b3b90997a4dc restarted failed!
[W 12:42:44.606 NotebookApp] Kernel deleted before session
aakhmetz
commented
8 years ago just checking, did you write the PATH to your new R environment in the bash profile?
robmarkcole
commented
8 years ago I am experiencing the crashing kernel, log below
[I 16:19:15.258 NotebookApp] Kernel started: 31882017-86c0-4f54-aba5-76cd8b7fa6f7
[1] "Got unhandled msg_type:" "comm_open"
Error in unlockBinding("base_display", displayenv) :
no binding for "base_display"
Calls: <Anonymous> ... <Anonymous> -> handle_shell -> <Anonymous> -> unlockBinding
Execution halted
[I 16:19:36.257 NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING:root:kernel 31882017-86c0-4f54-aba5-76cd8b7fa6f7 restartedPlease show conda list. Did you update r-irkernel?
robmarkcole
commented
8 years ago Hi yes irkernel is up to date
r-irkernel 0.7 r3.3.1_0 r
Last login: Thu Oct 6 16:28:39 on ttys006
Robins-MacBook-Air:~ robincole$ conda list
# packages in environment at /Users/robincole/anaconda3:
#
_nb_ext_conf 0.2.0 py35_0
alabaster 0.7.8 py35_0
anaconda 4.1.1 np111py35_0
anaconda-client 1.4.0 py35_0
anaconda-navigator 1.2.1 py35_0
appnope 0.1.0 py35_0
appscript 1.0.1 py35_0
argcomplete 1.0.0 py35_1
astropy 1.2.1 np111py35_0
babel 2.3.3 py35_0
backports 1.0 py35_0
beautifulsoup4 4.4.1 py35_0
bitarray 0.8.1 py35_0
blaze 0.10.1 py35_0
bokeh 0.12.0 py35_0
boto 2.40.0 py35_0
boto3 1.3.1 py35_0
botocore 1.4.52 py35_0
bottleneck 1.1.0 np111py35_0
cffi 1.6.0 py35_0
chest 0.2.3 py35_0
click 6.6 py35_0
clize 3.0.1 <pip>
cloudpickle 0.2.1 py35_0
clyent 1.2.2 py35_0
colorama 0.3.7 py35_0
conda 4.2.9 py35_0
conda-build 1.21.3 py35_0
conda-env 2.6.0 0
configobj 5.0.6 py35_0
contextlib2 0.5.3 py35_0
cryptography 1.4 py35_0
curl 7.49.0 0
cycler 0.10.0 py35_0
cython 0.24 py35_0
cytoolz 0.8.0 py35_0
dask 0.10.0 py35_0
datashape 0.5.2 py35_0
decorator 4.0.10 py35_0
dicompyler-core 0.5.2 <pip>
dill 0.2.5 py35_0
docutils 0.12 py35_2
dynd-python 0.7.2 py35_0
entrypoints 0.2.2 py35_0
et_xmlfile 1.0.1 py35_0
fastcache 1.0.2 py35_1
flask 0.11.1 py35_0
flask-cors 2.1.2 py35_0
freetype 2.5.5 1
get_terminal_size 1.0.0 py35_0
gevent 1.1.1 py35_0
Ghost.py 0.2.3 <pip>
glue-vispy-viewers 0.4 py35_0 conda-forge
glueviz 0.8.2 py35_1
greenlet 0.4.10 py35_0
gsl 1.16 2 r
h5py 2.6.0 np111py35_1
hdf5 1.8.16 0
heapdict 1.0.0 py35_1
icu 54.1 0
idna 2.1 py35_0
imageio 1.5 <pip>
imagesize 0.7.1 py35_0
ipykernel 4.3.1 py35_0
ipython 4.2.0 py35_1
ipython_genutils 0.1.0 py35_0
ipywidgets 4.1.1 py35_0
itsdangerous 0.24 py35_0
jbig 2.1 0
jdcal 1.2 py35_1
jedi 0.9.0 py35_1
jinja2 2.8 py35_1
jmespath 0.9.0 py35_0
jpeg 8d 1
jsonschema 2.5.1 py35_0
jupyter 1.0.0 py35_3
jupyter_client 4.3.0 py35_0
jupyter_console 4.1.1 py35_0
jupyter_core 4.1.0 py35_0
libdynd 0.7.2 0
libgcc 4.8.5 1 r
libpng 1.6.22 0
libtiff 4.0.6 2
libxml2 2.9.2 0
libxslt 1.1.28 2
llvmlite 0.11.0 py35_0
locket 0.2.0 py35_1
lxml 3.6.0 py35_0
markupsafe 0.23 py35_2
matplotlib 1.5.1 np111py35_0
mistune 0.7.2 py35_1
mkl 11.3.3 0
mkl-service 1.1.2 py35_2
mpmath 0.19 py35_1
multipledispatch 0.4.8 py35_0
nb_anacondacloud 1.1.0 py35_0
nb_conda 1.1.0 py35_0
nb_conda_kernels 1.0.3 py35_0
nbbrowserpdf 0.2.1 <pip>
nbconvert 4.2.0 py35_0
nbformat 4.0.1 py35_0
nbpresent 3.0.2 py35_0
ncurses 5.9 8 r
networkx 1.11 py35_0
nltk 3.2.1 py35_0
nose 1.3.7 py35_1
notebook 4.2.1 py35_0
numba 0.26.0 np111py35_0
numexpr 2.6.0 np111py35_0
numpy 1.11.1 py35_0
odo 0.5.0 py35_1
openpyxl 2.3.2 py35_0
openssl 1.0.2h 1
pandas 0.18.1 np111py35_0
pandoc 1.0.0b2 <pip>
partd 0.3.4 py35_0
path.py 8.2.1 py35_0
pathlib2 2.1.0 py35_0
patsy 0.4.1 py35_0
pcre 8.39 0
pep8 1.7.0 py35_0
pexpect 4.0.1 py35_0
pickleshare 0.7.2 py35_0
pillow 3.2.0 py35_1
pip 8.1.2 py35_0
plotly 1.12.9 <pip>
ply 3.8 py35_0
psutil 4.3.0 py35_0
ptyprocess 0.5.1 py35_0
py 1.4.31 py35_0
pyasn1 0.1.9 py35_0
pycosat 0.6.1 py35_1
pycparser 2.14 py35_1
pycrypto 2.6.1 py35_4
pycurl 7.43.0 py35_0
pydicom 0.9.9 <pip>
pyflakes 1.2.3 py35_0
pygments 2.1.3 py35_0
pyopengl 3.1.0 py35_0 conda-forge
pyopenssl 0.16.0 py35_0
pyparsing 2.1.4 py35_0
PyPDF2 1.26.0 <pip>
pyqt 4.11.4 py35_3
pytables 3.2.2 np111py35_4
pytest 2.9.2 py35_0
python 3.5.2 0
python-dateutil 2.5.3 py35_0
python-gantt 0.6.0 <pip>
python.app 1.2 py35_4
pytz 2016.4 py35_0
pytz 2016.6.1 <pip>
pyyaml 3.11 py35_4
pyzmq 15.2.0 py35_1
qt 4.8.7 3
qtconsole 4.2.1 py35_0
qtpy 1.0.2 py35_0
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 1a 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-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 1.4.2 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_0 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-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 r3.3.1_2 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 2
redis 3.2.0 0
redis-py 2.10.5 py35_0
requests 2.10.0 py35_0
requests 2.11.1 <pip>
rope 0.9.4 py35_1
ruamel_yaml 0.11.14 py35_0
scikit-image 0.12.3 np111py35_1
scikit-learn 0.17.1 np111py35_2
scipy 0.17.1 np111py35_1
seaborn 0.7.1 py35_0
setuptools 23.0.0 py35_0
sigtools 2.0.1 <pip>
simplegeneric 0.8.1 py35_1
singledispatch 3.4.0.3 py35_0
sip 4.16.9 py35_0
six 1.10.0 py35_0
snowballstemmer 1.2.1 py35_0
sockjs-tornado 1.0.3 py35_0
sphinx 1.4.1 py35_0
sphinx_rtd_theme 0.1.9 py35_0
spyder 2.3.9 py35_0
sqlalchemy 1.0.13 py35_0
sqlite 3.13.0 0
statsmodels 0.6.1 np111py35_1
svgwrite 1.1.8 <pip>
sympy 1.0 py35_0
terminado 0.6 py35_0
tk 8.5.18 0
toolz 0.8.0 py35_0
tornado 4.3 py35_1
traitlets 4.2.1 py35_0
unicodecsv 0.14.1 py35_0
watermark 1.3.3 <pip>
werkzeug 0.11.10 py35_0
wheel 0.29.0 py35_0
xlrd 1.0.0 py35_0
xlsxwriter 0.9.2 py35_0
xlwings 0.7.2 py35_0
xlwt 1.1.2 py35_0
xz 5.2.2 0
yaml 0.1.6 0
zeromq 4.1.3 0
zlib 1.2.8 3
Robins-MacBook-Air:~ robincole$ 
zenkavi
commented
8 years ago I'm having the same problem as @robmarkcole as well. Same error msg, same r-irkernel version
mingwandroid
commented
8 years ago @ijstokes You need to update your pcre. conda update pcre should see you right. I will pin it for the next rebuild of r-base.
ijstokes
commented
8 years ago @mingwandroid can you clarify: is "pinning" something different from a precise Conda package dependency specification? Right now I see pcre specified in the deps list for r-base but without a version number:
https://anaconda.org/r/r-base/files?sort=time&sort_order=desc
(clicking on the (i) icon). Are you suggesting that a version number needs to be added? Or something else?
mingwandroid
commented
8 years ago Yes, but it doesn't have to be so precise.
It is listed without any version pinning and is therefore happy to use any old version, including the broken one that you have in your environment.
The pinning is in fact already applied to the recipe:
https://github.com/conda/conda-recipes/blob/master/r-base/meta.yaml#L60
.. I do not plan to rebuild this until I next roll out an update to our R infrastructure since the last 3 bit-part updates to R (profiling then memory profiling and finally IRKernel 0.7) should all have been quick and safe, but they've turned out to be anything but.
The workaround is to use conda update pcre.
themerius
commented
8 years ago Yesterday I've installed the R kernel with conda create -n R-Env -c r r-essentials and also here the kernel dies.
The kernel dies with this errors in my case:
[I 09:38:50.535 NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING:root:kernel 308f3095-94db-44f6-97fa-ccdf42cf8b68 restarted
Error in unlockBinding("base_display", displayenv) :
no binding for "base_display"
Calls: <Anonymous> ... <Anonymous> -> handle_shell -> <Anonymous> -> unlockBinding
Execution haltedAlso I've tried to do conda update pcre, but unfortunately it is already the newest version.
robmarkcole
commented
8 years ago After installing pcre and launching a notebook with R, I get the following..
mingwandroid
commented
8 years ago @robmarkcole this is a separate issue (the original bug report was about OS X), you should really have opened another issue, though I will admit that you are not the first person to take this issue off in a tangential direction :-)
Assuming 64-bit Windows running 64-bit conda, can you please look in C:\Windows\System32 (or really %SYSTEMROOT%\System32) and see if you have a zlib1.dll in there? Many programs do this as a way of solving 'DLL hell', which works great for that piece software but not so great for any software that tries to co-exist harmoniously on the system (like Anaconda/Minconda).
Failing that, can you check your PATH and ensure that, if there any entries in it before %CONDA_PREFIX%\Library\mingw-w64\bin none of them contain a zlib1.dll?
Finally, conda list --show-channel-urls please!
robmarkcole
commented
8 years ago Hi @minwandroid, sorry I didn't appreciate it was a separate issue. I am running windows at work and mac on my research days :-)
zlib.dll is present.
PATH=C:\Windows\system32;
C:\Windows;
C:\Windows\System32\Wbem;
C:\Windows\System32\WindowsPowerShell\v1.0\;
C:\Program Files\Gemalto\GAC;
C:\Program Files\Gemalto\Classic Client\BIN;
C:\Program Files\Gemalto\GAC\;
C:\Program Files\MATLAB\R2014b\bin;
C:\Program Files\Windows Kits\8.1\Windows Performance Toolkit\;
C:\Program Files\Microsoft SQL Server\110\Tools\Binn\;
C:\Program Files\Microsoft SDKs\TypeScript\1.0\;
C:\Program Files\Microsoft SQL Server\120\Tools\Binn\;
C:\Program Files\Novell\ZENworks\bin;
C:\Users\...\AppData\Local\Continuum\Anaconda3;
C:\Users\...\AppData\Local\Continuum\Anaconda3\Scripts;C:\User
s\...\AppData\Local\Continuum\Anaconda3\Library\bin;
C:\Users\...\AppData\Local\Pandoc\;
C:\Users\..\AppData\Local\Programs\MiKTeX 2.9\miktex\bin\conda list --show-channel-urls (longer than command prompt can show..!)
curl 7.49.0 vc14_0 [vc14] defaults
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odo 0.5.0 py35_1 defaults
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openssl 1.0.2j vc14_0 [vc14] defaults
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pathlib2 2.1.0 py35_0 defaults
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pcre 8.39 0 defaults
pep8 1.7.0 py35_0 defaults
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pip 8.1.2 <pip>
pip 8.1.2 py35_0 defaults
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ply 3.9 py35_0 defaults
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pyqt 5.6.0 py35_0 defaults
pyreadline 2.1 py35_0 defaults
pytables 3.2.2 np111py35_4 defaults
pytest 2.9.2 py35_0 defaults
python 3.5.2 0 defaults
python-dateutil 2.5.3 py35_0 defaults
pytz 2016.6.1 py35_0 defaults
pywin32 220 py35_1 defaults
pyyaml 3.12 py35_0 defaults
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qt 5.6.0 vc14_0 [vc14] defaults
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qtconsole 4.2.1 py35_2 defaults
qtpy 1.1.2 py35_0 defaults
r 3.3.0 r3.3.0_1 r
r-assertthat 0.1 r3.3.0_2 r
r-base 3.3.0 0 r
r-base64enc 0.1_3 r3.3.0_0 r
r-bh 1.60.0_2 r3.3.0_0 r
r-bitops 1.0_6 r3.3.0_2 r
r-boot 1.3_18 r3.3.0_0 r
r-car 2.1_2 r3.3.0_0 r
r-caret 6.0_68 r3.3.0_0 r
r-catools 1.17.1 r3.3.0_2 r
r-chron 2.3_47 r3.3.0_0 r
r-class 7.3_14 r3.3.0_0 r
r-cluster 2.0.4 r3.3.0_0 r
r-codetools 0.2_14 r3.3.0_0 r
r-colorspace 1.2_6 r3.3.0_0 r
r-curl 0.9.7 r3.3.0_0 r
r-data.table 1.9.6 r3.3.0_0 r
r-dbi 0.4_1 r3.3.0_0 r
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r-htmltools 0.3.5 r3.3.0_0 r
r-htmlwidgets 0.6 r3.3.0_0 r
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r-httr 1.1.0 r3.3.0_0 r
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r-mime 0.4 r3.3.0_0 r
r-minqa 1.2.4 r3.3.0_2 r
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r-nlme 3.1_128 r3.3.0_0 r
r-nloptr 1.0.4 r3.3.0_2 r
r-nnet 7.3_12 r3.3.0_0 r
r-openssl 0.9.3 r3.3.0_0 r
r-pbdzmq 0.2_2 r3.3.0_0 r
r-pbkrtest 0.4_6 r3.3.0_0 r
r-plyr 1.8.3 r3.3.0_0 r
r-pryr 0.1.2 r3.3.0_0 r
r-quantmod 0.4_5 r3.3.0_2 r
r-quantreg 5.24 r3.3.0_0 r
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r-rcolorbrewer 1.1_2 r3.3.0_2 r
r-rcpp 0.12.5 r3.3.0_0 r
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r-recommended 3.3.0 r3.3.0_0 r
r-repr 0.7 r3.3.0_0 r
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r-rpart 4.1_10 r3.3.0_0 r
r-scales 0.4.0 r3.3.0_0 r
r-shiny 0.13.2 r3.3.0_0 r
r-sparsem 1.7 r3.3.0_0 r
r-spatial 7.3_11 r3.3.0_0 r
r-stringi 1.0_1 r3.3.0_0 r
r-stringr 1.0.0 r3.3.0_0 r
r-survival 2.39_4 r3.3.0_0 r
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r-uuid 0.1_2 r3.3.0_0 r
r-xtable 1.8_2 r3.3.0_0 r
r-xts 0.9_7 r3.3.0_2 r
r-yaml 2.1.13 r3.3.0_2 r
r-zoo 1.7_13 r3.3.0_0 r
requests 2.11.1 py35_0 defaults
rope 0.9.4 py35_1 defaults
ruamel_yaml 0.11.14 py35_0 defaults
scikit-image 0.12.3 np111py35_1 defaults
scikit-learn 0.17.1 np111py35_1 defaults
scipy 0.18.1 np111py35_0 defaults
seaborn 0.7.1 py35_0 defaults
setuptools 27.2.0 py35_1 defaults
simplegeneric 0.8.1 py35_1 defaults
singledispatch 3.4.0.3 py35_0 defaults
sip 4.18 py35_0 defaults
six 1.10.0 py35_0 defaults
snowballstemmer 1.2.1 py35_0 defaults
sockjs-tornado 1.0.3 py35_0 defaults
sphinx 1.4.6 py35_0 defaults
sphinx_rtd_theme 0.1.9 py35_0 defaults
spyder 3.0.0 py35_0 defaults
sqlalchemy 1.0.13 py35_0 defaults
statsmodels 0.6.1 np111py35_1 defaults
sympy 1.0 py35_0 defaults
tk 8.5.18 vc14_0 [vc14] defaults
toolz 0.8.0 py35_0 defaults
tornado 4.4.1 py35_0 defaults
traitlets 4.3.1 <pip>
traitlets 4.3.0 py35_0 defaults
traittypes 0.0.6 <pip>
unicodecsv 0.14.1 py35_0 defaults
vs2015_runtime 14.0.25123 0 defaults
watermark 1.3.3 <pip>
wcwidth 0.1.7 py35_0 defaults
werkzeug 0.11.11 py35_0 defaults
wheel 0.29.0 py35_0 defaults
widgetsnbextension 1.2.6 py35_0 defaults
widgetsnbextension 1.2.6 <pip>
win_unicode_console 0.5 py35_0 defaults
wrapt 1.10.6 py35_0 defaults
xlrd 1.0.0 py35_0 defaults
xlsxwriter 0.9.3 py35_0 defaults
xlwings 0.10.0 py35_0 defaults
xlwt 1.1.2 py35_0 defaults
zlib 1.2.8 vc14_3 [vc14] defaultszlib1.dll is present
Do you mean it is in C:\Windows\System32? That is fatal to any software that wants to use a different zlib1.dll. You need to find out what software put it there and uninstall it, and then, if you still have zlib1.dll in that folder, you need to delete it.
robmarkcole
commented
8 years ago Yes in System32. It was Date Modified in 2008, way before I took ownership of this (work) laptop. It appears to be the oldest file in System32. How could I find out which software installed it, or depends on it? I suppose I could delete it and see what happens, but since this is my work computer I may regret it..!
mingwandroid
commented
8 years ago You could rename it and see what breaks. I doubt it will render your system unusable, but I cannot 100% guarantee that. Alternatively, there's a Task Manager replacement called Process Hacker 2 [1]. It can also be run from a portable install [2] in a stand-alone fashion. It has a way to search for processes using DLLs.
If you run that, then click on Find handles or DLLs, you should be able to enter zlib1.dll into the Filter box and press the Find button. You should do this after you have launched (and are still executing) all your mission critical software as it only looks through the currently running processes. If nothing turns up, then this may give you some confidence to delete the file.
[1] http://processhacker.sourceforge.net/ [2] https://wj32.org/processhacker/rel/processhacker-2.39-bin.zip
robmarkcole
commented
8 years ago Since both those solutions require admin rights I got the IT dept on the phone, they deleted the dll and now R is working in jupyter :-)
mingwandroid
commented
8 years ago Great to hear. Thanks!
mingwandroid
commented
8 years ago A final point, ideally you would use the Anaconda Command Prompt to launch all of your conda software. Doing this guarantees that, for that session, the conda binary folders are put to the front of PATH which minimises chances of the wrong DLLs getting used, otherwise it is unfortunately pot-luck whether software will work or not depending on the relative installation order of software that modifies PATH during installation (and whether they prepend or append to it). The other systems implement slightly better techniques for shared library path resolution.
robmarkcole
commented
8 years ago On my mac, I still experience the death kernel, pcre is up to date..
conda update pcre
All requested packages already installed. packages in environment at /Users/robincole/anaconda3: pcre 8.39 0
ijstokes
commented
8 years ago @robmarkcole and @mingwandroid same here. conda update pcre moved me from 8.31 to 8.39 (nothing else updated), then my attempt to create a new Jupyter notebook with the R kernel failed as follows:
$ jupyter notebook
[W 05:46:53.776 NotebookApp] server_extensions is deprecated, use nbserver_extensions
[I 05:46:54.321 NotebookApp] [nb_conda_kernels] enabled, 17 kernels found
[I 05:46:54.932 NotebookApp] The port 8888 is already in use, trying another port.
[I 05:46:55.035 NotebookApp] ✓ nbpresent HTML export ENABLED
[W 05:46:55.035 NotebookApp] ✗ nbpresent PDF export DISABLED: No module named nbbrowserpdf.exporters.pdf
[W 05:46:55.071 NotebookApp] Error loading server extension ipyparallel.nbextension
Traceback (most recent call last):
File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/notebook/notebookapp.py", line 1049, in init_server_extensions
func(self)
File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/ipyparallel/nbextension/handlers.py", line 74, in load_jupyter_server_extension
install_nbextension(static, destination='ipyparallel', symlink=not windows, user=True)
File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/notebook/nbextensions.py", line 198, in install_nbextension
os.symlink(path, full_dest)
OSError: [Errno 17] File exists
[I 05:46:55.079 NotebookApp] [nb_conda] enabled
[I 05:46:55.154 NotebookApp] [nb_anacondacloud] enabled
[I 05:46:55.159 NotebookApp] Serving notebooks from local directory: /Users/ijstokes/teaching/python
[I 05:46:55.159 NotebookApp] 0 active kernels
[I 05:46:55.159 NotebookApp] The Jupyter Notebook is running at: http://localhost:8889/
[I 05:46:55.159 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[W 05:46:56.650 NotebookApp] 404 GET /nbextensions/ipyparallel/main.js?v=20161015054654 (::1) 10.93ms referer=http://localhost:8889/tree
[I 05:47:01.791 NotebookApp] Creating new notebook in
[I 05:47:06.245 NotebookApp] Kernel started: 78542f65-d751-48bd-8610-d87d2d71401e
Error in loadNamespace(name) : there is no package called ‘IRkernel’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[I 05:47:09.243 NotebookApp] KernelRestarter: restarting kernel (1/5)
Error in loadNamespace(name) : there is no package called ‘IRkernel’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[I 05:47:12.251 NotebookApp] KernelRestarter: restarting kernel (2/5)
Error in loadNamespace(name) : there is no package called ‘IRkernel’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[I 05:47:15.260 NotebookApp] KernelRestarter: restarting kernel (3/5)
Error in loadNamespace(name) : there is no package called ‘IRkernel’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[W 05:47:16.448 NotebookApp] Timeout waiting for kernel_info reply from 78542f65-d751-48bd-8610-d87d2d71401e
[I 05:47:18.270 NotebookApp] KernelRestarter: restarting kernel (4/5)
WARNING:root:kernel 78542f65-d751-48bd-8610-d87d2d71401e restarted
Error in loadNamespace(name) : there is no package called ‘IRkernel’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
[W 05:47:21.281 NotebookApp] KernelRestarter: restart failed
[W 05:47:21.282 NotebookApp] Kernel 78542f65-d751-48bd-8610-d87d2d71401e died, removing from map.
ERROR:root:kernel 78542f65-d751-48bd-8610-d87d2d71401e restarted failed!
[W 05:47:21.349 NotebookApp] Kernel deleted before session
[W 05:47:21.349 NotebookApp] 410 DELETE /api/sessions/cab45392-602e-492d-8334-743cef6a64b5 (::1) 2.56ms referer=http://localhost:8889/notebooks/Untitled.ipynb?kernel_name=ir
kzapfe
commented
8 years ago Hello team: I have the same problem here, with the newest anaconda just fresh installed a pair hours ago as date of this message. I am on a GNU/Linux machine x86_64.
anaconda 4.2.0 np111py35_0
conda 4.2.9 py35_0
nb_conda_kernels 2.0.0 py35_0
pcre 8.39 0 And r and r-essentials straight outta the conda installer:
r 3.3.1 r3.3.1_0 r
r-essentials 1.4.2 r3.3.1_0 r
r-irkernel 0.7 r3.3.1_0 rAlso, if I try to make it directly from R, I cannot install devtools. I get an error of the tune:
6: In install.packages("devtools") :
installation of package ‘devtools’ had non-zero exit statusIt seems that R cannot see where conda puts everything (specially tcl).
ijstokes
commented
8 years ago @kzapfe can you tell us if the following gives you a working R kernel in Jupyter:
conda create -n test_r -c r r-essentials jupyter
source activate test_r
jupyter notebookThen create a new notebook with the "R [conda default]" env or "R [conda test_r]" env and see if it works. We're having trouble figuring out what the source of this problem is as it appears to only affect some people in some configurations (I am one of those people for whom R is broken, so I'm motivated to find a solution).
kzapfe
commented
8 years ago Followed your instructions @ijstokes , no progress still.
Okey, keeps dying... messages on the shell are as follows:
[I 13:59:01.757 NotebookApp] Creating new notebook in
[I 13:59:02.787 NotebookApp] Kernel started: 0ca1fe0a-db09-4447-9be4-960cf6321bc3
[1] "Got unhandled msg_type:" "comm_info_request"
[1] "Got unhandled msg_type:" "comm_open"
[1] "Got unhandled msg_type:" "comm_open"
Error in unlockBinding("base_display", displayenv) :
no binding for "base_display"
Calls: <Anonymous> ... <Anonymous> -> handle_shell -> <Anonymous> -> unlockBinding
Execution halted
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
[I 13:59:14.787 NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING:root:kernel 0ca1fe0a-db09-4447-9be4-960cf6321bc3 restartedAs a side note: this also happens in other front-ends for Jupyter, such as qt console.
zenkavi
commented
8 years ago Hi, there is still no solution for this on Mac correct? My kernel is still dying with the following error. I tried updating pcre before but that didn't help
[I 12:57:01.313 NotebookApp] Kernel started: 5f894bb4-c34f-4694-a733-4fbaa878fbf5
[1] "Got unhandled msg_type:" "comm_open"
Error in unlockBinding("base_display", displayenv) :
no binding for "base_display"
Calls: <Anonymous> ... <Anonymous> -> handle_shell -> <Anonymous> -> unlockBinding
Execution halted
[I 12:57:13.316 NotebookApp] KernelRestarter: restarting kernel (1/5)
WARNING:root:kernel 5f894bb4-c34f-4694-a733-4fbaa878fbf5 restarted```
Can you do conda update r-rikernel and see if that works for you?
zenkavi
commented
8 years ago Yes
Fetching package metadata .......
# All requested packages already installed.
# packages in environment at /Users/zeynepenkavi/anaconda:
#
r-irkernel 0.7 r3.3.1_0 rYou are not using the R from Anaconda:
/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/bin/R
This looks like homebrew instead.
Please activate your conda environment (http://conda.pydata.org/docs/using/envs.html) and install r-essentials and jupyter.
seekshreyas
commented
8 years ago @mingwandroid : I think I am using conda virtual environment and it is activated. I checked and on
which r jupyter
I get this
/Users/shreyas/anaconda/envs/quasiexperiments/bin/jupyter
/Users/shreyas/anaconda/envs/quasiexperiments/bin/r@zenkavi, please try conda update -c r r-essentials and show me the output of that.
mingwandroid
commented
8 years ago @seekshreyas: Please show me the PATH from the command prompt from which you are launching jupyter:
echo $PATH
A minor nit, conda doesn't call refer to its environments as virutal environments, indeed conda doesn't work with normal virtual environments.
zenkavi
commented
8 years ago @mingwandroid Here's the output:
Fetching package metadata .......
# All requested packages already installed.
# packages in environment at /Users/zeynepenkavi/anaconda:
#
r-essentials 1.4.2 r3.3.1_0 r@zenkavi, I think that you may have missed -c r from your command-line, so conda is finding only the r-essentials package that you have already installed.
zenkavi
commented
8 years ago @mingwandroid my apologies. you were totally right. AND NOW IT'S WORKING! Thank you very much!
kzapfe
commented
8 years ago Okey, seems that there is an update avaiable now, I did
conda update -c r r-irkernel
karel@sofinha ~ $ conda update -c r r-irkernel
Fetching package metadata .........
Solving package specifications: ..........
Package plan for installation in environment /home/karel/anaconda3:
The following packages will be downloaded:
package | build
---------------------------|-----------------
r-memoise-1.0.0 | r3.3.1_0 23 KB r
r-crayon-1.3.1 | r3.3.1_0 599 KB r
r-irkernel-0.7 | r3.3.1_2 109 KB r
------------------------------------------------------------
Total: 731 KB
The following NEW packages will be INSTALLED:
r-crayon: 1.3.1-r3.3.1_0 r
r-memoise: 1.0.0-r3.3.1_0 r
The following packages will be UPDATED:
r-irkernel: 0.7-r3.3.1_0 r --> 0.7-r3.3.1_2 r
Proceed ([y]/n)? y
and it doesn't die inmediately anymore. I will throw something at it and see if it holds...
Well, it holds. Thank you everybody!
ijstokes
commented
8 years ago @mingwandroid I have R kernels working in my root environment now, thanks to conda update -c r r-essentials. Looks like I managed some kind of special maneuver and had r-essentials without r-base if I'm reading the Conda output correctly. I certainly did have r-base at one point recently...
The following NEW packages will be INSTALLED:
r-base: 3.3.1-0 r
r-crayon: 1.3.1-r3.3.1_0 r
r-memoise: 1.0.0-r3.3.1_0 r
The following packages will be UPDATED:
r-essentials: 1.4-0 r --> 1.4.3-r3.3.1_0 r
r-irdisplay: 0.3-r3.3.1_2 r --> 0.4.3-r3.3.1_2 r
r-irkernel: 0.6.1-r3.3.1_0 r --> 0.7-r3.3.1_2 r
csoja
commented
8 years ago Can this issue be closed?
ijstokes
commented
8 years ago @csoja I think so -- many of the people who reported ongoing problems are now saying that these various steps (in particular, updating pcre and r-irkernel) have solved the problem for them. It certainly has solved the problem for me. I'm closing it, but if anyone else is suffering after trying the steps described here (and it seems like it is the same issue) please request to reopen.
evankielley
commented
8 years ago Having the same issue. Although I just created a large Jupyter notebook yesterday, written in R, and gave a presentation with it, all went fine. Today for some reason, the kernel dies instantly. Both of my python kernels run fine.
I have tried all of your suggestions here but most involve updates and everything I have is up to date.
mingwandroid
commented
8 years ago @evankielley which OS are you using? Can you show the output from:
conda info
conda list --show-channel-urlsThanks for getting back to me.
I am running Ubuntu16.04 and I wiped my system clean of anaconda, jupyter, and R; then reinstalled; now the kernel works fine again.
If this happens anymore I'll be sure to post the info you requested.
Cheers!
On Nov 3, 2016 1:42 PM, "Ray Donnelly" notifications@github.com wrote:
@evankielley https://github.com/evankielley which OS are you using? Can you show the output from:
conda info conda list --show-channel-urls
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ContinuumIO/anaconda-issues/issues/999#issuecomment-258190710, or mute the thread https://github.com/notifications/unsubscribe-auth/ASVtSWKHm7ihNU0Za8nb3op95e4PsS7Rks5q6gf4gaJpZM4Jn1-1 .
yiulau
commented
8 years ago I have the same problem. Freshly installed r-essnetials and Jupyter in a conda environment but R kernel keeps dying.
(my-r-env) [yiulau@stat12 ~]$ conda info
Current conda install:
platform : linux-64
conda version : 4.2.9
conda is private : False
conda-env version : 4.2.9
conda-build version : 2.0.2
python version : 3.5.2.final.0
requests version : 2.11.1
root environment : /home/yiulau/anaconda3 (writable)
default environment : /home/yiulau/anaconda3/envs/my-r-env
envs directories : /home/yiulau/anaconda3/envs
package cache : /home/yiulau/anaconda3/pkgs
channel URLs : https://repo.continuum.io/pkgs/free/linux-64/
https://repo.continuum.io/pkgs/free/noarch/
https://repo.continuum.io/pkgs/pro/linux-64/
https://repo.continuum.io/pkgs/pro/noarch/
config file : None
offline mode : False
(my-r-env) [yiulau@stat12 ~]$ conda list --show-channel-urls
# packages in environment at /home/yiulau/anaconda3/envs/my-r-env:
#
bzip2 1.0.6 3 defaults
cairo 1.12.18 6 defaults
curl 7.49.0 1 defaults
fontconfig 2.11.1 6 defaults
freetype 2.5.5 1 defaults
glib 2.43.0 2 r
gsl 1.16 1 r
harfbuzz 0.9.35 6 r
icu 54.1 0 defaults
jbig 2.1 0 defaults
jpeg 8d 2 defaults
libffi 3.2.1 0 defaults
libgcc 4.8.5 1 r
libpng 1.6.22 0 defaults
libsodium 1.0.10 0 defaults
libtiff 4.0.6 2 defaults
libxml2 2.9.2 0 defaults
ncurses 5.9 8 r
openssl 1.0.2j 0 defaults
pango 1.36.8 3 r
pcre 8.39 0 defaults
pixman 0.32.6 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 3 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 1a 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 r3.3.1_3 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 r3.3.1_2 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 2 defaults
tk 8.5.18 0 defaults
xz 5.2.2 0 defaults
zeromq 4.1.5 0 defaults
zlib 1.2.8 3 defaults
(my-r-env) [yiulau@stat12 ~]$ lsb_release -a
LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description: CentOS release 6.8 (Final)
Release: 6.8
Codename: FinalI do not see jupyter in the list of installed packages. Holy need to install that into your environment.
yiulau
commented
8 years ago I have installed Jupyter now but it the problem is still there.
(my-r-env) [yiulau@stat12 ~]$ conda list --show-channel-urls
# packages in environment at /home/yiulau/anaconda3/envs/my-r-env:
#
_nb_ext_conf 0.3.0 py35_0 defaults
anaconda-client 1.5.3 py35_0 defaults
bzip2 1.0.6 3 defaults
cairo 1.12.18 6 defaults
clyent 1.2.2 py35_0 defaults
curl 7.49.0 1 defaults
dbus 1.10.10 0 defaults
decorator 4.0.10 py35_0 defaults
entrypoints 0.2.2 py35_0 defaults
expat 2.1.0 0 defaults
fontconfig 2.11.1 6 defaults
freetype 2.5.5 1 defaults
glib 2.43.0 2 r
gsl 1.16 1 r
gst-plugins-base 1.8.0 0 defaults
gstreamer 1.8.0 0 defaults
harfbuzz 0.9.35 6 r
icu 54.1 0 defaults
ipykernel 4.5.0 py35_0 defaults
ipython 5.1.0 py35_0 defaults
ipython_genutils 0.1.0 py35_0 defaults
ipywidgets 5.2.2 py35_0 defaults
jbig 2.1 0 defaults
jinja2 2.8 py35_1 defaults
jpeg 8d 2 defaults
jsonschema 2.5.1 py35_0 defaults
jupyter 1.0.0 py35_3 defaults
jupyter_client 4.4.0 py35_0 defaults
jupyter_console 5.0.0 py35_0 defaults
jupyter_core 4.2.0 py35_0 defaults
libffi 3.2.1 0 defaults
libgcc 4.8.5 1 r
libpng 1.6.22 0 defaults
libsodium 1.0.10 0 defaults
libtiff 4.0.6 2 defaults
libxcb 1.12 1 defaults
libxml2 2.9.2 0 defaults
markupsafe 0.23 py35_2 defaults
mistune 0.7.3 py35_0 defaults
nb_anacondacloud 1.2.0 py35_0 defaults
nb_conda 2.0.0 py35_0 defaults
nb_conda_kernels 2.0.0 py35_0 defaults
nbconvert 4.2.0 py35_0 defaults
nbformat 4.1.0 py35_0 defaults
nbpresent 3.0.2 py35_0 defaults
ncurses 5.9 8 r
notebook 4.2.3 py35_0 defaults
openssl 1.0.2j 0 defaults
pango 1.36.8 3 r
path.py 8.2.1 py35_0 defaults
pcre 8.39 0 defaults
pexpect 4.0.1 py35_0 defaults
pickleshare 0.7.4 py35_0 defaults
pip 9.0.0 py35_0 defaults
pixman 0.32.6 0 defaults
prompt_toolkit 1.0.8 py35_0 defaults
ptyprocess 0.5.1 py35_0 defaults
pygments 2.1.3 py35_0 defaults
pyqt 5.6.0 py35_0 defaults
python 3.5.2 0 defaults
python-dateutil 2.5.3 py35_0 defaults
pytz 2016.7 py35_0 defaults
pyyaml 3.12 py35_0 defaults
pyzmq 16.0.0 py35_0 defaults
qt 5.6.0 1 defaults
qtconsole 4.2.1 py35_1 defaults
r 3.3.1 r3.3.1_0 r
r-assertthat 0.1 r3.3.1_4 r
r-base 3.3.1 3 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 1a 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 r3.3.1_3 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 r3.3.1_2 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 2 defaults
requests 2.11.1 py35_0 defaults
setuptools 27.2.0 py35_0 defaults
simplegeneric 0.8.1 py35_1 defaults
sip 4.18 py35_0 defaults
six 1.10.0 py35_0 defaults
sqlite 3.13.0 0 defaults
terminado 0.6 py35_0 defaults
tk 8.5.18 0 defaults
tornado 4.4.2 py35_0 defaults
traitlets 4.3.1 py35_0 defaults
wcwidth 0.1.7 py35_0 defaults
wheel 0.29.0 py35_0 defaults
widgetsnbextension 1.2.6 py35_0 defaults
xz 5.2.2 0 defaults
yaml 0.1.6 0 defaults
zeromq 4.1.5 0 defaults
zlib 1.2.8 3 defaults
Hello. I have encountered a recurrent bug whenever I try to create an R notebook in Jupyter using the r-essentials package installer via conda. The problem is that the kernel immediately dies.
I followed the instructions published by @chdoig at https://www.continuum.io/blog/developer/jupyter-and-conda-r and also described in her webinar for ContinuumIO, "Open Data Science with R & Anaconda", available at http://go2.continuum.io/q0WX0C0q2g0Rdd01N0hC00l (video) and http://go2.continuum.io/tCWh1l0dXq02h00RNd0000D (slides).
Here are the steps I followed:
(1) Created a new environment and installed the r-essentials package and jupiter:
$ conda create -n R-Env -c r r-essentials$ source activate R-Env$ conda install jupyter(2) Ran Jupyter Notebook from this environment:
$ jupyter notebook(3) Chose to create new R notebook from the dropdown menu. The notebook will open, and Jupyter tries to connect to the kernel. Immediately, the kernel dies.
(4) I found several conversations on GitHub and elsewhere discussing problems with the R kernel via the r-essentials distribution. For examples, see
Unfortunately, none of these threads really end with a solution.
(5) Since the problem seems to be with IRkernel, I found these instructions at https://irkernel.github.io/installation/
In Terminal, I started R by typing
$ RThen, in the R console, I typed:
> install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'devtools', 'uuid', 'digest'))> devtools::install_github('IRkernel/IRkernel')> IRkernel::installspec()When I go back to the Terminal and change source to my R-Env environment, I then launch Jupyter Notebook and choose to create a new R notebook from the dropdown menu. SUCCESS! A new notebook is created, and it connects to the kernel without problems.
HOWEVER, the notebook is not seeing any of the packages installed in R-Env (from r-essentials). For example, typing
library(dplyr)in the Jupyter R notebook returns an error because the library is not found.In summary, when following @chdoig instructions, there is a reproducible error whereby the kernel dies in the Jupyter R notebook. If I add the instructions to make the IRkernel available to Jupyter, then the R notebook will open fine, but Jupyter is blind to the r-essentials packages.
Thoughts? Advice?
The kernel problem seems to be common to many people. I hope to find a solution, as I would love to use Jupyter for all my work in both Python and R, rather than needing to use RStudio.
Many thanks. -- Alexander.
System Info:
Mac OS X 10.11.6
$ conda infoCurrent conda install: platform : osx-64 conda version : 4.1.6 conda-env version : 2.5.1 conda-build version : 1.21.3 python version : 3.5.2.final.0 requests version : 2.10.0 root environment : /Applications/anaconda (writable) default environment : /Applications/anaconda envs directories : /Applications/anaconda/envs package cache : /Applications/anaconda/pkgs channel URLs : https://conda.anaconda.org/r/osx-64/ https://conda.anaconda.org/r/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/aa196/.condarc offline mode : False is foreign system : False
$ RR version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (64-bit)