As have been described previously, when running a cell with
%%R
I receive the following error:
ERROR:root:Cell magic `%%R` not found.
Trying
%load_ext rmagic
leads to:
C:\Anaconda2\envs\ipykernel_py2\lib\site-packages\IPython\extensions\rmagic.py:11:
UserWarning: The rmagic extension in IPython has moved to `rpy2.ipython`,
please see `rpy2` documentation.
warnings.warn("The rmagic extension in IPython has moved to "
Apparently, the command seems "deprecated". I then try:
%load_ext rpy2.ipython
This results in multiple errors, whereupon I check the folder C:\Anaconda2\envs\ipykernel_py2\lib\site-packages\IPython\extensions and find rmagic .py and .pyc, but no files related to rpy2.ipython:
I then try %load_ext rmagic again:
The rmagic extension is already loaded. To reload it, use:
%reload_ext rmagic.py
The error for %%R does not change.
Finally, I
pip install rpy2
upon which I receive an error when the installer runs Rterm.exe that
libgcc_s_dw2-1.dll (mentioned twice)
libbz2-1.dll
liblzma-5.dll
are missing on this computer and that I have to reinstall RTerm, which I guess is part of RTools. Eventually the stderr/stdout:
Collecting rpy2
Using cached rpy2-2.8.4.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "c:\users\user\appdata\local\temp\pip-build-1mtkwa\rpy2\setup.py",
line 331, in <module>
ri_ext = getRinterface_ext()
File "c:\users\user\appdata\local\temp\pip-build-1mtkwa\rpy2\setup.py", line 234,
in getRinterface_ext
if rexec.version[0] == 'development' or \
File "c:\users\user\appdata\local\temp\pip-build-1mtkwa\rpy2\setup.py",
line 160, in version
universal_newlines = True)
File "C:\Anaconda2\envs\ipykernel_py2\lib\subprocess.py",
line 574, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError:
Command '('C:\\Anaconda2\\R\\bin\\R', '--version')'
returned non-zero exit status -1073741515
R, RStudio, and R-Essentials (via conda) are installed on my computer. During the conda installation there is only a complaint about the p11-kit (PKCS 11), which I assume is unrelated.
Running >jupyter troubleshoot reveals that r-base has version number 0 (scroll down).
[31mDEPRECATION: The default format will switch to columns in the future. You can use --format=(legacy|columns) (or define a format=(legacy|columns) in your pip.conf under the [list] section) to disable this warning.[0m
$PATH:
C
\Anaconda2\Library\bin;C
\Anaconda2\Scripts;C
\Anaconda2\Library\bin;C
\Windows\system32;C
\Windows;C
\Windows\System32\Wbem;C
\Windows\System32\WindowsPowerShell\v1.0\;%JAVA%;%PYTHONPATH%;%PYTHONPATH%\Scripts;%PYTHONPATH%\Library\bin;%GITPATH%;C
\Program Files\MATLAB\R2016b\runtime\win64;C
\Program Files\MATLAB\R2016b\bin;C
\Users\user\AppData\Local\Microsoft\WindowsApps;C
\ProgramData\Oracle\Java\javapath;C
\Program Files\Git;%GITPATH\cmd%;C
\Program Files\Git\bin;C
\Anaconda2;C
\Anaconda2\Scripts;C
\Anaconda2\Library\bin;C
\ProgramData\che;C
\Program Files\R\R-3.3.2\bin;
As you can see, the PYTHONPATH is defined. This is against the recommendations of Continuum, but I do not see that this could be a culprit.
sys.path:
C:\Anaconda2\Scripts
C:\Anaconda2
C:\Anaconda2\python27.zip
C:\Anaconda2\DLLs
C:\Anaconda2\lib
C:\Anaconda2\lib\plat-win
C:\Anaconda2\lib\lib-tk
C:\Anaconda2\lib\site-packages
C:\Anaconda2\lib\site-packages\Sphinx-1.4.6-py2.7.egg
C:\Anaconda2\lib\site-packages\win32
C:\Anaconda2\lib\site-packages\win32\lib
C:\Anaconda2\lib\site-packages\Pythonwin
C:\Anaconda2\lib\site-packages\setuptools-27.2.0-py2.7.egg
sys.executable:
C:\Anaconda2\python.exe
sys.version:
2.7.12 |Anaconda 4.2.0 (32-bit)| (default, Jun 29 2016, 11:42:13) [MSC v.1500 32 bit (Intel)]
platform.platform():
Windows-10-10.0.14393
where jupyter:
C:\Anaconda2\Scripts\jupyter.exe
pip list:
alabaster (0.7.9)
anaconda-clean (1.0)
anaconda-client (1.5.1)
anaconda-navigator (1.3.1)
argcomplete (1.0.0)
astroid (1.4.7)
astropy (1.2.1)
Babel (2.3.4)
backports-abc (0.4)
backports.shutil-get-terminal-size (1.0.0)
backports.ssl-match-hostname (3.4.0.2)
beautifulsoup4 (4.5.1)
bitarray (0.8.1)
blaze (0.10.1)
bokeh (0.12.2)
boto (2.42.0)
Bottleneck (1.1.0)
cdecimal (2.3)
cffi (1.7.0)
chest (0.2.3)
click (6.6)
cloudpickle (0.2.1)
clyent (1.2.2)
colorama (0.3.7)
comtypes (1.1.2)
conda (4.2.13)
conda-build (2.0.2)
configobj (5.0.6)
configparser (3.5.0)
contextlib2 (0.5.3)
cryptography (1.5)
cycler (0.10.0)
Cython (0.24.1)
cytoolz (0.8.0)
dask (0.11.0)
datashape (0.5.2)
decorator (4.0.10)
dill (0.2.5)
docutils (0.12)
enum34 (1.1.6)
et-xmlfile (1.0.1)
ez-setup (0.9)
fastcache (1.0.2)
filelock (2.0.6)
Flask (0.11.1)
Flask-Cors (2.1.2)
funcsigs (1.0.2)
functools32 (3.2.3.post2)
futures (3.0.5)
gevent (1.1.2)
greenlet (0.4.10)
grin (1.2.1)
h5py (2.6.0)
HeapDict (1.0.0)
idna (2.1)
imagesize (0.7.1)
ipaddress (1.0.16)
ipykernel (4.5.0)
ipython (5.1.0)
ipython-genutils (0.1.0)
ipywidgets (5.2.2)
itsdangerous (0.24)
jdcal (1.2)
jedi (0.9.0)
Jinja2 (2.8)
jsonschema (2.5.1)
jupyter (1.0.0)
jupyter-client (4.4.0)
jupyter-console (5.0.0)
jupyter-core (4.2.0)
lazy-object-proxy (1.2.1)
llvmlite (0.13.0)
locket (0.2.0)
lxml (3.6.4)
MarkupSafe (0.23)
matplotlib (1.5.3)
menuinst (1.4.1)
mistune (0.7.3)
mpmath (0.19)
multipledispatch (0.4.8)
nb-anacondacloud (1.2.0)
nb-conda (2.0.0)
nb-conda-kernels (2.0.0)
nbconvert (4.2.0)
nbformat (4.1.0)
nbpresent (3.0.2)
networkx (1.11)
nltk (3.2.1)
nose (1.3.7)
notebook (4.2.3)
numba (0.28.1+0.gfe99fbc.dirty)
numexpr (2.6.1)
numpy (1.11.1)
odo (0.5.0)
openpyxl (2.3.2)
pandas (0.18.1)
partd (0.3.6)
path.py (0.0.0)
pathlib2 (2.1.0)
patsy (0.4.1)
pep8 (1.7.0)
pickleshare (0.7.4)
Pillow (3.3.1)
pip (9.0.1)
pkginfo (1.3.2)
ply (3.9)
prompt-toolkit (1.0.9)
psutil (4.3.1)
py (1.4.31)
pyasn1 (0.1.9)
pycosat (0.6.1)
pycparser (2.14)
pycrypto (2.6.1)
pycurl (7.43.0)
pyflakes (1.3.0)
Pygments (2.1.3)
pylint (1.5.4)
pyOpenSSL (16.0.0)
pyparsing (2.1.4)
pytest (2.9.2)
python-dateutil (2.5.3)
pytz (2016.6.1)
pywin32 (220)
PyYAML (3.12)
pyzmq (15.4.0)
QtAwesome (0.3.3)
qtconsole (4.2.1)
QtPy (1.1.2)
requests (2.11.1)
rope (0.9.4)
ruamel-yaml (-VERSION)
scikit-image (0.12.3)
scikit-learn (0.17.1)
scipy (0.18.1)
setuptools (27.2.0)
simplegeneric (0.8.1)
singledispatch (3.4.0.3)
six (1.10.0)
snowballstemmer (1.2.1)
sockjs-tornado (1.0.3)
sphinx (1.4.6)
spyder (3.0.0)
SQLAlchemy (1.0.13)
statsmodels (0.6.1)
sympy (1.0)
tables (3.2.2)
toolz (0.8.0)
tornado (4.4.1)
traitlets (4.3.0)
unicodecsv (0.14.1)
wcwidth (0.1.7)
Werkzeug (0.11.11)
wheel (0.29.0)
widgetsnbextension (1.2.6)
win-unicode-console (0.5)
wrapt (1.10.6)
xlrd (1.0.0)
XlsxWriter (0.9.3)
xlwings (0.10.0)
xlwt (1.1.2)
Extracts: >>conda list:
# packages in environment at C:\Anaconda2:
#
r 3.3.1 r3.3.1_0 r
r-assertthat 0.1 r3.3.1_2 r
r-base 3.3.1 0 r
r-base64enc 0.1_3 r3.3.1_0 r
r-bh 1.60.0_2 r3.3.1_0 r
r-bitops 1.0_6 r3.3.1_2 r
r-boot 1.3_18 r3.3.1_0 r
r-car 2.1_2 r3.3.1_0 r
r-caret 6.0_70 r3.3.1_0 r
r-catools 1.17.1 r3.3.1_2 r
r-chron 2.3_47 r3.3.1_0 r
r-class 7.3_14 r3.3.1_0 r
r-cluster 2.0.4 r3.3.1_0 r
r-codetools 0.2_14 r3.3.1_0 r
r-colorspace 1.2_6 r3.3.1_0 r
r-crayon 1.3.1 r3.3.1_0 r
r-curl 0.9.7 r3.3.1_0 r
r-data.table 1.9.6 r3.3.1_0 r
r-dbi 0.4_1 r3.3.1_0 r
r-dichromat 2.0_0 r3.3.1_2 r
r-digest 0.6.9 r3.3.1_0 r
r-dplyr 0.4.3 r3.3.1_0 r
r-essentials 1.4.2 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_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_2 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
I have also an installation of Sage. However, it runs from a virtual box and is currently not running.
I am not sure, but I would like to think that GNU GCC, mingw, and/or RTools breaks the bind to R, because of some bug in Continuum's current dist. At the same time, I don't know if the R-essentials are related at all to the use of %.
Where's the magic?
