R – No Magic [IP][y]: iPython -- 损坏的 python 内核?

R – No Magic [IP][y]: iPython -- Corrupt python kernel?

如前所述previously,当运行一个单元格

%%R

我收到以下错误:

ERROR:root:Cell magic `%%R` not found.

正在尝试

%load_ext rmagic

导致:

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 "

显然,该命令似乎是 "deprecated"。然后我尝试:

%load_ext rpy2.ipython

这会导致多个错误,因此我检查文件夹 C:\Anaconda2\envs\ipykernel_py2\lib\site-packages\IPython\extensions 并找到 rmagic .py.pyc,但没有与 rpy2.ipython 相关的文件:

然后我再次尝试 %load_ext rmagic

The rmagic extension is already loaded. To reload it, use:
    %reload_ext rmagic.py

%%R 的错误没有改变。


最后,我

pip install rpy2

当安装程序运行 Rterm.exe that

时我收到一个错误
libgcc_s_dw2-1.dll (mentioned twice)
libbz2-1.dll
liblzma-5.dll

在这台计算机上丢失了,我必须重新安装 RTerm,我猜它是 RTools 的一部分。最终 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

RRStudioR-Essentials(通过 conda ) 安装在我的电脑上。在 conda 安装期间,只有关于 p11-kit (PKCS 11) 的投诉,我认为这与此无关。

运行 >jupyter troubleshoot 显示 r-base 的版本号为 0(向下滚动)。

[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;

如您所见,PYTHONPATH 已定义。这违背了 Continuum 的建议,但我认为这不是罪魁祸首。

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)

摘录:>>conda 列表:

    # 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

我也安装了 Sage。但是,它是从虚拟框运行的,目前不是 运行。

我不确定,但我认为 GNU GCC、mingw、and/or RTools 打破了与 R 的绑定,因为 Continuum 当前 dist 中的一些错误。同时,我不知道 R-essentials 是否与 %.

的使用完全相关

魔法在哪里?

显然 rpy2 正在接管 IPython R 魔法扩展的角色。可能有问题的是您试图通过 pip 安装 rpy2,而不是在 IPython 环境中使用 miniconda。我从网络的不同部分听说 [下面的参考资料] 您需要在您的 conda 环境中安装 rpy2 才能使链接正常工作。它也可能会解决您的 .dll 查找问题。

我的建议(Windows):

activate ipykernel_py2
conda install -c r rpy2

如果效果不错,试试:

jupyter notebook

重要的是在 运行 jupyter 时处于 ipykernel_py2 环境中。

参考:

如果您已经完成 pip install rpy2 那么您需要在使用前加载扩展:

%load_ext rpy2.ipython
%%R