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September 7, 2016 04:13
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Save jbwhit/74fd2a6e51b784976f788e0302d1a54d to your computer and use it in GitHub Desktop.
Something has gone wrong, here is a minimum (not)-working example. The top is the failure in a Jupyter notebook; the bottom file is the installation.
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| $ conda create --name problem --channel r r-irkernel rpy2 python=3 jupyter notebook -y | |
| Fetching package metadata ........... | |
| Solving package specifications: .......... | |
| Package plan for installation in environment /Users/jonathan/miniconda3/envs/problem: | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| freetype-2.6.3 | 0 780 KB conda-forge | |
| The following NEW packages will be INSTALLED: | |
| appnope: 0.1.0-py35_0 | |
| backports.shutil_get_terminal_size: 1.0.0-py35_0 conda-forge | |
| ca-certificates: 2016.8.31-0 conda-forge | |
| certifi: 2016.8.31-py35_0 conda-forge | |
| curl: 7.49.1-1 conda-forge | |
| decorator: 4.0.10-py35_0 conda-forge | |
| entrypoints: 0.2.2-py35_0 conda-forge | |
| freetype: 2.6.3-0 conda-forge | |
| gsl: 1.16-2 r | |
| icu: 56.1-4 conda-forge | |
| ipykernel: 4.5.0-py35_0 conda-forge | |
| ipython: 5.1.0-py35_0 conda-forge | |
| ipython_genutils: 0.1.0-py35_0 conda-forge | |
| ipywidgets: 5.2.2-py35_0 conda-forge | |
| jinja2: 2.8-py35_1 conda-forge | |
| jpeg: 9b-0 conda-forge | |
| jsonschema: 2.5.1-py35_0 conda-forge | |
| jupyter: 1.0.0-py35_3 | |
| jupyter_client: 4.4.0-py35_0 conda-forge | |
| jupyter_console: 5.0.0-py35_0 conda-forge | |
| jupyter_core: 4.1.1-py35_1 conda-forge | |
| libgcc: 4.8.5-1 r | |
| libpng: 1.6.17-0 r | |
| libsodium: 1.0.10-0 conda-forge | |
| libtiff: 4.0.6-6 conda-forge | |
| libxml2: 2.9.2-1 r | |
| markupsafe: 0.23-py35_0 conda-forge | |
| mistune: 0.7.3-py35_0 conda-forge | |
| nbconvert: 4.2.0-py35_0 conda-forge | |
| nbformat: 4.1.0-py35_0 conda-forge | |
| ncurses: 5.9-8 r | |
| notebook: 4.2.2-py35_0 conda-forge | |
| openssl: 1.0.2h-2 conda-forge | |
| pcre: 8.38-1 conda-forge | |
| pexpect: 4.2.1-py35_0 conda-forge | |
| pickleshare: 0.7.3-py35_0 conda-forge | |
| pip: 8.1.2-py35_0 conda-forge | |
| prompt_toolkit: 1.0.7-py35_0 conda-forge | |
| ptyprocess: 0.5.1-py35_0 conda-forge | |
| pygments: 2.1.3-py35_1 conda-forge | |
| pyqt: 4.11.4-py35_4 | |
| python: 3.5.2-2 conda-forge | |
| python.app: 1.2-py35_4 | |
| pyzmq: 15.4.0-py35_0 conda-forge | |
| qt: 4.8.7-4 | |
| qtconsole: 4.2.1-py35_0 conda-forge | |
| r: 3.3.1-r3.3.1_0 r | |
| r-base: 3.3.1-0 r | |
| r-base64enc: 0.1_3-r3.3.1_0 r | |
| r-boot: 1.3_18-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-digest: 0.6.9-r3.3.1_0 r | |
| r-evaluate: 0.9-r3.3.1_0 r | |
| r-foreign: 0.8_66-r3.3.1_0 r | |
| r-irdisplay: 0.3-r3.3.1_2 r | |
| r-irkernel: 0.6.1-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-lattice: 0.20_33-r3.3.1_0 r | |
| r-magrittr: 1.5-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-mgcv: 1.8_12-r3.3.1_0 r | |
| r-nlme: 3.1_128-r3.3.1_0 r | |
| r-nnet: 7.3_12-r3.3.1_0 r | |
| r-pbdzmq: 0.2_3-r3.3.1_0 r | |
| r-r6: 2.1.2-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-rpart: 4.1_10-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-uuid: 0.1_2-r3.3.1_0 r | |
| readline: 6.2-0 conda-forge | |
| rpy2: 2.8.2-py35r3.3.1_1 r | |
| setuptools: 26.1.1-py35_0 conda-forge | |
| simplegeneric: 0.8.1-py35_0 conda-forge | |
| sip: 4.18-py35_0 conda-forge | |
| six: 1.10.0-py35_0 conda-forge | |
| sqlite: 3.13.0-1 conda-forge | |
| terminado: 0.6-py35_0 conda-forge | |
| tk: 8.5.19-0 conda-forge | |
| tornado: 4.4.1-py35_1 conda-forge | |
| traitlets: 4.2.2-py35_0 conda-forge | |
| wcwidth: 0.1.7-py35_0 conda-forge | |
| wheel: 0.29.0-py35_0 conda-forge | |
| widgetsnbextension: 1.2.6-py35_3 conda-forge | |
| xz: 5.2.2-0 conda-forge | |
| zeromq: 4.1.5-0 conda-forge | |
| zlib: 1.2.8-1 r | |
| Fetching packages ... | |
| freetype-2.6.3 100% |#############################################################################################| Time: 0:00:00 838.97 kB/s | |
| Extracting packages ... | |
| [ COMPLETE ]|################################################################################################################| 100% | |
| Linking packages ... | |
| [ COMPLETE ]|################################################################################################################| 100% | |
| No psutil available. | |
| To proceed, please conda install psutil# | |
| # To activate this environment, use: | |
| # $ source activate problem | |
| # | |
| # To deactivate this environment, use: | |
| # $ source deactivate | |
| # | |
| # ~/github/jupyter-tips-and-tricks | |
| $ source activate problem | |
| (problem) | |
| # ~/github/jupyter-tips-and-tricks | |
| $ jupyter notebook | |
| [W 20:22:21.424 NotebookApp] Unrecognized JSON config file version, assuming version 1 | |
| [I 20:22:22.649 NotebookApp] The port 8888 is already in use, trying another port. | |
| [W 20:22:22.678 NotebookApp] Error loading server extension jupyter_nbextensions_configurator | |
| Traceback (most recent call last): | |
| File "/Users/jonathan/miniconda3/envs/problem/lib/python3.5/site-packages/notebook/notebookapp.py", line 1046, in init_server_extensions | |
| mod = importlib.import_module(modulename) | |
| File "/Users/jonathan/miniconda3/envs/problem/lib/python3.5/importlib/__init__.py", line 126, in import_module | |
| return _bootstrap._gcd_import(name[level:], package, level) | |
| File "<frozen importlib._bootstrap>", line 986, in _gcd_import | |
| File "<frozen importlib._bootstrap>", line 969, in _find_and_load | |
| File "<frozen importlib._bootstrap>", line 956, in _find_and_load_unlocked | |
| ImportError: No module named 'jupyter_nbextensions_configurator' | |
| [I 20:22:22.701 NotebookApp] Serving notebooks from local directory: /Users/jonathan/github/jupyter-tips-and-tricks | |
| [I 20:22:22.701 NotebookApp] 0 active kernels | |
| [I 20:22:22.701 NotebookApp] The Jupyter Notebook is running at: http://localhost:8889/ | |
| [I 20:22:22.701 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). | |
| [W 20:22:25.071 NotebookApp] 404 GET /nbextensions/nbextensions_configurator/tree_tab/main.js?v=20160906202221 (::1) 12.75ms referer=http://localhost:8889/tree | |
| [W 20:22:27.144 NotebookApp] 404 GET /nbextensions/nbextensions_configurator/tree_tab/main.js?v=20160906202221 (::1) 1.43ms referer=http://localhost:8889/tree/deliver | |
| [I 20:22:32.394 NotebookApp] Copying deliver/01-Tips-and-tricks.ipynb to /deliver |
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My
install-log.bash: