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ResolvePackageNotFound causing Binder launch to fail

See original GitHub issue

Every time I try to launch my repo via (or the auto-generated badge I put into the README file) using my conda environment.yml config file, I seem to hit a wall at step 39/44 with the error The command '/bin/sh -c conda env update -n root -f "environment.yml" && conda clean -tipsy && conda list -n root' returned a non-zero code: 1

It seems like it’s not finding these packages, but most of them (e.g. pandas) are extremely common, so I doubt that’s the issue. Any help would be much appreciated! Here is the last piece of the Build Log that includes the referenced error message:

Step 39/44 : RUN conda env update -n root -f "environment.yml" && conda clean -tipsy && conda list -n root
 ---> Running in ebe9a67762e4
Solving environment: ...working... failed

  - jsonschema==2.6.0=py36hb385e00_0
  - libedit==3.1.20181209=hb402a30_0
  - tornado==5.1.1=py36h1de35cc_0
  - mistune==0.8.4=py36h1de35cc_0
  - readline==7.0=h1de35cc_5
  - markupsafe==1.1.1=py36h1de35cc_0
  - wcwidth==0.1.7=py36h8c6ec74_0
  - cryptography==2.5=py36ha12b0ac_0
  - libffi==3.2.1=h475c297_4
  - xz==5.2.4=h1de35cc_4
  - ncurses==6.1=h0a44026_1
  - python==3.6.8=haf84260_0
  - pyzmq==18.0.0=py36h0a44026_0
  - cffi==1.12.1=py36hb5b8e2f_0
  - traitlets==4.3.2=py36h65bd3ce_0
  - libsodium==1.0.16=h3efe00b_0
  - openssl==1.1.1b=h1de35cc_0
  - sqlite==3.26.0=ha441bb4_0
  - ipython_genutils==0.2.0=py36h241746c_0
  - nbformat==4.4.0=py36h827af21_0
  - tk==8.6.8=ha441bb4_0
  - yaml==0.1.7=hc338f04_2
  - zlib==1.2.11=h1de35cc_3
  - zeromq==4.3.1=h0a44026_3
  - nodejs==10.13.0=h0a44026_0
  - lxml==4.3.1=py36hef8c89e_0
  - libgfortran==3.0.1=h93005f0_2
  - libpng==1.6.36=ha441bb4_0
  - libxslt==1.1.33=h33a18ac_0
  - icu==58.2=h4b95b61_1
  - kiwisolver==1.0.1=py36h0a44026_0
  - libcxxabi==4.0.1=hcfea43d_1
  - mkl_fft==1.0.10=py36h5e564d8_0
  - scikit-learn==0.20.2=py36h27c97d8_0
  - libxml2==2.9.9=hab757c2_0
  - statsmodels==0.9.0=py36h1d22016_0
  - et_xmlfile==1.0.1=py36h1315bdc_0
  - libiconv==1.15=hdd342a3_7
  - freetype==2.9.1=hb4e5f40_0
  - numpy==1.15.4=py36hacdab7b_0
  - scipy==1.2.1=py36h1410ff5_0
  - mkl_random==1.0.2=py36h27c97d8_0
  - pyyaml==3.13=py36h1de35cc_0
  - numpy-base==1.15.4=py36h6575580_0
  - cycler==0.10.0=py36hfc81398_0
  - pandas==0.24.1=py36h0a44026_0
  - libcxx==4.0.1=hcfea43d_1
  - matplotlib==3.0.2=py36h54f8f79_0
  - appnope==0.1.0=py36hf537a9a_0

Removing intermediate container ebe9a67762e4
The command '/bin/sh -c conda env update -n root -f "environment.yml" && conda clean -tipsy && conda list -n root' returned a non-zero code: 1

Issue Analytics

  • State:closed
  • Created 5 years ago
  • Comments:12 (8 by maintainers)

github_iconTop GitHub Comments

emigre459commented, Mar 2, 2019

OK, using conda env export --no-builds -f environment.yml and removing the packages that are still causing issues with the build (reproduced below for reference) manually from the environment.yml file seemed to do the trick. Thank you both for your help!

In case it’s not specified elsewhere in the docs, I’d also note that I was using *.yaml as my file extension earlier and had to change it to *.yml for Binder. Maybe I’m uncommon in that regard, but it might be a good “gotcha” to also warn people about.

@choldgraf, I’m going to submit a pull request to modify the README for your conda repo to reflect this (and include the packages I removed, for OSX users to have a shortcut at least), and can use the same language for your conda-freeze repo if you like, @betatim. Just let me know if that’s useful. Regardless, I’m going to close this issue since I think we’ve hit upon the current solution, prior to a jupyter-repo2docker freeze command being developed.

  - libcxxabi=4.0.1
  - appnope=0.1.0
  - libgfortran=3.0.1
  - libcxx=4.0.1
choldgrafcommented, Mar 1, 2019

hey @emigre459 - it looks like you created your environment.yml file using conda. This actually creates a set of dependencies that are too specific. For example, many of those =py36xxxxx parts are OS-dependent etc. Can you try the same list but keeping the level specificity to version numbers?

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