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bioc version #3

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kmsteinberg opened this Issue Dec 5, 2018 · 7 comments

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kmsteinberg commented Dec 5, 2018

Hi Jake,

I think the bioc issue from kindred also affects pubrunner:

pip install pubrunner
Collecting pubrunner
  Using cached https://files.pythonhosted.org/packages/cb/2e/f4c4efccacea847f0f61eb1adcf871983a61185daaa4cb5e86972698dedd/pubrunner-0.5.1.tar.gz
Collecting six (from pubrunner)
  Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting gitpython (from pubrunner)
  Using cached https://files.pythonhosted.org/packages/fe/e5/fafe827507644c32d6dc553a1c435cdf882e0c28918a5bab29f7fbebfb70/GitPython-2.1.11-py2.py3-none-any.whl
Collecting pyyaml (from pubrunner)
  Using cached https://files.pythonhosted.org/packages/9e/a3/1d13970c3f36777c583f136c136f804d70f500168edc1edea6daa7200769/PyYAML-3.13.tar.gz
Collecting wget (from pubrunner)
  Using cached https://files.pythonhosted.org/packages/47/6a/62e288da7bcda82b935ff0c6cfe542970f04e29c756b0e147251b2fb251f/wget-3.2.zip
Collecting requests (from pubrunner)
  Using cached https://files.pythonhosted.org/packages/ff/17/5cbb026005115301a8fb2f9b0e3e8d32313142fe8b617070e7baad20554f/requests-2.20.1-py2.py3-none-any.whl
Collecting ftputil (from pubrunner)
  Using cached https://files.pythonhosted.org/packages/0d/ab/8e5cc3199b16c37d926b5d8091fbaf9b2734a7b2c5579ee96d063f319a2a/ftputil-3.4.tar.gz
Collecting bioc==1.2.2 (from pubrunner)
  Could not find a version that satisfies the requirement bioc==1.2.2 (from pubrunner) (from versions: 1.0.dev22, 1.0.dev23, 1.0.dev24, 1.0.dev25, 1.0.dev27, 1.0.dev28, 1.0.dev29, 1.0.dev30, 1.0.dev31, 1.0.dev32, 1.0, 1.1.dev1, 1.1.dev2, 1.1.dev3, 1.2.3, 1.2.4, 1.3, 1.3.1)
No matching distribution found for bioc==1.2.2 (from pubrunner)

Thanks,
Karyn

jakelever added a commit that referenced this issue Dec 6, 2018

@jakelever jakelever self-assigned this Dec 6, 2018

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jakelever commented Dec 6, 2018

Nice catch. I've added a cronjob to Travis to try to spot these changes and I've updated the dependencies. Try upgrading pubrunner to v0.5.2 and see if that works.

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kmsteinberg commented Dec 7, 2018

Hi Jake,

I am having some issues installing pubrunner v0.5.2. I have to run setup.py because my default python is 2.7. Here is the error:

Installed /work/testdata/biomarker/kmeltzst_test/lib/python3.6/site-packages/pubrunner-0.5.2-py3.6.egg
Processing dependencies for pubrunner==0.5.2
Searching for jsonschema
Reading https://pypi.python.org/simple/jsonschema/
Downloading https://files.pythonhosted.org/packages/47/e1/afd760aa29665e61142811ef6ea8b8f79e43574ac8427473a11f6e918a10/jsonschema-3.0.0a3.tar.gz#sha256=dfd8426040892c8d0ef6da574085f282569f189cb24b70091a66c21c12d6705e
Best match: jsonschema 3.0.0a3
Processing jsonschema-3.0.0a3.tar.gz
Writing /tmp/easy_install-pvsjvlwr/jsonschema-3.0.0a3/setup.cfg
Running jsonschema-3.0.0a3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-pvsjvlwr/jsonschema-3.0.0a3/egg-dist-tmp-xlyxpsra
/opt/python/current/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'use_scm_version'
  warnings.warn(msg)
warning: install_lib: 'build/lib' does not exist -- no Python modules to install

zip_safe flag not set; analyzing archive contents...
Removing /work/testdata/biomarker/kmeltzst_test/lib/python3.6/site-packages/UNKNOWN-0.0.0-py3.6.egg
Moving UNKNOWN-0.0.0-py3.6.egg to /work/testdata/biomarker/kmeltzst_test/lib/python3.6/site-packages
UNKNOWN 0.0.0 is already the active version in easy-install.pth

Installed /work/testdata/biomarker/kmeltzst_test/lib/python3.6/site-packages/UNKNOWN-0.0.0-py3.6.egg
error: The 'jsonschema' distribution was not found and is required by snakemake
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jakelever commented Dec 7, 2018

Hi, unfortunately PubRunner can only work with Python 3. This is due to Snakemake (which PubRunner makes heavy use of) requiring Python 3. There should have been an error message on install so I'll investigate why that didn't appear. Let me know if you need any help getting it working with Python 3.

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kmsteinberg commented Dec 7, 2018

Hi,

Sorry I should have been more specific. I have python3.6 but it just isn't my system's default python version (and, sadly, I am not root).

So I cloned the git repo and ran python3.6 pubrunner/setup.py install --prefix /work/testdata/biomarker/kmeltzst_test/python3.6/. That was when I got the above jsonschema error.

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jakelever commented Dec 8, 2018

Hmm. I'll have to dig into this as I've only tested installation through pip. Unfortunately I'm away from a computer for a few days so can't do much at the moment.

You could try setting up Python 3.6 using virtualenv so that python and pip point to v3 versions. Example commands below:

  • pip install virtualenv
  • virtualenv -p python3.6 py3
  • source py3/bin/activate
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kmsteinberg commented Dec 10, 2018

Great--thanks, Jake. I am new to both text mining and python so I appreciate the assistance!

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jakelever commented Dec 11, 2018

Excellent. Let me know if there are any more issues.

@jakelever jakelever closed this Dec 18, 2018

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