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cgat-developers / cgat-flow

cgat-flow repository
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Update .travis.yml for xvfb and re-order conda channels #105

Closed sebastian-luna-valero closed 5 years ago

sebastian-luna-valero commented 5 years ago

Travis has changed the default Ubuntu from Trusty to Xenial, which changed the way xvfb works, and I have updated .travis.yml accordingly; https://docs.travis-ci.com/user/gui-and-headless-browsers/#using-xvfb-to-run-tests-that-require-a-gui

On the other hand, conda's dependency resolution were causing Linux builds to time out. In my opinion, this is due to the change introduced in https://github.com/cgat-developers/cgat-flow/pull/99 and I have reverted that change to reset the recommended channel order.

The remaining issue is the Exception: Buffer for this type not yet supported, which seems to be explained here: https://bitbucket.org/rpy2/rpy2/issues/572/valueerror-buffer-for-this-type-not-yet

The solution would be either to pin numpy and rpy2, or to wait for new versions of rpy2 to be uploaded to conda-forge. Any preferences?

Also, skipping the tests for pipeline_splicing seems to help. For some reason I have in my mind pipeline_splicing was not Py3 ready? Could someone confirm, please?

Acribbs commented 5 years ago

Thanks @sebastian-luna-valero! I think skipping tests at the moment would be the best option as there are a bunch of python scripts associated with DEXSeq that are python 2 only. It doesn't seem like there is even a GitHub page to raise an issue as its quite an old project.

When the next version of rpy2 is released we can remove the skipping.