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Tests involving Bioconductor objects #9

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DarwinAwardWinner opened this issue Dec 8, 2012 · 2 comments
Open

Tests involving Bioconductor objects #9

DarwinAwardWinner opened this issue Dec 8, 2012 · 2 comments

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@DarwinAwardWinner
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Currently all tests are using primitive vectors and/or lists. Since the goal is for the parallel functions to work on anything implementing c, [, and [[, we should add tests that work on Bioconductor vector-like classes, such as IRanges, SimpleList, GRangesList, and XStringSet, etc.

Issues to be addressed:

  • How can we use a package in a test without making BiocParallel depend on that package?
  • We should benchmark to see what kind of speedup is achieved with various backends. For a big complex object like GRanges, there might be a lot of overhead from transferring data between workers, as well as the splitting and joining operations. This wouldn't be part of the normal tests though.
@DarwinAwardWinner
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@ttriche here's the test issue. Feel free to add any self-contained test code that illustrates a use case.

@DarwinAwardWinner
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Here's an example test: 54cec90

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