User: peter.kharchenko

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Posts by peter.kharchenko

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Comment: C: S4Vectors masks/breaks regular Matrix functions
... I came to the same solution (explicitly qualifying the package). I see how promoting new functions to generics can cause problems. I have little experience with declaring generics, but thought there was a way to "append" new classes to an existing generic rather than overwrite it. Thanks for the exp ...
written 2.8 years ago by peter.kharchenko30
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Answer: A: S4Vectors masks/breaks regular Matrix functions
... I came to the same solution (explicitly qualifying the package). I see how promoting new functions to generics can cause problems. I have little experience with declaring generics, but thought there was a way to "append" new classes to an existing generic rather than overwrite it. Thanks for the exp ...
written 2.8 years ago by peter.kharchenko30
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S4Vectors masks/breaks regular Matrix functions
... Dear All,   Just wanted to point out that S4Vectors blocks regular Matrix package operations. Matrix is, perhaps, the most popular sparse matrix package for R, and it would be nice if S4Vectors (which is required by many/most of Bioconductor packages) wouldn't break it. Specific example of how mask ...
s4vectors matrix written 2.8 years ago by peter.kharchenko30
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BiocParallel::bplapply() performance issue
... We had to switch to using bplapply() and in the later version of the package started to encounter serious performance issues. Here's an example using low number of cores (workers): Here's evaluation of a simple function using lapply, mclapply and bplapply with one worker:  > system.time(lapply ...
biocparallel written 4.0 years ago by peter.kharchenko30 • updated 4.0 years ago by Martin Morgan ♦♦ 24k

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For BiocParallel::bplapply() performance issue

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