From #bioc-builds > Books now being built on macOS in devel? @ 馃挰
The timeout happens in OSCA.workflows in the hca-bone-marrow.Rmd chapter in the integration chunk when batchelor::fastMNN() is called. This call spans five R processes that use 14.1g each and the load falls to < 1. So it looks like batchelor::fastMNN() gets stuck, but it's stuck doing what? It doesn't seem to be I/O. This only happens with openblas-openmp. I want to investigate this more. Note that this indirectly causes the timeouts you see for the other sub-books (OSCA.basic, OSCA.multisample and *OSCA.advanced) because for all of them rebook::preCompileBook() gets stuck waiting for OSCA.workflows to compute and cache the stuff that they need in order to proceed.
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```{r integration} |
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library(batchelor) |
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library(BiocNeighbors) |
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set.seed(1010001) |
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merged.bone <- fastMNN(sce.bone, batch = sce.bone$Donor, subset.row = top.bone, |
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BSPARAM=BiocSingular::RandomParam(deferred = TRUE), |
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BNPARAM=AnnoyParam(), |
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BPPARAM=bpp) |
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reducedDim(sce.bone, 'MNN') <- reducedDim(merged.bone, 'corrected') |
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``` |
From #bioc-builds > Books now being built on macOS in devel? @ 馃挰
OSCA.workflows/inst/book/hca-bone-marrow.Rmd
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