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From #bioc-builds > Books now being built on macOS in devel? @ 💬
The timeout happens in OSCA.workflows in the
hca-bone-marrow.Rmdchapter in theintegrationchunk whenbatchelor::fastMNN()is called. This call spans five R processes that use 14.1g each and the load falls to < 1. So it looks likebatchelor::fastMNN()gets stuck, but it's stuck doing what? It doesn't seem to be I/O. This only happens withopenblas-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 themrebook::preCompileBook()gets stuck waiting for OSCA.workflows to compute and cache the stuff that they need in order to proceed.
OSCA.workflows/inst/book/hca-bone-marrow.Rmd
Lines 111 to 122 in 9bb4528
| ```{r integration} | |
| library(batchelor) | |
| library(BiocNeighbors) | |
| set.seed(1010001) | |
| merged.bone <- fastMNN(sce.bone, batch = sce.bone$Donor, subset.row = top.bone, | |
| BSPARAM=BiocSingular::RandomParam(deferred = TRUE), | |
| BNPARAM=AnnoyParam(), | |
| BPPARAM=bpp) | |
| reducedDim(sce.bone, 'MNN') <- reducedDim(merged.bone, 'corrected') | |
| ``` |