Closed ycl6 closed 3 years ago
Hi, I encounter an error that is similar to the one I reported in scater's repo when I ran emptyDrops.
emptyDrops
Error in .local(x, ...): cluster already started Traceback: 1. emptyDrops(mat, BPPARAM = bpp) 2. emptyDrops(mat, BPPARAM = bpp) 3. .local(m, ...) 4. testEmptyDrops(m, lower = lower, round = FALSE, test.ambient = test.ambient, . ..., BPPARAM = BPPARAM) 5. bpstart(BPPARAM) 6. bpstart(BPPARAM) 7. .local(x, ...) 8. stop("cluster already started") Error in serialize(data, node$con, xdr = FALSE): ignoring SIGPIPE signal Traceback: 1. emptyDrops(mat, BPPARAM = bpp) 2. emptyDrops(mat, BPPARAM = bpp) 3. .local(m, ...) 4. bpstop(BPPARAM) 5. bpstop(BPPARAM) 6. .bpstop_impl(x) 7. .bpstop_nodes(x) 8. .send_to(cluster, i, .DONE()) 9. .send_to(cluster, i, .DONE()) 10. parallel:::sendData(backend[[node]], value) 11. sendData.SOCK0node(backend[[node]], value) 12. serialize(data, node$con, xdr = FALSE)
I noticed in the source codes
https://github.com/MarioniLab/DropletUtils/blob/71296b6021fc04edf257309c9858dbbc150cf9e2/R/emptyDrops.R#L190
and
https://github.com/MarioniLab/DropletUtils/blob/71296b6021fc04edf257309c9858dbbc150cf9e2/R/emptyDrops.R#L370
probably should be like below as LTLA pointed out in my original issue in scater
if (.bpNotSharedOrUp(BPPARAM)) {
Thanks, fixed.
Hi, I encounter an error that is similar to the one I reported in scater's repo when I ran
emptyDrops
.I noticed in the source codes
https://github.com/MarioniLab/DropletUtils/blob/71296b6021fc04edf257309c9858dbbc150cf9e2/R/emptyDrops.R#L190
and
https://github.com/MarioniLab/DropletUtils/blob/71296b6021fc04edf257309c9858dbbc150cf9e2/R/emptyDrops.R#L370
probably should be like below as LTLA pointed out in my original issue in scater