Load the data

Setting SC3 parameters...
Setting a range of k...
Calculating distances between the cells...
starting worker pid=9833 on localhost:11267 at 21:54:28.710
Loading required package: SC3
loaded SC3 and set parent environment
Loading required package: foreach
Loading required package: rngtools
Loading required package: pkgmaker
Loading required package: registry

Attaching package: ‘pkgmaker’

The following object is masked from ‘package:base’:

    isNamespaceLoaded

Performing transformations and calculating eigenvectors...
starting worker pid=9843 on localhost:11267 at 21:54:33.550
Loading required package: SC3
loaded SC3 and set parent environment

 *** caught segfault ***
address 0xee12000, cause 'memory not mapped'

Traceback:
 1: .Call("SC3_norm_laplacian", PACKAGE = "SC3", A)
 2: norm_laplacian(dists)
 3: transformation(get(hash.table[i, 1], dists), hash.table[i, 2])
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
 8: try({    tmp <- transformation(get(hash.table[i, 1], dists), hash.table[i,         2])    tmp[, 1:max(n_dim)]})
 9: eval(expr, envir, enclos)
10: eval(.doSnowGlobals$expr, envir = .doSnowGlobals$exportenv)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(eval(.doSnowGlobals$expr, envir = .doSnowGlobals$exportenv),     error = function(e) e)
15: (function (args) {    lapply(names(args), function(n) assign(n, args[[n]], pos = .doSnowGlobals$exportenv))    tryCatch(eval(.doSnowGlobals$expr, envir = .doSnowGlobals$exportenv),         error = function(e) e)})(quote(list(i = 4L)))
16: do.call(msg$data$fun, msg$data$args, quote = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(do.call(msg$data$fun, msg$data$args, quote = TRUE),     error = handler)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch({    msg <- recvData(master)    if (msg$type == "DONE") {        closeNode(master)        break    }    else if (msg$type == "EXEC") {        success <- TRUE        handler <- function(e) {            success <<- FALSE            structure(conditionMessage(e), class = c("snow-try-error",                 "try-error"))        }        t1 <- proc.time()        value <- tryCatch(do.call(msg$data$fun, msg$data$args,             quote = TRUE), error = handler)        t2 <- proc.time()        value <- list(type = "VALUE", value = value, success = success,             time = t2 - t1, tag = msg$data$tag)        msg <- NULL        sendData(master, value)        value <- NULL    }}, interrupt = function(e) NULL)
25: slaveLoop(makeSOCKmaster(master, port, timeout, useXDR))
26: parallel:::.slaveRSOCK()
An irrecoverable exception occurred. R is aborting now ...
Error in unserialize(socklist[[n]]) : error reading from connection

hemberg-lab / SC3

Error running sc3() - Error in unserialize(socklist[[n]]) : error reading from connection #33

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