Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("adjclust")
  > 
  > test_check("adjclust")
  
   *** caught segfault ***
  address 0x559bf191e568, cause 'memory not mapped'
  
  Traceback:
   1: ..getNamespace(c("methods", "4.3.0"), "<unknown>")
   2: (function (n) {    if (existsInFrame(n, envenv))         envenv[[n]]    else {        e <- mkenv()        envenv[[n]] <- e        key <- env[[n]]        ekey <- if (is.list(key))             key$eagerKey        else key        data <- lazyLoadDBfetch(ekey, datafile, compressed, envhook)        parent.env(e) <- if (!is.null(data$enclos))             data$enclos        else emptyenv()        list2env(data$bindings, e)        if (!is.null(data$attributes))             attributes(e) <- data$attributes        if (!is.null(data$isS4) && data$isS4)             .Internal(setS4Object(e, TRUE, TRUE))        if (is.list(key)) {            expr <- quote(lazyLoadDBfetch(KEY, datafile, compressed,                 envhook))            .Internal(makeLazy(names(key$lazyKeys), key$lazyKeys,                 expr, parent.env(environment()), e))        }        if (!is.null(data$locked) && data$locked)             .Internal(lockEnvironment(e, FALSE))        e    }})("env::52")
   3: (function (n) {    if (existsInFrame(n, envenv))         envenv[[n]]    else {        e <- mkenv()        envenv[[n]] <- e        key <- env[[n]]        ekey <- if (is.list(key))             key$eagerKey        else key        data <- lazyLoadDBfetch(ekey, datafile, compressed, envhook)        parent.env(e) <- if (!is.null(data$enclos))             data$enclos        else emptyenv()        list2env(data$bindings, e)        if (!is.null(data$attributes))             attributes(e) <- data$attributes        if (!is.null(data$isS4) && data$isS4)             .Internal(setS4Object(e, TRUE, TRUE))        if (is.list(key)) {            expr <- quote(lazyLoadDBfetch(KEY, datafile, compressed,                 envhook))            .Internal(makeLazy(names(key$lazyKeys), key$lazyKeys,                 expr, parent.env(environment()), e))        }        if (!is.null(data$locked) && data$locked)             .Internal(lockEnvironment(e, FALSE))        e    }})("env::51")
   4: (function (n) {    if (existsInFrame(n, envenv))         envenv[[n]]    else {        e <- mkenv()        envenv[[n]] <- e        key <- env[[n]]        ekey <- if (is.list(key))             key$eagerKey        else key        data <- lazyLoadDBfetch(ekey, datafile, compressed, envhook)        parent.env(e) <- if (!is.null(data$enclos))             data$enclos        else emptyenv()        list2env(data$bindings, e)        if (!is.null(data$attributes))             attributes(e) <- data$attributes        if (!is.null(data$isS4) && data$isS4)             .Internal(setS4Object(e, TRUE, TRUE))        if (is.list(key)) {            expr <- quote(lazyLoadDBfetch(KEY, datafile, compressed,                 envhook))            .Internal(makeLazy(names(key$lazyKeys), key$lazyKeys,                 expr, parent.env(environment()), e))        }        if (!is.null(data$locked) && data$locked)             .Internal(lockEnvironment(e, FALSE))        e    }})("env::50")
   5: (function (n) {    if (existsInFrame(n, envenv))         envenv[[n]]    else {        e <- mkenv()        envenv[[n]] <- e        key <- env[[n]]        ekey <- if (is.list(key))             key$eagerKey        else key        data <- lazyLoadDBfetch(ekey, datafile, compressed, envhook)        parent.env(e) <- if (!is.null(data$enclos))             data$enclos        else emptyenv()        list2env(data$bindings, e)        if (!is.null(data$attributes))             attributes(e) <- data$attributes        if (!is.null(data$isS4) && data$isS4)             .Internal(setS4Object(e, TRUE, TRUE))        if (is.list(key)) {            expr <- quote(lazyLoadDBfetch(KEY, datafile, compressed,                 envhook))            .Internal(makeLazy(names(key$lazyKeys), key$lazyKeys,                 expr, parent.env(environment()), e))        }        if (!is.null(data$locked) && data$locked)             .Internal(lockEnvironment(e, FALSE))        e    }})("env::42")
   6: (function (n) {    if (existsInFrame(n, envenv))         envenv[[n]]    else {        e <- mkenv()        envenv[[n]] <- e        key <- env[[n]]        ekey <- if (is.list(key))             key$eagerKey        else key        data <- lazyLoadDBfetch(ekey, datafile, compressed, envhook)        parent.env(e) <- if (!is.null(data$enclos))             data$enclos        else emptyenv()        list2env(data$bindings, e)        if (!is.null(data$attributes))             attributes(e) <- data$attributes        if (!is.null(data$isS4) && data$isS4)             .Internal(setS4Object(e, TRUE, TRUE))        if (is.list(key)) {            expr <- quote(lazyLoadDBfetch(KEY, datafile, compressed,                 envhook))            .Internal(makeLazy(names(key$lazyKeys), key$lazyKeys,                 expr, parent.env(environment()), e))        }        if (!is.null(data$locked) && data$locked)             .Internal(lockEnvironment(e, FALSE))        e    }})("env::41")
   7: (function (n) {    if (existsInFrame(n, envenv))         envenv[[n]]    else {        e <- mkenv()        envenv[[n]] <- e        key <- env[[n]]        ekey <- if (is.list(key))             key$eagerKey        else key        data <- lazyLoadDBfetch(ekey, datafile, compressed, envhook)        parent.env(e) <- if (!is.null(data$enclos))             data$enclos        else emptyenv()        list2env(data$bindings, e)        if (!is.null(data$attributes))             attributes(e) <- data$attributes        if (!is.null(data$isS4) && data$isS4)             .Internal(setS4Object(e, TRUE, TRUE))        if (is.list(key)) {            expr <- quote(lazyLoadDBfetch(KEY, datafile, compressed,                 envhook))            .Internal(makeLazy(names(key$lazyKeys), key$lazyKeys,                 expr, parent.env(environment()), e))        }        if (!is.null(data$locked) && data$locked)             .Internal(lockEnvironment(e, FALSE))        e    }})("env::40")
   8: .updateMethodsInTable(fdef, where, attach)
   9: methods::cacheMetaData(ns, TRUE, ns)
  10: loadNamespace(package, lib.loc)
  11: doTryCatch(return(expr), name, parentenv, handler)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: tryCatchList(expr, classes, parentenv, handlers)
  14: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return && !quietly)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
  15: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,     warn.conflicts = warn.conflicts, quietly = quietly, mask.ok = mask.ok,     exclude = exclude, include.only = include.only, attach.required = attach.required)
  16: doTryCatch(return(expr), name, parentenv, handler)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: tryCatchList(expr, classes, parentenv, handlers)
  19: tryCatch(library(package, lib.loc = lib.loc, character.only = TRUE,     logical.return = TRUE, warn.conflicts = warn.conflicts, quietly = quietly,     mask.ok = mask.ok, exclude = exclude, include.only = include.only,     attach.required = attach.required), error = function(e) e)
  20: require("snpStats")
  21: check_snp()
  22: eval(code, test_env)
  23: eval(code, test_env)
  24: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  25: doTryCatch(return(expr), name, parentenv, handler)
  26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  27: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  28: doTryCatch(return(expr), name, parentenv, handler)
  29: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  30: tryCatchList(expr, classes, parentenv, handlers)
  31: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  32: test_code(desc, code, env = parent.frame(), reporter = reporter)
  33: test_that("snpClust gives results identical to those of adjclust 0.3.0",     {        check_snp()        pathname <- system.file("extdata", "res_adjclust_0.3.0.rds",             package = "adjclust")        prevfit <- readRDS(pathname)        data("ld.example", package = "snpStats")        h <- 100        ld.ceph <- snpStats::ld(ceph.1mb, depth = h, stats = "R.squared")        p <- ncol(ceph.1mb)        nSamples <- nrow(ceph.1mb)        h <- 100        ceph.1mb[4, 286]@.Data[1, 1] <- as.raw(3)        ld.ceph <- snpStats::ld(ceph.1mb, depth = h, stats = "R.squared",             symmetric = TRUE)        ld.ceph <- round(ld.ceph, digits = 10)        expect_identical(unname(diag(ld.ceph)), rep(0, p))        expect_message(snpClust(ld.ceph, h = 100), "Note: forcing the diagonal of the LD similarity matrix to be 1",             all = FALSE)        diag(ld.ceph) <- rep(1, p)        fit <- snpClust(ld.ceph, h = 100)        expect_equal(cumsum(fit$height), prevfit$height, tolerance = 1e-05)    })
  34: eval(code, test_env)
  35: eval(code, test_env)
  36: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  37: doTryCatch(return(expr), name, parentenv, handler)
  38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  39: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  40: doTryCatch(return(expr), name, parentenv, handler)
  41: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  42: tryCatchList(expr, classes, parentenv, handlers)
  43: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  44: test_code(NULL, exprs, env)
  45: source_file(path, env(env), wrap = wrap)
  46: FUN(X[[i]], ...)
  47: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  48: doTryCatch(return(expr), name, parentenv, handler)
  49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  50: tryCatchList(expr, classes, parentenv, handlers)
  51: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  52: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
  53: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package)
  54: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap, load_package = load_package, parallel = parallel)
  55: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  56: test_check("adjclust")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault