Running ‘testthat.R’ [7s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("adjclust")
  > 
  > test_check("adjclust")
  
   *** caught segfault ***
  address 0x30, cause 'memory not mapped'
  
  Traceback:
   1: length(private$stack)
   2: self$skips$push(result)
   3: x$add_result(...)
   4: FUN(X[[i]], ...)
   5: lapply(objects, f)
   6: o_apply(self$reporters, "add_result", context = context, test = test,     result = result)
   7: reporter$add_result(context = reporter$.context, test = test,     result = e)
   8: register_expectation(e, debug_end)
   9: (function (e) {    handled <<- TRUE    debug_end <- if (inherits(e, "skip_empty"))         -1    else 2    register_expectation(e, debug_end)    signalCondition(e)})(list(message = "Reason: 'snpStats' package not available"))
  10: stop(cond)
  11: skip("'snpStats' package not available")
  12: check_snp()
  13: eval(code, test_env)
  14: eval(code, test_env)
  15: 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)
  16: doTryCatch(return(expr), name, parentenv, handler)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  19: doTryCatch(return(expr), name, parentenv, handler)
  20: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  21: tryCatchList(expr, classes, parentenv, handlers)
  22: 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) {    })
  23: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
  24: 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$height, tolerance = 1e-05)    })
  25: eval(code, test_env)
  26: eval(code, test_env)
  27: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  28: doTryCatch(return(expr), name, parentenv, handler)
  29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  31: doTryCatch(return(expr), name, parentenv, handler)
  32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  33: tryCatchList(expr, classes, parentenv, handlers)
  34: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  35: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  36: source_file(path, env = env(env), desc = desc, error_call = error_call)
  37: FUN(X[[i]], ...)
  38: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  39: doTryCatch(return(expr), name, parentenv, handler)
  40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  41: tryCatchList(expr, classes, parentenv, handlers)
  42: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  43: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  44: 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,     desc = desc, load_package = load_package, error_call = error_call)
  45: 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,     load_package = load_package, parallel = parallel)
  46: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  47: test_check("adjclust")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault