Running ‘spelling.R’
  Running ‘testthat.R’ [71s/116s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bigsnpr)
  Loading required package: bigstatsr
  > 
  > for (k in 1:9)
  +   test_check("bigsnpr", filter = paste0(k, '-'))
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On Solaris (1)
  
  [ FAIL 0 | WARN 0 | SKIP 1 | PASS 223 ]
  
   *** caught segfault ***
  address f824013c, cause 'invalid permissions'
  
  Traceback:
   1: bed_clumping_chr(obj.bed, keep, ind_row = ind.row, ind_col = ind.chr,     center = center, scale = scale, ordInd = ord, rankInd = match(seq_along(ord),         ord), pos = pos.chr, size = size * 1000, thr = thr.r2,     ncores = ncores)
   2: bedClumpingChr(obj.bed, S, ind.chr, ind.row, size, infos.pos,     thr.r2, ncores)
   3: FUN(X[[i]], ...)
   4: lapply(split(ind.noexcl, infos.chr[ind.noexcl]), function(ind.chr) {    bedClumpingChr(obj.bed, S, ind.chr, ind.row, size, infos.pos,         thr.r2, ncores)})
   5: unlist(lapply(split(ind.noexcl, infos.chr[ind.noexcl]), function(ind.chr) {    bedClumpingChr(obj.bed, S, ind.chr, ind.row, size, infos.pos,         thr.r2, ncores)}), use.names = FALSE)
   6: sort(unlist(lapply(split(ind.noexcl, infos.chr[ind.noexcl]),     function(ind.chr) {        bedClumpingChr(obj.bed, S, ind.chr, ind.row, size, infos.pos,             thr.r2, ncores)    }), use.names = FALSE))
   7: bed_clumping(obj.bed, ind.row = ind.row, exclude = setdiff(cols_along(obj.bed),     ind.col), thr.r2 = thr.r2, size = size, ncores = ncores)
   8: bed_autoSVD(obj.bed, verbose = FALSE)
   9: eval_bare(expr, quo_get_env(quo))
  10: quasi_label(enquo(object), label, arg = "object")
  11: expect_is(obj.svd <- bed_autoSVD(obj.bed, verbose = FALSE), "big_SVD")
  12: eval(code, test_env)
  13: eval(code, test_env)
  14: 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)
  15: doTryCatch(return(expr), name, parentenv, handler)
  16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  17: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  18: doTryCatch(return(expr), name, parentenv, handler)
  19: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  20: tryCatchList(expr, classes, parentenv, handlers)
  21: 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) {    })
  22: test_code(desc, code, env = parent.frame(), reporter = reporter)
  23: test_that("bed_autoSVD() works", {    obj.bed <- bed(snp_writeBed(test, bedfile = tempfile(fileext = ".bed")))    expect_output(bed_autoSVD(obj.bed, thr.r2 = NA), "Skipping clumping.")    expect_is(obj.svd <- bed_autoSVD(obj.bed, verbose = FALSE),         "big_SVD")    expect_identical(attr(obj.svd, "lrldr"), LD.wiki34[0, 1:3])    skip_if(is_cran)    obj.svd2 <- bed_autoSVD(obj.bed, size = 5, verbose = FALSE)    expect_gt(length(attr(obj.svd2, "subset")), length(attr(obj.svd,         "subset")))    obj.svd4 <- bed_autoSVD(obj.bed, roll.size = 0, verbose = FALSE)    expect_lt(length(attr(obj.svd4, "subset")), length(attr(obj.svd,         "subset")))    obj.svd5 <- bed_autoSVD(obj.bed, thr.r2 = 1, roll.size = 0,         verbose = FALSE)    expect_gt(min(diag(cor(obj.svd5$u, obj.svd$u))[1:3]^2), 0.98)    obj.svd6 <- bed_autoSVD(obj.bed, thr.r2 = NA, roll.size = 0,         verbose = FALSE)    expect_equal(obj.svd6, obj.svd5)    obj.svd7 <- bed_autoSVD(obj.bed, alpha.tukey = 0.999, roll.size = 0,         verbose = FALSE)    expect_lt(length(attr(obj.svd7, "subset")), length(attr(obj.svd6,         "subset")))    expect_output(bed_autoSVD(obj.bed, alpha.tukey = 0.999999999,         roll.size = 0, verbose = TRUE), "Maximum number of iterations reached.")})
  24: eval(code, test_env)
  25: eval(code, test_env)
  26: 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)
  27: doTryCatch(return(expr), name, parentenv, handler)
  28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  30: doTryCatch(return(expr), name, parentenv, handler)
  31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  32: tryCatchList(expr, classes, parentenv, handlers)
  33: 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) {    })
  34: test_code(NULL, exprs, env)
  35: source_file(path, child_env(env), wrap = wrap)
  36: FUN(X[[i]], ...)
  37: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  38: force(code)
  39: doWithOneRestart(return(expr), restart)
  40: withOneRestart(expr, restarts[[1L]])
  41: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  42: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
  43: test_files(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)
  44: 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)
  45: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  46: test_check("bigsnpr", filter = paste0(k, "-"))
  An irrecoverable exception occurred. R is aborting now ...