Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxonomizr)
  > library(data.table)
  > library(RSQLite)
  > test_check("taxonomizr")
  
   *** caught segfault ***
  address 0x6c, cause 'memory not mapped'
  
  Traceback:
   1: .C("taxaTrim", c(tmp, "/dev/full"), PACKAGE = "taxonomizr")
   2: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   3: withCallingHandlers({    code    NULL}, error = function(cnd) {    if (can_entrace(cnd)) {        cnd <- cnd_entrace(cnd)    }    return_from(env, cnd)})
   4: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),     ...)
   5: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
   6: expect_error(.C("taxaTrim", c(tmp, "/dev/full"), PACKAGE = "taxonomizr"),     "write")
   7: eval(code, test_env)
   8: eval(code, test_env)
   9: 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)
  10: doTryCatch(return(expr), name, parentenv, handler)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  13: doTryCatch(return(expr), name, parentenv, handler)
  14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  15: tryCatchList(expr, classes, parentenv, handlers)
  16: 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) {    })
  17: test_code(desc, code, env = parent.frame(), reporter = reporter)
  18: test_that("Test trimTaxa", {    expect_error(taxonomizr:::trimTaxa("NotARealFile", "test"),         "file")    expect_error(.C("taxaTrim", c("NotARealFile", "test"), PACKAGE = "taxonomizr"),         "file")    tmp <- tempfile()    out <- c("head\t1\t2\t3", "a\t2\t3\t4", "b\t3\t4\t5", "c\t4\t5\t6")    writeLines(out, tmp)    tmpDir <- tempfile()    dir.create(tmpDir)    expect_error(.C("taxaTrim", c(tmp, tmpDir), PACKAGE = "taxonomizr"),         "output file")    file.remove(tmpDir)    tmpPerm <- tempfile()    file.create(tmpPerm)    if (Sys.chmod(tmpPerm, "0000") && file.access(tmpPerm, 6) ==         -1 && any(class(tryCatch(readLines(tmpPerm), error = function(xx) xx)) ==         "error") && any(class(tryCatch(writeLines("ABC", tmpPerm),         error = function(xx) xx)) == "error")) {        expect_error(.C("taxaTrim", c(tmpPerm, tmp), PACKAGE = "taxonomizr"),             "input file")        expect_error(.C("taxaTrim", c(tmp, tmpPerm), PACKAGE = "taxonomizr"),             "output file")    }    file.remove(tmpPerm)    if (file.exists("/dev/full")) {        expect_error(.C("taxaTrim", c(tmp, "/dev/full"), PACKAGE = "taxonomizr"),             "write")        expect_error(taxonomizr:::trimTaxa(tmp, "/dev/full"),             "write")    }    tmp2 <- tempfile()    expect_error(taxonomizr:::trimTaxa(tmp, tmp2), NA)    expect_equal(readLines(tmp2), c("2\t3", "3\t4", "4\t5"))    writeLines(c(out, "1\t2\t3\t4\t5"), tmp)    expect_error(taxonomizr:::trimTaxa(tmp, tmp2), "line")    file.remove(tmp2)    tmp2 <- tempfile()    gzHandle <- gzfile(tmp)    writeLines(out, gzHandle)    close(gzHandle)    expect_error(taxonomizr:::trimTaxa(tmp, tmp2), NA)    expect_equal(readLines(tmp2), c("2\t3", "3\t4", "4\t5"))    file.remove(tmp2)    tmp2 <- tempfile()    expect_error(taxonomizr:::trimTaxa(tmp, tmp2, 2), NA)    expect_equal(readLines(tmp2), c("2", "3", "4"))    file.remove(tmp2)    tmp2 <- tempfile()    expect_error(taxonomizr:::trimTaxa(tmp, tmp2, c(2, 4)), NA)    expect_equal(readLines(tmp2), c("2\t4", "3\t5", "4\t6"))    expect_error(taxonomizr:::trimTaxa(tmp, tmp2, c(2, 4)), NA)    expect_equal(readLines(tmp2), rep(c("2\t4", "3\t5", "4\t6"),         2))    with_mock(`R.utils::gunzip` = function(...) {    }, expect_error(taxonomizr:::trimTaxa(tmp, tmp2), "unzip"))    out <- c("head\t1\t2\t3", "a\t2\t3\t4", "b\t3\t4\t5\tJUNK",         "c\t4\t5\t6")    writeLines(out, tmp)    expect_error(.C("taxaTrim", c(tmp, tmp2), PACKAGE = "taxonomizr"),         "Malformed.*3")    out <- c("head\t1\t2\t3", "a\t2\t3\t4", "b\t3\t4\t5", "c\t4\t5")    writeLines(out, tmp)    expect_error(.C("taxaTrim", c(tmp, tmp2), PACKAGE = "taxonomizr"),         "Malformed.*4")})
  19: eval(code, test_env)
  20: eval(code, test_env)
  21: 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)
  22: doTryCatch(return(expr), name, parentenv, handler)
  23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  25: doTryCatch(return(expr), name, parentenv, handler)
  26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  27: tryCatchList(expr, classes, parentenv, handlers)
  28: 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) {    })
  29: test_code(NULL, exprs, env)
  30: source_file(path, child_env(env), wrap = wrap)
  31: FUN(X[[i]], ...)
  32: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  33: doTryCatch(return(expr), name, parentenv, handler)
  34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  35: tryCatchList(expr, classes, parentenv, handlers)
  36: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  37: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
  38: 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)
  39: 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)
  40: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  41: test_check("taxonomizr")
  An irrecoverable exception occurred. R is aborting now ...