Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BioInstaller)
  > 
  > 
  > test_check("BioInstaller")
  cloning into '/tmp/Rtmp88FHKo/working_dir/Rtmpt3MuSz/github_demo0'...
  
   *** caught segfault ***
  address 0xc800010009, cause 'memory not mapped'
  
  Traceback:
   1: git2r::clone(github_url, destdir)
   2: git.download(name, download.dir, version, github_url, use_git2r,     recursive_clone, verbose)
   3: install.github(name = "github_demo", destdir = destdir, download.dir = destdir,     verbose = F)
   4: eval(code, test_env)
   5: eval(code, test_env)
   6: 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)
   7: doTryCatch(return(expr), name, parentenv, handler)
   8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  10: doTryCatch(return(expr), name, parentenv, handler)
  11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  12: tryCatchList(expr, classes, parentenv, handlers)
  13: 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) {    })
  14: test_code(desc, code, env = parent.frame())
  15: test_that("install.github", {    x <- tryCatch(RCurl::getURL("https://github.com"), error = function(e) {        message("Connect Github failed. Please check the network.")        NULL    })    if (!is.null(x)) {        destdir <- sprintf("%s/github_demo0", tempdir())        destdir <- normalizePath(destdir, "/", FALSE)        x <- install.github(name = "github_demo", destdir = destdir,             download.dir = destdir, verbose = F)        expect_that(x, equals(TRUE))        unlink(destdir, recursive = T, TRUE)        destdir <- sprintf("%s/github_demo1", tempdir())        destdir <- normalizePath(destdir, "/", FALSE)        x <- suppressWarnings(install.github(show.all.versions = T,             verbose = F))        expect_that(x, equals(FALSE))        destdir <- sprintf("%s/bwa", tempdir())        destdir <- normalizePath(destdir, "/", FALSE)        x <- install.github(name = "bwa", show.all.versions = T,             verbose = F)        expect_that(is.character(x), equals(TRUE))        unlink(destdir, recursive = T, TRUE)        x <- tryCatch(install.github(name = list(), show.all.versions = T,             verbose = F), error = function(e) {            return(FALSE)        })        expect_that(is.character(x), equals(FALSE))        unlink(destdir, recursive = T, TRUE)        destdir <- sprintf("%s/github_demo2", tempdir())        destdir <- normalizePath(destdir, "/", FALSE)        x <- install.github(name = "github_demo", destdir = destdir,             download.dir = destdir, verbose = F, download.only = TRUE)        expect_that(x, equals(TRUE))        unlink(destdir, recursive = T, TRUE)    }    else {        message("Please check RCurl::getURL('https://github.com')")    }})
  16: eval(code, test_env)
  17: eval(code, test_env)
  18: 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)
  19: doTryCatch(return(expr), name, parentenv, handler)
  20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  22: doTryCatch(return(expr), name, parentenv, handler)
  23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  24: tryCatchList(expr, classes, parentenv, handlers)
  25: 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) {    })
  26: test_code(NULL, exprs, env)
  27: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  28: force(code)
  29: doWithOneRestart(return(expr), restart)
  30: withOneRestart(expr, restarts[[1L]])
  31: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  32: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        reporter$start_file(basename(path))        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        reporter$.end_context()        reporter$end_file()    })
  33: FUN(X[[i]], ...)
  34: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  35: force(code)
  36: doWithOneRestart(return(expr), restart)
  37: withOneRestart(expr, restarts[[1L]])
  38: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  39: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  40: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  41: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  42: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  43: test_check("BioInstaller")
  An irrecoverable exception occurred. R is aborting now ...