Running ‘testthat.R’ [4s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RDML)
  > 
  > test_check("RDML")
  ── 1. Error: RDML can be created from BioRad .rdml (@test_rdml_new.R#7)  ───────
  LOGICAL() can only be applied to a 'logical', not a 'unknown type #12'
  1: RDML$new(filename) at testthat/test_rdml_new.R:7
  2: .subset2(public_bind_env, "initialize")(...)
  3: fromRDML()
  4: list.map(rdml.doc %>>% xml_find_all("/rdml:rdml/rdml:id", rdml.env$ns), id ~ rdmlIdType$new(publisher = getTextValue(tree = id, 
         path = "./rdml:publisher"), serialNumber = getTextValue(tree = id, path = "./rdml:serialNumber"), 
         MD5Hash = getTextValue(tree = id, path = "./rdml:MD5Hash"))) %>>% list.names(.$publisher)
  5: list.map(rdml.doc %>>% xml_find_all("/rdml:rdml/rdml:id", rdml.env$ns), id ~ rdmlIdType$new(publisher = getTextValue(tree = id, 
         path = "./rdml:publisher"), serialNumber = getTextValue(tree = id, path = "./rdml:serialNumber"), 
         MD5Hash = getTextValue(tree = id, path = "./rdml:MD5Hash")))
  6: list.map.internal(.data, substitute(expr), parent.frame())
  7: map(fun, list(.data, .data, seq_along(.data), xnames))
  8: .mapply(f, dots, more)
  9: (function (.data, id, .i, .name) 
     {
         eval(.expr, .evalwith(.data), environment())
     })(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], dots[[4L]][[1L]])
  10: eval(.expr, .evalwith(.data), environment())
  11: eval(.expr, .evalwith(.data), environment())
  12: rdmlIdType$new(publisher = getTextValue(tree = id, path = "./rdml:publisher"), serialNumber = getTextValue(tree = id, 
         path = "./rdml:serialNumber"), MD5Hash = getTextValue(tree = id, path = "./rdml:MD5Hash"))
  13: .subset2(public_bind_env, "initialize")(...)
  14: (function (MD5Hash) 
     {
         if (missing(MD5Hash)) 
             return(private$.MD5Hash)
         assert(checkNull(MD5Hash), checkString(MD5Hash))
         private$.MD5Hash <- MD5Hash
     })(.Primitive("quote")(""))
  15: assert(checkNull(MD5Hash), checkString(MD5Hash))
  16: assertChoice(combine, c("or", "and"))
  17: checkChoice(x, choices, null.ok, fmatch)
  18: qassert(null.ok, "B1")
  
  
   *** caught segfault ***
  address 8, cause 'memory not mapped'
  
  Traceback:
   1: qassert(classes, "S+")
   2: checkClass(x, classes, ordered, null.ok)
   3: assertClass(id, "idType")
   4: (function (id) {    if (missing(id))         return(private$.id)    assertClass(id, "idType")    private$.id <- id})(.Primitive("quote")(<environment>))
   5: .subset2(public_bind_env, "initialize")(...)
   6: sampleType$new(id = idType$new(id), description = getTextValue(sample,     "./rdml:description"), documentation = lapply(sample %>>%     xml_find_all("./rdml:documentation", rdml.env$ns), function(doc) genIdRef(doc)),     xRef = list.map(sample %>>% xml_find_all("./rdml:xRef", rdml.env$ns),         xRef ~ xRefType$new(name = getTextValue(xRef, "./rdml:name"),             id = getTextValue(xRef, "./rdml:id"))), annotation = c(list.map(sample %>>%         xml_find_all("./rdml:annotation", rdml.env$ns), annotation ~         annotationType$new(property = getTextValue(annotation,             "./rdml:property"), value = getTextValue(annotation,             "./rdml:value"))), if (!is.null(conditions.sep)) {        val <- gsub(sprintf("^.*%s(.*)$", conditions.sep), "\\1",             id)        if (length(val) != 0) {            annotationType$new(property = "condition", value = val)        }    }), type = sampleTypeType$new(type), interRunCalibrator = getLogicalValue(sample,         "./rdml:interRunCalibrator"), quantity = tryCatch(quantityType$new(value = getNumericValue(sample,         "./rdml:quantity/rdml:value"), unit = quantityUnitType$new(getTextValue(sample,         "./rdml:quantity/rdml:unit"))), error = function(e) NULL),     calibratorSample = getLogicalValue(sample, "./rdml:calibaratorSample"),     cdnaSynthesisMethod = cdnaSynthesisMethodType$new(enzyme = getTextValue(sample,         "./rdml:cdnaSynthesisMethod/rdml:enzyme"), primingMethod = primingMethodType$new(getTextValue(sample,         "./rdml:cdnaSynthesisMethod/rdml:primingMethod")), dnaseTreatment = getLogicalValue(sample,         "./rdml:cdnaSynthesisMethod/rdml:dnaseTreatment"), thermalCyclingConditions = tryCatch(genIdRef(xml_find_first(sample,         "./rdml:cdnaSynthesisMethod/rdml:thermalCyclingConditions",         ns = rdml.env$ns)), error = function(e) NULL)), templateQuantity = tryCatch(templateQuantityType$new(conc = getNumericValue(sample,         "./rdml:templateQuantity/rdml:conc"), nucleotide = nucleotideType$new(getTextValue(sample,         "./rdml:templateQuantity/rdml:nucleotide"))), error = function(e) NULL))
   7: eval(.expr, .evalwith(.data), environment())
   8: eval(.expr, .evalwith(.data), environment())
   9: (function (.data, sample, .i, .name) {    eval(.expr, .evalwith(.data), environment())})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], dots[[4L]][[1L]])
  10: .mapply(f, dots, more)
  11: map(fun, list(.data, .data, seq_along(.data), xnames))
  12: list.map.internal(.data, substitute(expr), parent.frame())
  13: list.map(rdml.doc %>>% xml_find_all("/rdml:rdml/rdml:sample",     rdml.env$ns), sample ~ {    type <- getTextValue(sample, "./rdml:type")    if (type == "ntp")         return(NULL)    id <- xml_attr(sample, "id")    sampleType$new(id = idType$new(id), description = getTextValue(sample,         "./rdml:description"), documentation = lapply(sample %>>%         xml_find_all("./rdml:documentation", rdml.env$ns), function(doc) genIdRef(doc)),         xRef = list.map(sample %>>% xml_find_all("./rdml:xRef",             rdml.env$ns), xRef ~ xRefType$new(name = getTextValue(xRef,             "./rdml:name"), id = getTextValue(xRef, "./rdml:id"))),         annotation = c(list.map(sample %>>% xml_find_all("./rdml:annotation",             rdml.env$ns), annotation ~ annotationType$new(property = getTextValue(annotation,             "./rdml:property"), value = getTextValue(annotation,             "./rdml:value"))), if (!is.null(conditions.sep)) {            val <- gsub(sprintf("^.*%s(.*)$", conditions.sep),                 "\\1", id)            if (length(val) != 0) {                annotationType$new(property = "condition", value = val)            }        }), type = sampleTypeType$new(type), interRunCalibrator = getLogicalValue(sample,             "./rdml:interRunCalibrator"), quantity = tryCatch(quantityType$new(value = getNumericValue(sample,             "./rdml:quantity/rdml:value"), unit = quantityUnitType$new(getTextValue(sample,             "./rdml:quantity/rdml:unit"))), error = function(e) NULL),         calibratorSample = getLogicalValue(sample, "./rdml:calibaratorSample"),         cdnaSynthesisMethod = cdnaSynthesisMethodType$new(enzyme = getTextValue(sample,             "./rdml:cdnaSynthesisMethod/rdml:enzyme"), primingMethod = primingMethodType$new(getTextValue(sample,             "./rdml:cdnaSynthesisMethod/rdml:primingMethod")),             dnaseTreatment = getLogicalValue(sample, "./rdml:cdnaSynthesisMethod/rdml:dnaseTreatment"),             thermalCyclingConditions = tryCatch(genIdRef(xml_find_first(sample,                 "./rdml:cdnaSynthesisMethod/rdml:thermalCyclingConditions",                 ns = rdml.env$ns)), error = function(e) NULL)),         templateQuantity = tryCatch(templateQuantityType$new(conc = getNumericValue(sample,             "./rdml:templateQuantity/rdml:conc"), nucleotide = nucleotideType$new(getTextValue(sample,             "./rdml:templateQuantity/rdml:nucleotide"))), error = function(e) NULL))})
  14: list.map(rdml.doc %>>% xml_find_all("/rdml:rdml/rdml:sample",     rdml.env$ns), sample ~ {    type <- getTextValue(sample, "./rdml:type")    if (type == "ntp")         return(NULL)    id <- xml_attr(sample, "id")    sampleType$new(id = idType$new(id), description = getTextValue(sample,         "./rdml:description"), documentation = lapply(sample %>>%         xml_find_all("./rdml:documentation", rdml.env$ns), function(doc) genIdRef(doc)),         xRef = list.map(sample %>>% xml_find_all("./rdml:xRef",             rdml.env$ns), xRef ~ xRefType$new(name = getTextValue(xRef,             "./rdml:name"), id = getTextValue(xRef, "./rdml:id"))),         annotation = c(list.map(sample %>>% xml_find_all("./rdml:annotation",             rdml.env$ns), annotation ~ annotationType$new(property = getTextValue(annotation,             "./rdml:property"), value = getTextValue(annotation,             "./rdml:value"))), if (!is.null(conditions.sep)) {            val <- gsub(sprintf("^.*%s(.*)$", conditions.sep),                 "\\1", id)            if (length(val) != 0) {                annotationType$new(property = "condition", value = val)            }        }), type = sampleTypeType$new(type), interRunCalibrator = getLogicalValue(sample,             "./rdml:interRunCalibrator"), quantity = tryCatch(quantityType$new(value = getNumericValue(sample,             "./rdml:quantity/rdml:value"), unit = quantityUnitType$new(getTextValue(sample,             "./rdml:quantity/rdml:unit"))), error = function(e) NULL),         calibratorSample = getLogicalValue(sample, "./rdml:calibaratorSample"),         cdnaSynthesisMethod = cdnaSynthesisMethodType$new(enzyme = getTextValue(sample,             "./rdml:cdnaSynthesisMethod/rdml:enzyme"), primingMethod = primingMethodType$new(getTextValue(sample,             "./rdml:cdnaSynthesisMethod/rdml:primingMethod")),             dnaseTreatment = getLogicalValue(sample, "./rdml:cdnaSynthesisMethod/rdml:dnaseTreatment"),             thermalCyclingConditions = tryCatch(genIdRef(xml_find_first(sample,                 "./rdml:cdnaSynthesisMethod/rdml:thermalCyclingConditions",                 ns = rdml.env$ns)), error = function(e) NULL)),         templateQuantity = tryCatch(templateQuantityType$new(conc = getNumericValue(sample,             "./rdml:templateQuantity/rdml:conc"), nucleotide = nucleotideType$new(getTextValue(sample,             "./rdml:templateQuantity/rdml:nucleotide"))), error = function(e) NULL))}) %>>% list.filter(!is.null(.))
  15: list.map(rdml.doc %>>% xml_find_all("/rdml:rdml/rdml:sample",     rdml.env$ns), sample ~ {    type <- getTextValue(sample, "./rdml:type")    if (type == "ntp")         return(NULL)    id <- xml_attr(sample, "id")    sampleType$new(id = idType$new(id), description = getTextValue(sample,         "./rdml:description"), documentation = lapply(sample %>>%         xml_find_all("./rdml:documentation", rdml.env$ns), function(doc) genIdRef(doc)),         xRef = list.map(sample %>>% xml_find_all("./rdml:xRef",             rdml.env$ns), xRef ~ xRefType$new(name = getTextValue(xRef,             "./rdml:name"), id = getTextValue(xRef, "./rdml:id"))),         annotation = c(list.map(sample %>>% xml_find_all("./rdml:annotation",             rdml.env$ns), annotation ~ annotationType$new(property = getTextValue(annotation,             "./rdml:property"), value = getTextValue(annotation,             "./rdml:value"))), if (!is.null(conditions.sep)) {            val <- gsub(sprintf("^.*%s(.*)$", conditions.sep),                 "\\1", id)            if (length(val) != 0) {                annotationType$new(property = "condition", value = val)            }        }), type = sampleTypeType$new(type), interRunCalibrator = getLogicalValue(sample,             "./rdml:interRunCalibrator"), quantity = tryCatch(quantityType$new(value = getNumericValue(sample,             "./rdml:quantity/rdml:value"), unit = quantityUnitType$new(getTextValue(sample,             "./rdml:quantity/rdml:unit"))), error = function(e) NULL),         calibratorSample = getLogicalValue(sample, "./rdml:calibaratorSample"),         cdnaSynthesisMethod = cdnaSynthesisMethodType$new(enzyme = getTextValue(sample,             "./rdml:cdnaSynthesisMethod/rdml:enzyme"), primingMethod = primingMethodType$new(getTextValue(sample,             "./rdml:cdnaSynthesisMethod/rdml:primingMethod")),             dnaseTreatment = getLogicalValue(sample, "./rdml:cdnaSynthesisMethod/rdml:dnaseTreatment"),             thermalCyclingConditions = tryCatch(genIdRef(xml_find_first(sample,                 "./rdml:cdnaSynthesisMethod/rdml:thermalCyclingConditions",                 ns = rdml.env$ns)), error = function(e) NULL)),         templateQuantity = tryCatch(templateQuantityType$new(conc = getNumericValue(sample,             "./rdml:templateQuantity/rdml:conc"), nucleotide = nucleotideType$new(getTextValue(sample,             "./rdml:templateQuantity/rdml:nucleotide"))), error = function(e) NULL))}) %>>% list.filter(!is.null(.)) %>>% list.names(.$id$id)
  16: fromRDML()
  17: .subset2(public_bind_env, "initialize")(...)
  18: RDML$new(filename)
  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(desc, code, env = parent.frame())
  30: test_that("RDML can be created from StepOne .rdml", {    filename <- paste0(PATH, "/extdata/", "stepone_std.rdml")    rdml <- RDML$new(filename)    expect_class(rdml, "RDML")})
  31: eval(code, test_env)
  32: eval(code, test_env)
  33: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  34: doTryCatch(return(expr), name, parentenv, handler)
  35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  36: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  37: doTryCatch(return(expr), name, parentenv, handler)
  38: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  39: tryCatchList(expr, classes, parentenv, handlers)
  40: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  41: test_code(NULL, exprs, env)
  42: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  43: force(code)
  44: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        end_context()    })
  45: FUN(X[[i]], ...)
  46: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  47: force(code)
  48: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  49: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  50: 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)
  51: 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)
  52: test_check("RDML")
  An irrecoverable exception occurred. R is aborting now ...