Running 'testthat.R' [49s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library("testthat")
  > #library("vcfR")
  > #
  > #
  > test_check("vcfR")
  Loading required package: vcfR
  
     *****       ***   vcfR   ***       *****
     This is vcfR 1.8.0 
       browseVignettes('vcfR') # Documentation
       citation('vcfR') # Citation
     *****       *****      *****       *****
  
  Failed with error:  'ICU init failed: U_FILE_ACCESS_ERROR'
  -- 1. Failure: vcfR2genind works (@test_conversion.R#15)  ----------------------
  `my_genind` inherits from `matrix` not `genind`.
  
  -- 2. Error: vcfR2genlight works (@test_conversion.R#22)  ----------------------
  package or namespace load failed for 'adegenet' in inDL(x, as.logical(local), as.logical(now), ...):
   ICU init failed: U_FILE_ACCESS_ERROR
  1: suppressMessages(library(adegenet)) at testthat/test_conversion.R:22
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: library(adegenet)
  4: tryCatch({
         attr(package, "LibPath") <- which.lib.loc
         ns <- loadNamespace(package, lib.loc)
         env <- attachNamespace(ns, pos = pos, deps)
     }, error = function(e) {
         P <- if (!is.null(cc <- conditionCall(e))) 
             paste(" in", deparse(cc)[1L])
         else ""
         msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), 
             P, conditionMessage(e))
         if (logical.return) 
             message(paste("Error:", msg), domain = NA)
         else stop(msg, call. = FALSE, domain = NA)
     })
  5: tryCatchList(expr, classes, parentenv, handlers)
  6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7: value[[3L]](cond)
  8: stop(msg, call. = FALSE, domain = NA)
  
  -- 3. Error: vcfR2tidy works (@test_vcfRtidy.R#80)  ----------------------------
  ICU init failed: U_FILE_ACCESS_ERROR
  1: vcfR2tidy(vcf, info_only = FALSE) at testthat/test_vcfRtidy.R:80
  2: do.call(what = extract_info_tidy, args = info_dots)
  3: (function (x, info_fields = NULL, info_types = TRUE, info_sep = ";") 
     {
         if (!is.null(info_fields) && any(duplicated(info_fields))) 
             stop("Requesting extraction of duplicate info_field names")
         if (class(x) != "vcfR") 
             stop("Expecting x to be a vcfR object, not a ", class(x))
         vcf <- x
         x <- as.data.frame(x@fix, stringsAsFactors = FALSE) %>% tibble::as.tibble()
         if (is.null(info_fields)) {
             info_df <- vcfR::vcf_field_names(vcf, tag = "INFO")
             info_fields <- info_df$ID
         }
         if (!is.null(info_types) && length(info_types) == 1 && info_types[1] == TRUE) {
             info_df <- vcfR::vcf_field_names(vcf, tag = "INFO") %>% dplyr::filter_(~ID %in% 
                 info_fields)
             info_types <- guess_types(info_df)
         }
         ret <- stringr::str_split(string = x$INFO, pattern = info_sep) %>% lapply(function(x) {
             y <- stringr::str_split(x, pattern = "=", n = 2)
             vals <- unlist(lapply(y, function(z) z[2]))
             names(vals) <- unlist(lapply(y, function(z) z[1]))
             unname(vals[info_fields])
         }) %>% unlist
         if (is.null(ret)) {
             ret <- matrix(nrow = 0, ncol = length(info_fields), byrow = TRUE)
         }
         else {
             ret <- matrix(ret, ncol = length(info_fields), byrow = TRUE)
         }
         ret <- as.data.frame(ret, stringsAsFactors = FALSE) %>% setNames(info_fields) %>% 
             tibble::as.tibble()
         if (!is.null(info_types)) {
             ns <- info_types[!is.na(info_types) & info_types == "n"]
             is <- info_types[!is.na(info_types) & info_types == "i"]
             fs <- info_types[!is.na(info_types) & info_types == "f"]
             if (length(ns) > 0) {
                 ret[names(ns)] <- lapply(ret[names(ns)], as.numeric)
             }
             if (length(is) > 0) {
                 ret[names(is)] <- lapply(ret[names(is)], as.integer)
             }
             proc_flag <- function(x, INFO) {
                 x2 <- rep(FALSE, times = length(INFO))
                 x2[grep(x, INFO)] <- TRUE
                 x2
             }
             if (length(fs) > 0) {
                 ret[names(fs)] <- lapply(names(fs), proc_flag, x$INFO)
             }
         }
         if (nrow(ret) > 0) {
             ret <- cbind(Key = 1:nrow(ret), ret) %>% tibble::as.tibble()
         }
         else {
             ret <- cbind(Key = vector(mode = "integer", length = 0), ret) %>% tibble::as.tibble()
         }
         ret
     })(x = <S4 object of class structure("vcfR", package = "vcfR")>)
  4: stringr::str_split(string = x$INFO, pattern = info_sep) %>% lapply(function(x) {
         y <- stringr::str_split(x, pattern = "=", n = 2)
         vals <- unlist(lapply(y, function(z) z[2]))
         names(vals) <- unlist(lapply(y, function(z) z[1]))
         unname(vals[info_fields])
     }) %>% unlist
  5: eval(lhs, parent, parent)
  6: eval(lhs, parent, parent)
  7: stringr::str_split
  8: getExportedValue(pkg, name)
  9: asNamespace(ns)
  10: getNamespace(ns)
  11: tryCatch(loadNamespace(name), error = function(e) stop(e))
  12: tryCatchList(expr, classes, parentenv, handlers)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: value[[3L]](cond)
  
  -- 4. Error: extract_info_tidy works (@test_vcfRtidy.R#104)  -------------------
  ICU init failed: U_FILE_ACCESS_ERROR
  1: extract_info_tidy(vcf, info_fields = c("AC", "AN", "MQ"), info_types = c(AN = "i", 
         MQ = "n")) at testthat/test_vcfRtidy.R:104
  2: stringr::str_split(string = x$INFO, pattern = info_sep) %>% lapply(function(x) {
         y <- stringr::str_split(x, pattern = "=", n = 2)
         vals <- unlist(lapply(y, function(z) z[2]))
         names(vals) <- unlist(lapply(y, function(z) z[1]))
         unname(vals[info_fields])
     }) %>% unlist
  3: eval(lhs, parent, parent)
  4: eval(lhs, parent, parent)
  5: stringr::str_split
  6: getExportedValue(pkg, name)
  7: asNamespace(ns)
  8: getNamespace(ns)
  9: tryCatch(loadNamespace(name), error = function(e) stop(e))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  
  -- 5. Error: extract_info_tidy works with Flags (@test_vcfRtidy.R#116)  --------
  ICU init failed: U_FILE_ACCESS_ERROR
  1: extract_info_tidy(vcfR_test, info_types = TRUE) at testthat/test_vcfRtidy.R:116
  2: stringr::str_split(string = x$INFO, pattern = info_sep) %>% lapply(function(x) {
         y <- stringr::str_split(x, pattern = "=", n = 2)
         vals <- unlist(lapply(y, function(z) z[2]))
         names(vals) <- unlist(lapply(y, function(z) z[1]))
         unname(vals[info_fields])
     }) %>% unlist
  3: eval(lhs, parent, parent)
  4: eval(lhs, parent, parent)
  5: stringr::str_split
  6: getExportedValue(pkg, name)
  7: asNamespace(ns)
  8: getNamespace(ns)
  9: tryCatch(loadNamespace(name), error = function(e) stop(e))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  
  == testthat results  ===========================================================
  OK: 463 SKIPPED: 0 FAILED: 5
  1. Failure: vcfR2genind works (@test_conversion.R#15) 
  2. Error: vcfR2genlight works (@test_conversion.R#22) 
  3. Error: vcfR2tidy works (@test_vcfRtidy.R#80) 
  4. Error: extract_info_tidy works (@test_vcfRtidy.R#104) 
  5. Error: extract_info_tidy works with Flags (@test_vcfRtidy.R#116) 
  
  Error: testthat unit tests failed
  Execution halted