Running ‘test-all.R’ [8s/10s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(biofiles)
  Loading required package: Rcpp
  
  Attaching package: 'biofiles'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > test_check("biofiles")
  ── 1. Error: getSequence works for gbFeatures (@test-07-gbRecord.r#60)  ────────
  unable to find an inherited method for function 'windows' for signature '"DNAString"'
  1: getSequence(x) at testthat/test-07-gbRecord.r:60
  2: getSequence(x)
  3: .local(x, ...)
  4: .seq_access(x)
  5: merge_seq(seq, x, SEQFUN)
  6: XVector::subseq(x = seq, start = start(x), end = end(x))
  7: XVector::subseq(x = seq, start = start(x), end = end(x))
  8: narrow(x, start = start, end = end, width = width)
  9: narrow(x, start = start, end = end, width = width)
  10: mendoapply(narrow, x, start, end, width, MoreArgs = list(use.names = use.names))
  11: mapply(FUN, ..., MoreArgs = MoreArgs, SIMPLIFY = FALSE)
  12: standardGeneric("mapply")
  13: eval(mc, env)
  14: eval(mc, env)
  15: eval(mc, env)
  16: mapply(FUN = FUN, ..., MoreArgs = MoreArgs, SIMPLIFY = SIMPLIFY)
  17: (new("standardGeneric", .Data = function (x, start = NA, end = NA, width = NA, use.names = TRUE) 
     standardGeneric("narrow"), generic = structure("narrow", package = "IRanges"), package = "IRanges", 
         group = list(), valueClass = character(0), signature = "x", default = NULL, skeleton = (function (x, 
             start = NA, end = NA, width = NA, use.names = TRUE) 
         stop("invalid call in method dispatch to 'narrow' (no default method)", domain = NA))(x, 
             start, end, width, use.names)))(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], 
         dots[[4L]][[1L]], use.names = TRUE)
  18: (new("standardGeneric", .Data = function (x, start = NA, end = NA, width = NA, use.names = TRUE) 
     standardGeneric("narrow"), generic = structure("narrow", package = "IRanges"), package = "IRanges", 
         group = list(), valueClass = character(0), signature = "x", default = NULL, skeleton = (function (x, 
             start = NA, end = NA, width = NA, use.names = TRUE) 
         stop("invalid call in method dispatch to 'narrow' (no default method)", domain = NA))(x, 
             start, end, width, use.names)))(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], 
         dots[[4L]][[1L]], use.names = TRUE)
  19: windows(x, start = start, end = end, width = width)
  20: (function (classes, fdef, mtable) 
     {
         methods <- .findInheritedMethods(classes, fdef, mtable)
         if (length(methods) == 1L) 
             return(methods[[1L]])
         else if (length(methods) == 0L) {
             cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
             stop(gettextf("unable to find an inherited method for function %s for signature %s", 
                 sQuote(fdef@generic), sQuote(cnames)), domain = NA)
         }
         else stop("Internal error in finding inherited methods; didn't return a unique method", 
             domain = NA)
     })(list(structure("DNAString", package = "Biostrings")), new("standardGeneric", .Data = function (x, 
         start = NA, end = NA, width = NA) 
     standardGeneric("windows"), generic = structure("windows", package = "IRanges"), 
         package = "IRanges", group = list(), valueClass = character(0), signature = "x", 
         default = NULL, skeleton = (function (x, start = NA, end = NA, width = NA) 
         stop("invalid call in method dispatch to 'windows' (no default method)", domain = NA))(x, 
             start, end, width)), <environment>)
  21: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
         sQuote(fdef@generic), sQuote(cnames)), domain = NA)
  
  ── 2. Error: Sequence, and Seqinfo can be extracted (@test-08-gbRecord.r#15)  ──
  unable to find an inherited method for function 'windows' for signature '"DNAString"'
  1: expect_is(getSequence(x), "DNAStringSet") at testthat/test-08-gbRecord.r:15
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: getSequence(x)
  5: getSequence(x)
  6: .local(x, ...)
  7: .seq_access(x)
  8: Reduce(append, lapply(x, merge_seq, seq = seq, SEQFUN = SEQFUN))
  9: lapply(x, merge_seq, seq = seq, SEQFUN = SEQFUN)
  10: FUN(X[[i]], ...)
  ...
  17: standardGeneric("mapply")
  18: eval(mc, env)
  19: eval(mc, env)
  20: eval(mc, env)
  21: mapply(FUN = FUN, ..., MoreArgs = MoreArgs, SIMPLIFY = SIMPLIFY)
  22: (new("standardGeneric", .Data = function (x, start = NA, end = NA, width = NA, use.names = TRUE) 
     standardGeneric("narrow"), generic = structure("narrow", package = "IRanges"), package = "IRanges", 
         group = list(), valueClass = character(0), signature = "x", default = NULL, skeleton = (function (x, 
             start = NA, end = NA, width = NA, use.names = TRUE) 
         stop("invalid call in method dispatch to 'narrow' (no default method)", domain = NA))(x, 
             start, end, width, use.names)))(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], 
         dots[[4L]][[1L]], use.names = TRUE)
  23: (new("standardGeneric", .Data = function (x, start = NA, end = NA, width = NA, use.names = TRUE) 
     standardGeneric("narrow"), generic = structure("narrow", package = "IRanges"), package = "IRanges", 
         group = list(), valueClass = character(0), signature = "x", default = NULL, skeleton = (function (x, 
             start = NA, end = NA, width = NA, use.names = TRUE) 
         stop("invalid call in method dispatch to 'narrow' (no default method)", domain = NA))(x, 
             start, end, width, use.names)))(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], 
         dots[[4L]][[1L]], use.names = TRUE)
  24: windows(x, start = start, end = end, width = width)
  25: (function (classes, fdef, mtable) 
     {
         methods <- .findInheritedMethods(classes, fdef, mtable)
         if (length(methods) == 1L) 
             return(methods[[1L]])
         else if (length(methods) == 0L) {
             cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
             stop(gettextf("unable to find an inherited method for function %s for signature %s", 
                 sQuote(fdef@generic), sQuote(cnames)), domain = NA)
         }
         else stop("Internal error in finding inherited methods; didn't return a unique method", 
             domain = NA)
     })(list(structure("DNAString", package = "Biostrings")), new("standardGeneric", .Data = function (x, 
         start = NA, end = NA, width = NA) 
     standardGeneric("windows"), generic = structure("windows", package = "IRanges"), 
         package = "IRanges", group = list(), valueClass = character(0), signature = "x", 
         default = NULL, skeleton = (function (x, start = NA, end = NA, width = NA) 
         stop("invalid call in method dispatch to 'windows' (no default method)", domain = NA))(x, 
             start, end, width)), <environment>)
  26: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
         sQuote(fdef@generic), sQuote(cnames)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 268 SKIPPED: 1 FAILED: 2
  1. Error: getSequence works for gbFeatures (@test-07-gbRecord.r#60) 
  2. Error: Sequence, and Seqinfo can be extracted (@test-08-gbRecord.r#15) 
  
  Error: testthat unit tests failed
  Execution halted