Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(pagoo)
  Loading required package: S4Vectors
  Loading required package: stats4
  Loading required package: BiocGenerics
  Loading required package: parallel
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:parallel':
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from 'package:stats':
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  
  Attaching package: 'S4Vectors'
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  Loading required package: Biostrings
  Loading required package: IRanges
  
  Attaching package: 'IRanges'
  
  The following object is masked from 'package:grDevices':
  
      windows
  
  Loading required package: XVector
  Loading required package: GenomeInfoDb
  
  Attaching package: 'Biostrings'
  
  The following object is masked from 'package:base':
  
      strsplit
  
  Loading required package: ggplot2
  > 
  > test_check("pagoo")
  == Failed tests ================================================================
  -- Error (test_input.R:101:3): Class of data fields (active bindings) are the expected --
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_is(p$genes, "SplitDataFrameList") test_input.R:101:2
    2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
    3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    4. \-(function () ...
    5.   +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    6.   \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    7.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
    8.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.       \-S4Vectors:::.local(x, f, drop, ...)
   10.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   11.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   12.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_input.R:110:3): Data fields (active bindings) are consistent ----
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_equal(length(p$genes), nrow(p$clusters)) test_input.R:110:2
    2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
    3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    4. \-(function () ...
    5.   +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    6.   \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    7.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
    8.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.       \-S4Vectors:::.local(x, f, drop, ...)
   10.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   11.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   12.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_input.R:119:3): $save_pangenomeRDS() and load_pangenome() works --
  Error: error in evaluating the argument 'skeleton' in selecting a method for function 'relist': 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-p$save_pangenomeRDS(out_rds) test_input.R:119:2
    2. | +-base::split(sqs, mcols(sqs)$org)
    3. | \-S4Vectors::split(sqs, mcols(sqs)$org)
    4. |   +-S4Vectors::splitAsList(x, f, drop = drop, ...)
    5. |   \-S4Vectors::splitAsList(x, f, drop = drop, ...)
    6. |     \-S4Vectors:::.local(x, f, drop, ...)
    7. |       \-IRanges:::default_splitAsList(x, f, drop = drop)
    8. |         \-IRanges:::as.factor2(f)
    9. |           +-IRanges::PartitioningByEnd(relist(g))
   10. |           | \-methods::is(x, "List")
   11. |           +-utils::relist(g)
   12. |           \-IRanges::relist(g)
   13. |             +-utils::relist(...)
   14. |             \-IRanges::PartitioningByEnd(attr(flesh, "ends"))
   15. |               \-IRanges:::.numeric2end(x, NG)
   16. |                 \-S4Vectors:::isNotSorted(x)
   17. \-base::.handleSimpleError(...)
   18.   \-base:::h(simpleError(msg, call))
  -- Error (test_input.R:167:3): Adding gene metadata after object creation works. --
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_is(p$genes, "DFrameList") test_input.R:167:2
    2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
    3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    4. \-(function () ...
    5.   +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    6.   \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    7.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
    8.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.       \-S4Vectors:::.local(x, f, drop, ...)
   10.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   11.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   12.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_methods-plots.R:29:3): methods return expected objects ----------
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-p$core_seqs_4_phylo() test_methods-plots.R:29:2
    2. | \-base::unlist(self$core_sequences, use.names = FALSE)
    3. +-(function () ...
    4. | \-base::unlist(self$core_genes)
    5. \-(function () ...
    6.   +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    7.   \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    8.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.       \-S4Vectors:::.local(x, f, drop, ...)
   11.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   12.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   13.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_subset.R:8:3): predefined subsets for $genes are consistent -----
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_is(p$core_genes, is(p$genes)) test_subset.R:8:2
    2. | \-base::stopifnot(is.character(class))
    3. +-methods::is(p$genes)
    4. \-(function () ...
    5.   +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    6.   \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    7.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
    8.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.       \-S4Vectors:::.local(x, f, drop, ...)
   10.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   11.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   12.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_subset.R:19:3): predefined subsets for $clusters are consistent --
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_is(p$shell_genes, is(p$clusters)) test_subset.R:19:2
    2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
    3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    4. \-(function () ...
    5.   +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    6.   \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    7.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
    8.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.       \-S4Vectors:::.local(x, f, drop, ...)
   10.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   11.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   12.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_subset.R:28:3): predefined subsets for $sequences are consistent --
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_is(p$core_sequences, is(p$sequences)) test_subset.R:28:2
    2. | \-base::stopifnot(is.character(class))
    3. +-methods::is(p$sequences)
    4. +-(function () ...
    5. | \-base::unlist(self$genes)
    6. \-(function () ...
    7.   +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    8.   \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    9.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.       \-S4Vectors:::.local(x, f, drop, ...)
   12.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   13.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   14.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_subset.R:54:3): vector/list notation for subset works -----------
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_equal(p[1], p[clus_1_char]) test_subset.R:54:2
    2. | +-testthat::compare(act$val, exp$val, ...)
    3. | \-testthat:::compare.default(act$val, exp$val, ...)
    4. |   +-base::all.equal(x, y, ...)
    5. |   \-base::all.equal.environment(x, y, ...)
    6. |     \-base::as.list.environment(target, all.names = all.names, sorted = TRUE)
    7. \-(function () ...
    8.   +-base::split(df, df$cluster, drop = TRUE)
    9.   \-S4Vectors::split(df, df$cluster, drop = TRUE)
   10.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
   12.       \-S4Vectors:::.local(x, f, drop, ...)
   13.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   14.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   15.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_subset.R:78:3): matrix notation for subset works ----------------
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_equal(p[1, 1], p[orgs_1_char, clus_1_char]) test_subset.R:78:2
    2. | +-testthat::compare(act$val, exp$val, ...)
    3. | \-testthat:::compare.default(act$val, exp$val, ...)
    4. |   +-base::all.equal(x, y, ...)
    5. |   \-base::all.equal.environment(x, y, ...)
    6. |     \-base::as.list.environment(target, all.names = all.names, sorted = TRUE)
    7. \-(function () ...
    8.   +-base::split(df, df$cluster, drop = TRUE)
    9.   \-S4Vectors::split(df, df$cluster, drop = TRUE)
   10.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
   12.       \-S4Vectors:::.local(x, f, drop, ...)
   13.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   14.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   15.             \-S4Vectors:::isNotSorted(f)
  -- Error (test_subset.R:103:3): dropping/recovering organisms works ------------
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       x
    1. +-testthat::expect_false(...) test_subset.R:103:2
    2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
    3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    4. +-as.character(todrop) %in% as.character(unlist(p$genes, use.names = FALSE)$org)
    5. +-base::unlist(p$genes, use.names = FALSE)
    6. \-(function () ...
    7.   +-base::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    8.   \-S4Vectors::split(data[, , drop = FALSE], f = data$cluster, drop = TRUE)
    9.     +-S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.     \-S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.       \-S4Vectors:::.local(x, f, drop, ...)
   12.         \-IRanges:::default_splitAsList(x, f, drop = drop)
   13.           \-IRanges:::.splitAsList_by_factor(x, f, drop)
   14.             \-S4Vectors:::isNotSorted(f)
  
  [ FAIL 11 | WARN 0 | SKIP 0 | PASS 72 ]
  Error: Test failures
  Execution halted