Running ‘testthat.R’ [20s/30s]
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
  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:
       █
    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$cluster, drop = TRUE)
    7.     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
    8.     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.       └─S4Vectors:::.local(x, f, drop, ...)
   10.         └─IRanges:::default_splitAsList(x, f, drop = drop)
   11.           └─IRanges:::.splitAsList_by_factor(x, f, drop)
   12.             └─S4Vectors:::isNotSorted(f)
  ── Error (test_input.R:110:3): Data fields (active bindings) are consistent ────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_equal(length(p$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): $save_pangenomeRDS() and load_pangenome() works ──
  Error: error in evaluating the argument 'skeleton' in selecting a method for function 'relist': 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─p$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:
       █
    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$cluster, drop = TRUE)
    7.     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
    8.     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
    9.       └─S4Vectors:::.local(x, f, drop, ...)
   10.         └─IRanges:::default_splitAsList(x, f, drop = drop)
   11.           └─IRanges:::.splitAsList_by_factor(x, f, drop)
   12.             └─S4Vectors:::isNotSorted(f)
  ── Error (test_methods-plots.R:29:3): methods return expected objects ──────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─p$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 $genes are consistent ─────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_is(p$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 $clusters are consistent ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_is(p$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 $sequences are consistent ──
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_is(p$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$cluster, drop = TRUE)
    9.     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.       └─S4Vectors:::.local(x, f, drop, ...)
   12.         └─IRanges:::default_splitAsList(x, f, drop = drop)
   13.           └─IRanges:::.splitAsList_by_factor(x, f, drop)
   14.             └─S4Vectors:::isNotSorted(f)
  ── Error (test_subset.R:54:3): vector/list notation for subset works ───────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_equal(p[1], p[clus_1_char]) test_subset.R:54:2
    2. │ ├─testthat::compare(act$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$cluster, drop = TRUE)
   10.     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   12.       └─S4Vectors:::.local(x, f, drop, ...)
   13.         └─IRanges:::default_splitAsList(x, f, drop = drop)
   14.           └─IRanges:::.splitAsList_by_factor(x, f, drop)
   15.             └─S4Vectors:::isNotSorted(f)
  ── Error (test_subset.R:78:3): matrix notation for subset works ────────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_equal(p[1, 1], p[orgs_1_char, clus_1_char]) test_subset.R:78:2
    2. │ ├─testthat::compare(act$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$cluster, drop = TRUE)
   10.     ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.     └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   12.       └─S4Vectors:::.local(x, f, drop, ...)
   13.         └─IRanges:::default_splitAsList(x, f, drop = drop)
   14.           └─IRanges:::.splitAsList_by_factor(x, f, drop)
   15.             └─S4Vectors:::isNotSorted(f)
  ── Error (test_subset.R:103:3): dropping/recovering organisms works ────────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. ├─testthat::expect_false(...) test_subset.R:103:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─as.character(todrop) %in% as.character(unlist(p$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