Running ‘testthat.R’ [11s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(valr)
  > 
  > test_check("valr")
  ── 1. Failure: ensure that absdist is calculated with respect to input tbls issu
  any(orig[, c(1:5)] != res[, c(1:5)]) isn't true.
  
  ── 2. Failure: check that strand closest works (strand = TRUE) (@test_closest.r#
  nrow(res) not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 3. Failure: check that same strand is reported (strand = TRUE (@test_closest.
  all(pred == res) isn't true.
  
  ── 4. Error: Make sure non-overlapping ties are reported with strand = T  (@test
  '==' only defined for equally-sized data frames
  1: expect_true(all(pred == res)) at testthat/test_closest.r:402
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: Ops.data.frame(pred, res)
  5: stop(gettextf("%s only defined for equally-sized data frames", sQuote(.Generic)), 
         domain = NA)
  
  ── 5. Error: Make sure non-overlapping ties are reported with strand_opp = T  (@
  '==' only defined for equally-sized data frames
  1: expect_true(all(pred == res)) at testthat/test_closest.r:411
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: Ops.data.frame(pred, res)
  5: stop(gettextf("%s only defined for equally-sized data frames", sQuote(.Generic)), 
         domain = NA)
  
  ── 6. Failure: ensure that subtraction is done with respect to input tbls issue#
  all(res$group.x == res$group.y) isn't true.
  
  ── 7. Failure: test closest forcing -s yet no matching strands on chrom (@test_c
  nrow(res) == 0 isn't true.
  
  ── 8. Failure: Make sure non-overlapping ties are reported, with strand option (
  nrow(res) == 1 isn't true.
  
  ── 9. Failure: Make sure non-overlapping ties are reported, with strand-oppo opt
  nrow(res) == 1 isn't true.
  
  ── 10. Error: basic cluster works (@test_cluster.r#20)  ────────────────────────
  Need at least one column for `hash()`
  1: bed_cluster(x) at testthat/test_cluster.r:20
  2: merge_impl(res, max_dist, collapse = FALSE)
  
  ── 11. Error: stranded cluster works (@test_cluster.r#27)  ─────────────────────
  Need at least one column for `hash()`
  1: bed_cluster(group_by(x, strand)) at testthat/test_cluster.r:27
  2: merge_impl(res, max_dist, collapse = FALSE)
  
  ── 12. Error: cluster ids are not repeated per group issue #171 (@test_cluster.r
  Need at least one column for `hash()`
  1: bed_cluster(x) at testthat/test_cluster.r:42
  2: merge_impl(res, max_dist, collapse = FALSE)
  
  ── 13. Failure: coverage of stranded tbls can be calc (@test_coverage.r#81)  ───
  all(res == pred) isn't true.
  
  ── 14. Failure:  strand_opp coverage works (strand_opp = TRUE) (@test_coverage.r
  all(res == pred) isn't true.
  
  ── 15. Failure: ensure that coverage is calculated with respect to input tbls is
  res[1, ".ints"] == 0 isn't true.
  
  ── 16. Error: glyphs are rendered (@test_glyph.r#10)  ──────────────────────────
  Need at least one column for `hash()`
  1: bed_glyph(bed_merge(x)) at testthat/test_glyph.r:10
  2: bed_cluster(ys)
  3: merge_impl(res, max_dist, collapse = FALSE)
  
  ── 17. Error: glyph labels are applied (@test_glyph.r#15)  ─────────────────────
  Need at least one column for `hash()`
  1: bed_glyph(bed_merge(x, id = n()), label = "id") at testthat/test_glyph.r:15
  2: bed_cluster(ys)
  3: merge_impl(res, max_dist, collapse = FALSE)
  
  ── 18. Error: expr arguments do not need to be x and/or y (@test_glyph.r#31)  ──
  Need at least one column for `hash()`
  1: bed_glyph(bed_intersect(a, b)) at testthat/test_glyph.r:31
  2: bed_cluster(ys)
  3: merge_impl(res, max_dist, collapse = FALSE)
  
  ── 19. Failure: input x groups are used for comparing intervals issue #108 (@tes
  all(res$group.x == res$group.y) isn't true.
  
  ── 20. Failure: tbls grouped by strand are processed (@test_intersect.r#183)  ──
  nrow(res) not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 21. Failure: groups are respected when passing multiple y tbl_intervals  (@te
  nrow(res) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ── 22. Failure: unmatched groups are included when invert = TRUE (@test_intersec
  `res` not equal to `pred`.
  Different number of rows
  
  ── 23. Failure: jaccard with grouped inputs are calculated (@test_jaccard.r#40) 
  nrow(res) not equal to 24.
  1/1 mismatches
  [1] 1 - 24 == -23
  
  ── 24. Failure: jaccard with grouped inputs are calculated (@test_jaccard.r#41) 
  "chrom" %in% names(res) isn't true.
  
  ── 25. Failure: x/y groupings are respected (@test_map.r#27)  ──────────────────
  all(res == pred, na.rm = TRUE) isn't true.
  
  ── 26. Failure: input groups are maintained in the output tbl issue #108 (@test_
  all(x$group %in% res$group) isn't true.
  
  ── 27. Failure: intervals can be merged by strand (@test_merge.r#100)  ─────────
  nrow(res) not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  
  ── 28. Failure: Test stranded merge with bedPlus files that have strand (@test_m
  res$end not equal to c(20000, 25000).
  Lengths differ: 1 is not 2
  
  ── 29. Failure: grouping is respected (@test_partition.r#201)  ─────────────────
  all(c("+" %in% res$strand, "-" %in% res$strand)) isn't true.
  
  ── 30. Failure: grouping is respected (@test_partition.r#202)  ─────────────────
  nrow(res) not equal to 8.
  1/1 mismatches
  [1] 9 - 8 == 1
  
  ── 31. Failure: summary functions are executed per group (@test_partition.r#237)
  sum(res$count) not equal to 196.
  1/1 mismatches
  [1] 198 - 196 == 2
  
  ── 32. Failure: summary functions are executed per group (@test_partition.r#238)
  nrow(res) not equal to 7.
  1/1 mismatches
  [1] 6 - 7 == -1
  
  ── 33. Failure: reldist respects groups (#108) (@test_reldist.r#61)  ───────────
  nrow(res) == 1 isn't true.
  
  ── 34. Failure: shift by strand works (@test_shift.r#85)  ──────────────────────
  all(...) isn't true.
  
  ── 35. Failure: shift by strand and fraction works (@test_shift.r#102)  ────────
  all(...) isn't true.
  
  ── 36. Failure: tbls grouped by strand are processed (@test_subtract.r#133)  ───
  all(res == a) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 382 SKIPPED: 3 FAILED: 36
  1. Failure: ensure that absdist is calculated with respect to input tbls issue#108 (@test_absdist.r#95) 
  2. Failure: check that strand closest works (strand = TRUE) (@test_closest.r#121) 
  3. Failure: check that same strand is reported (strand = TRUE (@test_closest.r#143) 
  4. Error: Make sure non-overlapping ties are reported with strand = T  (@test_closest.r#402) 
  5. Error: Make sure non-overlapping ties are reported with strand_opp = T  (@test_closest.r#411) 
  6. Failure: ensure that subtraction is done with respect to input tbls issue#108 (@test_closest.r#467) 
  7. Failure: test closest forcing -s yet no matching strands on chrom (@test_closest.r#481) 
  8. Failure: Make sure non-overlapping ties are reported, with strand option (@test_closest.r#522) 
  9. Failure: Make sure non-overlapping ties are reported, with strand-oppo option (@test_closest.r#536) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted