CRAN Package Check Results for Package valr

Last updated on 2018-11-20 13:46:45 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4.2 180.53 109.67 290.20 OK
r-devel-linux-x86_64-debian-gcc 0.4.2 158.94 88.07 247.01 OK
r-devel-linux-x86_64-fedora-clang 0.4.2 333.10 NOTE
r-devel-linux-x86_64-fedora-gcc 0.4.2 359.23 OK
r-devel-windows-ix86+x86_64 0.4.2 424.00 258.00 682.00 OK
r-patched-linux-x86_64 0.4.2 185.44 106.33 291.77 OK
r-patched-solaris-x86 0.4.2 399.30 OK
r-release-linux-x86_64 0.4.2 201.75 106.53 308.28 OK
r-release-windows-ix86+x86_64 0.4.2 316.00 223.00 539.00 OK
r-release-osx-x86_64 0.4.2 NOTE
r-oldrel-windows-ix86+x86_64 0.4.1 372.00 169.00 541.00 ERROR
r-oldrel-osx-x86_64 0.4.2 NOTE

Check Details

Version: 0.4.2
Check: installed package size
Result: NOTE
     installed size is 16.0Mb
     sub-directories of 1Mb or more:
     libs 14.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.4.1
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'valr-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: bed_closest
    > ### Title: Identify closest intervals.
    > ### Aliases: bed_closest
    >
    > ### ** Examples
    >
    > x <- trbl_interval(
    + ~chrom, ~start, ~end,
    + 'chr1', 100, 125
    + )
    >
    > y <- trbl_interval(
    + ~chrom, ~start, ~end,
    + 'chr1', 25, 50,
    + 'chr1', 140, 175
    + )
    >
    > bed_glyph(bed_closest(x, y))
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Error in merge_impl(res, max_dist, collapse = FALSE) :
     Need at least one column for `hash()`
    Calls: bed_glyph -> bed_cluster -> merge_impl -> .Call
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.4.1
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'valr-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: bed_closest
    > ### Title: Identify closest intervals.
    > ### Aliases: bed_closest
    >
    > ### ** Examples
    >
    > x <- trbl_interval(
    + ~chrom, ~start, ~end,
    + 'chr1', 100, 125
    + )
    >
    > y <- trbl_interval(
    + ~chrom, ~start, ~end,
    + 'chr1', 25, 50,
    + 'chr1', 140, 175
    + )
    >
    > bed_glyph(bed_closest(x, y))
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Error in merge_impl(res, max_dist, collapse = FALSE) :
     Need at least one column for `hash()`
    Calls: bed_glyph -> bed_cluster -> merge_impl -> .Call
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.4.1
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [15s]
    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
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.4.1
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [20s]
    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
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.4.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Quitting from lines 124-136 (valr.Rmd)
    Error: processing vignette 'valr.Rmd' failed with diagnostics:
    Need at least one column for `hash()`
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64