dplyr 1.0.0
romainfrancois opened this issue · 1 comments
romainfrancois commented
In addition to #12, we see these issues when testing this package against the soon to be released dplyr 1.0.0:
[master*] 219.2 MiB ❯ revdepcheck::revdep_details(revdep = "tidytree")
══ Reverse dependency check ══════════════════════════════════ tidytree 0.3.1 ══
Status: BROKEN
── Newly failing
✖ checking examples ... ERROR
✖ checking tests ...
── Before ──────────────────────────────────────────────────────────────────────
0 errors ✔ | 0 warnings ✔ | 0 notes ✔
── After ───────────────────────────────────────────────────────────────────────
❯ checking examples ... ERROR
Running examples in ‘tidytree-Ex.R’ failed
The error most likely occurred in:
> ### Name: as.treedata
> ### Title: as.treedata
> ### Aliases: as.treedata as.treedata.tbl_tree
>
> ### ** Examples
>
> library(ape)
> set.seed(2017)
> tree <- rtree(4)
> d <- tibble(label = paste0('t', 1:4),
+ trait = rnorm(4))
> x <- as_tibble(tree)
> full_join(x, d, by = 'label') %>% as.treedata
Warning: `mutate_()` is deprecated as of dplyr 0.7.0.
Please use `mutate()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error in get(x, envir = ns, inherits = FALSE) :
object 'mutate.tbl_df' not found
Calls: %>% ... mutate_.tbl_df -> mutate -> mutate.tbl_tree -> <Anonymous> -> get
Execution halted
❯ checking tests ...
See below...
── Test failures ───────────────────────────────────────────────── testthat ────
> library(testthat)
> library(tidytree)
Attaching package: 'tidytree'
The following object is masked from 'package:stats':
filter
>
> test_check("tidytree")
── 1. Error: conversion to table is reversible (@test-access-related-nodes.R#56)
object 'mutate.tbl_df' not found
Backtrace:
1. testthat::expect_equal(as.phylo(as_tibble(bi_tree)), bi_tree)
5. tidytree:::as.phylo.tbl_tree(as_tibble(bi_tree))
6. [ `%<>%`(...) ] with 7 more calls
15. dplyr:::mutate_.tbl_df(., isTip = ~(!node %in% parent))
17. tidytree:::mutate.tbl_tree(.data, !!!dots)
18. utils::getFromNamespace("mutate.tbl_df", "dplyr")
19. base::get(x, envir = ns, inherits = FALSE)
── 2. Failure: child works for bifurcating trees (@test-access-related-nodes.R#6
child(as_tibble(bi_tree), 1) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 3. Failure: child works for non-bifurcating trees (@test-access-related-nodes
child(as_tibble(multi_tree), 1) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 4. Failure: offspring works on bifurcating trees (@test-access-related-nodes.
offspring(as_tibble(bi_tree), 1) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 5. Failure: offspring works on non-bifurcating trees (@test-access-related-no
offspring(as_tibble(multi_tree), 1) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 6. Failure: parent works for bifurcating trees (@test-access-related-nodes.R#
parent(as_tibble(bi_tree), 11) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 7. Failure: parent works for non-bifurcating trees (@test-access-related-node
parent(as_tibble(multi_tree), 11) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 8. Failure: ancestor works for bifurcating trees (@test-access-related-nodes.
ancestor(as_tibble(bi_tree), 11) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 9. Failure: ancestor works for non-bifurcating trees (@test-access-related-no
ancestor(as_tibble(multi_tree), 11) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 10. Failure: MRCA works for bifurcating trees (@test-access-related-nodes.R#1
MRCA(as_tibble(multi_tree), 11, 5) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 11. Failure: MRCA works for non-bifurcating trees (@test-access-related-nodes
MRCA(as_tibble(multi_tree), 11, 5) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 12. Failure: sibling works for bifurcating trees (@test-access-related-nodes.
sibling(as_tibble(bi_tree), 11) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
── 13. Failure: sibling works for non-bifurcating trees (@test-access-related-no
sibling(as_tibble(multi_tree), 11) not equal to `empty_tbl`.
Attributes: < Component "class": Lengths (4, 3) differ (string compare on first 3) >
Attributes: < Component "class": 3 string mismatches >
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 31 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 13 ]
1. Error: conversion to table is reversible (@test-access-related-nodes.R#56)
2. Failure: child works for bifurcating trees (@test-access-related-nodes.R#64)
3. Failure: child works for non-bifurcating trees (@test-access-related-nodes.R#73)
4. Failure: offspring works on bifurcating trees (@test-access-related-nodes.R#81)
5. Failure: offspring works on non-bifurcating trees (@test-access-related-nodes.R#87)
6. Failure: parent works for bifurcating trees (@test-access-related-nodes.R#93)
7. Failure: parent works for non-bifurcating trees (@test-access-related-nodes.R#99)
8. Failure: ancestor works for bifurcating trees (@test-access-related-nodes.R#105)
9. Failure: ancestor works for non-bifurcating trees (@test-access-related-nodes.R#111)
1. ...
Error: testthat unit tests failed
Execution halted
2 errors ✖ | 0 warnings ✔ | 0 notes ✔
romainfrancois commented
Thanks. Hopefully these changes also are fine with the current dplyr version, so should be safe to release.