Changes after revdep checks of dplyr 0.8.0 RC

[romainfrancois]

This fixes two problems that were identified as part of reverse dependency checks of dplyr 0.8.0 release candidate. https://github.com/tidyverse/dplyr/blob/revdep_dplyr_0_8_0_RC/revdep/problems.md#naniar

• n() must be imported or prefixed like any other function. In the PR, I've changed 1:n() to dplyr::row_number() as naniar seems to prefix all dplyr functions.

• update_shadow was only restoring the class attributes, changed so that it restores all attributes, this was causing problems when data was a grouped_df. This likely was a problem before too, but dplyr 0.8.0 is stricter about what is a grouped data frame.

[romainfrancois]

For reference:

> revdep_details(revdep = "naniar")
══ Reverse dependency check ═══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════ naniar 0.4.1 ══

Status: BROKEN

── Newly failing

✖ checking examples ... ERROR
✖ checking tests ...

── Before ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
0 errors ✔ | 0 warnings ✔ | 0 notes ✔

── After ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
❯ checking examples ... ERROR
  Running examples in ‘naniar-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: gg_miss_case
  > ### Title: Plot the number of missings per case (row)
  > ### Aliases: gg_miss_case
  > 
  > ### ** Examples
  > 
  > 
  > gg_miss_case(airquality)
  Error in n() : could not find function "n"
  Calls: gg_miss_case ... <Anonymous> -> <Anonymous> -> mutate.tbl_df -> mutate_impl
  Execution halted

❯ checking tests ...
  See below...

── Test failures ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── testthat ────

> library(testthat)
> library(naniar)
> 
> test_check("naniar")
── 1. Error: (unknown) (@test-gg-miss-case.R#5)  ───────────────────────────────
could not find function "n"
1: gg_miss_case(airquality) at testthat/test-gg-miss-case.R:5
2: x %>% miss_case_summary(order = TRUE) %>% dplyr::mutate(case = 1:n()) %>% gg_miss_case_create(show_pct = show_pct) at /Users/romain/git/release/dplyr/revdep/checks.noindex/naniar/new/naniar.Rcheck/00_pkg_src/naniar/R/gg-miss-case.R:40
3: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
4: eval(quote(`_fseq`(`_lhs`)), env, env)
5: eval(quote(`_fseq`(`_lhs`)), env, env)
6: `_fseq`(`_lhs`)
7: freduce(value, `_function_list`)
8: function_list[[i]](value)
9: dplyr::mutate(., case = 1:n())
10: mutate.tbl_df(., case = 1:n()) at /Users/romain/git/tidyverse/dplyr/R/manip.r:416
11: mutate_impl(.data, dots) at /Users/romain/git/tidyverse/dplyr/R/tbl-df.r:91

── 2. Error: (unknown) (@test-special-missing-values.R#131)  ───────────────────
`.data` is a corrupt grouped_df, the `"groups"` attribute must be a data frame
1: airquality %>% bind_shadow() %>% dplyr::group_by(Month) %>% recode_shadow(Ozone = .where(Wind <= 
       5 ~ "broken_machine")) at testthat/test-special-missing-values.R:131
2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
3: eval(quote(`_fseq`(`_lhs`)), env, env)
4: eval(quote(`_fseq`(`_lhs`)), env, env)
5: `_fseq`(`_lhs`)
6: freduce(value, `_function_list`)
7: withVisible(function_list[[k]](value))
8: function_list[[k]](value)
9: recode_shadow(., Ozone = .where(Wind <= 5 ~ "broken_machine"))
10: data %>% update_shadow(unlist(suffix, use.names = FALSE)) %>% dplyr::mutate(!!!magic_shade_case_when) at /Users/romain/git/release/dplyr/revdep/checks.noindex/naniar/new/naniar.Rcheck/00_pkg_src/naniar/R/shadow-recode.R:235
11: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
12: eval(quote(`_fseq`(`_lhs`)), env, env)
13: eval(quote(`_fseq`(`_lhs`)), env, env)
14: `_fseq`(`_lhs`)
15: freduce(value, `_function_list`)
16: withVisible(function_list[[k]](value))
17: function_list[[k]](value)
18: dplyr::mutate(., !!!magic_shade_case_when)
19: mutate.tbl_df(., !!!magic_shade_case_when) at /Users/romain/git/tidyverse/dplyr/R/manip.r:416
20: mutate_impl(.data, dots) at /Users/romain/git/tidyverse/dplyr/R/tbl-df.r:91

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 469 SKIPPED: 15 FAILED: 2
1. Error: (unknown) (@test-gg-miss-case.R#5) 
2. Error: (unknown) (@test-special-missing-values.R#131) 

Error: testthat unit tests failed
Execution halted

2 errors ✖ | 0 warnings ✔ | 0 notes ✔

[romainfrancois]

I believe the error is spurious

[njtierney]

Thanks for this, @romainfrancois ! I'll take a look on my machine and try and work out those errors.

Thanks for finding that issue with class vs attributes - I had sort of equated the two in my head, need to read up on the differences.

[romainfrancois]

In short the class is one attribute

[njtierney]

That actually really helps trigger my understanding of this, I know what I'm looking for to learn more about this now, thanks! :)

[njtierney]

OK so I get no errors on my machine, although I did only submit a patch release a few weeks ago, so I might try and include this in the next release for 0.5.0 around the end of Jan.