dplyr 1.1.0 revdep tracker

[DavisVaughan]

No description provided.

[hadley]

I'll take these ones:

na_if() vctrs update #6329

• circumplex: Fix for dev dplyr jmgirard/circumplex#18
• forestmangr: Fix for dev dplyr sollano/forestmangr#5
• hlaR: Fix for dev dplyr LarsenLab/hlaR#3
• huito: from inti::tarpuy_design
• inti: Fix for dev dplyr Flavjack/inti#11
• itraxR: Looks like CRAN version had a problem that was fixed here in dev version. Related to na_if() on a data frame tombishop1/itraxR@5de1717
• JumpeR: Partial fix for dev dplyr gpilgrim2670/JumpeR#3
• naniar: Fixes for dev dplyr njtierney/naniar#305
• skater: Fix for dev dplyr signaturescience/skater#57
• suddengains: Fix for dev dplyr milanwiedemann/suddengains#31
• SwimmeR: Some fixes for dev dplyr gpilgrim2670/SwimmeR#5

[DavisVaughan]

vctrs

• GauPro: vctrs ordering with matrix col issue Issue with vec_order_radix() and matrix columns r-lib/vctrs#1753

na_if() vctrs update #6329

• dbGaPCheckup: Apply na_if() to numeric columns lwheinsberg/dbGaPCheckup#1
• tidyplus: Convert to character early cran/tidyplus#1 and email
• ggblanket: Only na_if() double or integer columns davidhodge931/ggblanket#269
• fqar: Specifically call na_if() on columns equitable-equations/fqar#2

From join updates #5910

Assuming that most of these "produced warning" failures are from the new multi match join warning.

• comperes: Use expect_no_message() over expect_silent() echasnovski/comperes#7
• dodgr: Use expect_no_message() over expect_silent() UrbanAnalyst/dodgr#198
• exuber: Suppress multiple match warning where it causes test errors kvasilopoulos/exuber#23
• lans2r: Use expect_no_message() over expect_silent() KopfLab/lans2r#4
• modeldb: Disappeared after is_direct() changes
• multicolor: Use as.vector() not as_vector() to drop matrix class aedobbyn/multicolor#25
• parsnip: Disappeared after is_direct() changes
• sfnetworks: Error due to sfc not being orderable (tackling in vctrs) Rewrite vec_joint_proxy_order() with a more conservative heuristic r-lib/vctrs#1558
• stars: Disappeared on rerun
• Tplyr: Disappeared on rerun
• gratia: Suppress multiple match warning gavinsimpson/gratia#203
• isoorbi: Disappeared on rerun
• PHEindicatormethods: Don't index into unpredictably sized object ukhsa-collaboration/PHEindicatormethods#72
• PKNCA: Capture output using snapshots billdenney/pknca#198
• tidytransit: Suppress multiple match warning r-transit/tidytransit#191
• MBNMAtime: Silence join warnings causing problems in tests cran/MBNMAtime#1

Misc

• headliner: Only filter() if cond is provided rjake/headliner#121
• dtplyr: Use snapshots for errors that dplyr owns now dtplyr#404
• chronicler: Prefer chronicler::pick() in vignette b-rodrigues/chronicler#8
• skimr: Submit new version of skimr to CRAN soon? ropensci/skimr#721 - already fixed, need release
• MetAlyzer: Fix partial ungrouping #6607
• FRK: andrewzm/FRK@6c186df#r93113457 Fixed by the dev
• questionr: Official notice of impending dplyr 1.1.0 release sfirke/janitor#506 fixed already by janitor dev
• admiral: Drop names in if_else() pharmaverse/admiral#1638
• simplevis: Add backwards compatible code for storms update StatisticsNZ/simplevis#455
• tfrmt: Fix for dev dplyr GSK-Biostatistics/tfrmt#346
• recipes: Fixes for dev dplyr tidymodels/recipes#1070
• textrecipes: Unname before handing off to c_across() tidymodels/textrecipes#207

rename_with() now checks function output length

• topr: Only try renaming if >0 columns are selected totajuliusd/topr#2
• logitr: Use vec_paste0() helper for better recycling ddsjoberg/gtsummary#1404

distinct() and sticky columns?

• panelr: Early convert to tibble before calling distinct() jacob-long/panelr#50

slice_*() strictness about n

• kmscv: Round before handing off to slice_sample() cran/kmscv#1

slice() errors on named args

• forceR There is no argument named n Peter-T-Ruehr/forceR#2

Set operations #6354

• IPEDSuploadables: Conditionally add possibly missing columns AlisonLanski/IPEDSuploadables#102

slice() with no args now drops all rows

• rsample: Remove overly strict test tidymodels/rsample#380

From between updates #6260

• brolgar: between() cast error in tests — Fix for dev dplyr njtierney/brolgar#113
• cubble: between() cast error in vignette (double to character) — Fixes for dev dplyr huizezhang-sherry/cubble#11
• gmgm: between() cast error in tests (double to integer) — Fixes for the dev version of dplyr jeremyroos/gmgm#1
• helda: between() cast error in examples — Fix for dev dplyr Redcart/helda#12
• presenter: Unknown vignette failure — Fix for dev dplyr Harrison4192/presenter#1
• respR: between() cast error in examples (double to integer) — Fix for dev dplyr januarharianto/respR#187

arrange() radix ordering #6263

• dexter: Relied on arrange() and group_by() %>% summarize() having the same ordering Call arrange() after group_by() + summarize() dexter-psychometrics/dexter#6

data_frame_() removal #6277

• rabhit: Imported data_frame_() but never actually used it https://bitbucket.org/yaarilab/rabhit/issues/4/remove-data_frame_-import-from-dplyr

dplyr::tbl_sum() removal in favor of pillar::tbl_sum() #6284

• groupr: Use pillar::tbl_sum() rather than dplyr::tbl_sum() ngriffiths21/groupr#5
• tabxplor Use pillar::tbl_sum() rather than dplyr::tbl_sum() BriceNocenti/tabxplor#2

case_when() uses vctrs #6300

• epocakir: Uses case_when(~ ordered, TRUE ~ NA_integer_). Needs to use GFR_stages[NA_integer_] for default. Use correctly typed missing values alwinw/epocakir#41
• huxtable: Tries to use a mix of matrix and vector logicals on the LHS. Should probably un-dim, apply case-when, then re-dim. Convert to vectors before calling case_when() hughjonesd/huxtable#234
• unpivotr: case_when() was being used to return calls, but now requires vector types. It was also making this vctrs bug pop up, but was easily worked around vec_ptype2(<character>, <character>)  r-lib/vctrs#1300 dplyr 1.1.0 compatibility nacnudus/unpivotr#58

if_else() uses vctrs #6317

• dm: chore: Use correctly typed missing value for lists cynkra/dm#1686
• hablar: Remove overly strict test davidsjoberg/hablar#16
• PVplr: Use correct typed NA cran/PVplr#1 and email
• rsample: Use more appropriate NULL handling for unique_ind tidymodels/rsample#341
• seecolor: Use base ifelse() with matrices lovestat/seecolor#1

lead() and lag() update #6336

• ferrn: Typo in lead() argument default huizezhang-sherry/ferrn#8
• nonmemica: wrangle is causing this to break
• statar: Passing invalid argument to lag() matthieugomez/statar#35
• wrangle: Convert to double early cran/wrangle#1

n_distinct() doesn't allow named args

• track2KBA: Remove named arg from n_distinct() BirdLifeInternational/track2kba#46

Join check_dots_unused() (our fault) #6599

• disk.frame Breakage with upcoming dplyr 1.1.0  DiskFrame/disk.frame#390
• table.express Move check into methods and switch to empty dots check #6605
• tidytree: Use inject() to splice in dots YuLab-SMU/tidytree#29 this one had a bug too

Join check dots their fault

• ethnobotanyR: na.rm is not an argument to left_join() CWWhitney/ethnobotanyR#29
• wcep: Remove invalid argument cran/wcep#1
• fastqcr: Remove extra args in left_join() kassambara/fastqcr#23
• ndi Fix faulty join args idblr/ndi#7

Weird ranking functions missing links issue

I think CRAN will ignore this so I'm marking it complete.

• heemod: Links to row_number() which previously was [dplyr:ranking]{dplyr::row_number()} but now row_number() is on a different help page

group_labels_details() weirdness? can't reproduce locally

These all seemed to be related to some old bugs in group_labels_details() that have disappeared on a rerun of the revdeps. I had my suspicions about them already because I couldn't reproduce locally, so i think they are fine.

• GDPuc:
• gmgm:
• NHSRplotthedots:

False alarm?

• SVMMaj: Looks like a bad tolerance issue in a test

---

Issues below this were walked back in dplyr itself, but we are tracking them here anyways.

Would be broken by nth(), first(), last() vctrs update if we made first(list(1)) use vec_slice() #6331

• DataFakeR: %>% tidygraph::pull(table) %>% dplyr::first() on a list-col, expecting first() to give the first element
• dyngen: Through GillespieSSA2, does str_split(" ") %>% first() expecting to get the first element of the list
• dynwrap: Programmatic usage of first() on a list, expecting to get the first element
• GillespieSSA2: does str_split(" ") %>% first() expecting to get the first element of the list (see also dyngen)
• phenofit: last() on a list, expecting the last list element
• TidyMultiqc: first() on a list expecting to get the first element
• xpose: first() on a list expecting to get the first element

Would be broken by funs() deprecation #6389

• AQuadtree: dplyr::summarise_at(qt2.act@data, sum.2, funs(sum))
• bootnet: dplyr::summarize_each(., funs(fun(., digits = digits)))
• caffsim: dplyr::summarise_at(., vars(value), funs(mean, sd, min, max))
• carpenter: dplyr::mutate_all(., dplyr::funs(as.character))
• clustrd: dplyr::summarise_all(., funs(mean))
• coefplot: dplyr::mutate_at(...) some usage of funs in there
• cometExactTest: dplyr::summarise_all(., funs(sum))
• funModeling: dplyr::summarise_each_(., funs(group_func), vars_to_keep)
• geosimilarity: dplyr::summarise_all(., funs(mean))
• GFE: base::ifelse(type == "Jackknife", funs(varJack), funs(var))
• glmdisc: dplyr::mutate_at(., dplyr::vars("X1", "X2"), dplyr::funs(as.integer))
• graphicalVAR: dplyr::mutate_at(., funs(shift), .vars = vars)
• IBCF.MTME: dplyr::mutate_if(., is.numeric, funs(round(., digits)))
• interplot: in vignette
• ipft: dplyr::summarise_all(., funs(mean))
• Lahman: dplyr::summarise_each(., funs(sum))
• missCompare: dplyr::summarise_all(., funs(mymean))
• MRFcov: dplyr::summarise_all(., dplyr::funs(sd(.)))
• MSiP: dplyr::summarise_each(., funs(max(.)))
• ncappc: dplyr::mutate_all(., dplyr::funs(as.numeric(as.character(.))))
• PAC: dplyr::summarise_all(., funs(sum))
• PDtoolkit: dplyr::summarise_at(...)
• phase1PRMD: dplyr::mutate_at(...)
• PPforest: in vignette
• prevtoinc: dplyr::mutate_all(., dplyr::funs(unlist))
• prozor: dplyr::mutate_at(pepinfo, peptide, dplyr::funs(as.character))
• psychonetrics: dplyr::summarise_at(., funs(mean(., na.rm = TRUE)), .vars = vars)
• randomForestExplainer: dplyr::summarize_at(., vars, funs(max(., na.rm = TRUE)))
• ruler: in vignette
• sfc: mutate_each(funs(as.character(.)))
• sjmisc: dplyr::summarise_all(...)
• sjPlot: in vignette
• skynet: dplyr::mutate_all(., funs(ifelse(is.na(.), 0, .)))
• staRdom: in vignette
• statVisual: dplyr::summarise_at(...)
• tabularaster: in vignette
• tidyboot: dplyr::summarise_at(., vars(mean), funs(ci_upper, mean, ci_lower))
• useful: mutate_at(...)
• xray: mutate_all(...)

Weird bind_rows() or bind_cols() missing links issue

• blsR: Links to bind_rows() which previously was [dplyr:bind]{dplyr::bind_rows()} but now bind_rows() has its own help page
• dtrackr:
• ffp:
• getLattes:
• jstable:
• mark:
• mrgsim.parallel:
• RKorAPClient:
• salesforcer
• sf:
• sftime:
• sjmisc:
• skimr:
• slackr:
• soiltestcorr:
• styler:
• tidygraph:
• tsibble:

Would be broken by slice_*() check_dots_empty() in generic

• tidyterra: slice_sample.SpatRaster(.keep_extent = TRUE) extra argument counted as dots

[lionel-]

nth(), first(), last() vctrs update #6331

• confoundr: "Can't convert default to match type of x ", first(x, default = "NA") with double x - Compatibility with dplyr 1.1.0 jwjackson/confoundr#3
• divseg: Does dplyr::first(dplyr::cur_data()) expecting to get the first col of the data frame? Should use pull(). - Compatibility with dplyr 1.1.0 christopherkenny/divseg#1
• finnts: dplyr::filter(Date==max(Date)) %>% dplyr::last() on a df where they should have used pull(-1) - Compatibility with dplyr 1.1.0 microsoft/finnts#117
• FRK: Not sure, possibly related but hard to diagnose - Compatibility with dplyr 1.1.0 andrewzm/FRK#7
• janitor: dplyr::last(dat) on a data frame expecting last column, should use pull() - address breaking change in dplyr::last() sfirke/janitor#491
• questionr: Broken because of janitor
• tidygraph: dplyr::count() %>% dplyr::first() on a data frame, expecting first column, should use pull() - Use pull(1) instead of first() thomasp85/tidygraph#168
• phenofit: Compatibility with dplyr 1.1.0 eco-hydro/phenofit#14

select_vars() deprecation #6389

• extdplyr: dplyr::select_vars(colnames(data), ...) - No online repo, sent mail with a link to lionel-/extdplyr@a3cc769
• NobBS: No online repo, sent mail with a link to lionel-/NobBS@d7e4607

n_distinct() doesn't allow 0 args

• arrow: test-dplyr-summarize.R:301 - GH-14947 [R] Compatibility with dplyr 1.1.0 apache/arrow#14948

Join check_dots_unused() (actual bug)

• iNZightTools: calling anti_join() with suffix arg but that doesn't exist - Only supply suffix to join_ functions that support it iNZightVIT/iNZightTools#196
• lillies: all.x arg that doesn't exist dplyr::left_join(LYL, ages_onset, by = "age", all.x = T) Sent mail linking to lionel-/lillies@6d0d31f
• mudata2: prefix arg that doesn't exist, supposedly meant suffix? - Compatibility with dplyr 1.1.0 paleolimbot/mudata2#34
• overviewR: by.x and by.y args that don't exist - Don't supply unknown arguments to full_join() cosimameyer/overviewR#38
• tidyquery: Looks like they might be calling anti_join() or something like it with suffix=, which doesn't exist. - Don't supply unknown arguments to dplyr join functions ianmcook/tidyquery#29
• dtrackr: Calls semi_join() with suffix= argument. - Compatibility with dplyr 1.1.0 terminological/dtrackr#30

distinct() returns columns in requested order now #6156

• romic: issue in test-conversion.R where expected column order is different - Compatibility with dplyr 1.1.0 calico/romic#41
• tidyCDISC: - Tweak order of arguments supplied to distinct() Biogen-Inc/tidyCDISC#144

Misc

• starschemar: Looks like that have superclassed data.frame, something we don't support. x must be a vector, not a <tbl_df/tbl/data.frame/dimension_table> object - Sent mail with link to lionel-/starschemar@a392623

Unknown

• r2dii.analysis: some calculation in tests is off, but very complex chain of calculations to get there - Fix partial ungrouping #6607
• RNeXML: sort(meta.cont[, "Meta"]) not equal to sort(unique(meta.nested[, "meta"])) in test_meta_extract.R:204 - Compatibility with dplyr 1.1.0 ropensci/RNeXML#254

na_if() vctrs update #6329

• ontologics: Can't convert y <character> to match type of x <tbl_df> - Compatibility with dplyr 1.1.0 luckinet/ontologics#27
• tabshiftr: Can't convert y <character> to match type of x <double> - Only map na_if() on compatible vectors luckinet/tabshiftr#3

[lionel-]

New problems revealed in revdep checks of #6550:

New exported where() function causes an import conflict

Caused by #6609. where() is also exported by ape and imager packages.

• ggmuller - Resolve name conflict for where() between dplyr and ape robjohnnoble/ggmuller#19
• LARGB - Sent mail linking to lionel-/LARGB@2ed45f6
• treeplyr - Resolve name conflict for where() between ape and dplyr uyedaj/treeplyr#9

[DavisVaughan]

From 24ea5ae

• arrow - [R] dplyr 1.1.0 compatibility  apache/arrow#33894 (New version on CRAN Dec 6)
• autoGO - Don't import where() from ape cran/autoGO#1 and email (on CRAN Jan 16)
• injurytools - Preemptively use multiple = "all" in left_join() lzumeta/injurytools#1 (on CRAN Jan 25)
• metacore - Expressions using <- can overwrite active bindings in the data mask #6666. Don't use an anonymous function in across() atorus-research/metacore#72
• sift - Use a slightly more relaxed check for the old variant of cross join #6665

[DavisVaughan]

3 more detected only by CRAN's checks. We aren't sure how they slipped through ours.

• DecomposeR - Use lapply() rather than sapply() cran/DecomposeR#1 and email
• eHDPrep - Compatibility with dplyr 1.1.0 overton-group/eHDPrep#3
• SIPmg - Only apply na_if() to specific columns ZielsLab/SIPmg#1

[hadley]

On CRAN 🥳