reverse dependency checks for 0.7.0

[simonpcouch]

A thread to document working through reverse dependency checks for 0.7.0. broom changes will be pushed to the 0-7-0-9000-revdeps branch and I'll link out to issues/PRs on other repositories when relevant.

• [x] allestimates

Package is not hosted on CRAN. The package doesn't provide model objects that broom provides tidier methods for. Email sent to maintainer at zhiqiang.wang@menzies.edu.au.

* Version: 0.1.6 * Source code: https://github.com/cran/allestimates * Date/Publication: 2020-02-05 16:30:12 UTC * Number of recursive dependencies: 75 Run `revdep_details(,"allestimates")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘allestimates-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: all_cox
  > ### Title: Estimates all possible effect estimates using Cox Proportional
  > ###   Hazards regression models
  > ### Aliases: all_cox
  > 
  > ### ** Examples
  > 
  > vlist <- c("Age", "Sex", "Married", "BMI", "Education", "Income")
  > results <- all_cox(crude = "Surv(t0, t1, Endpoint) ~ Diabetes", xlist = vlist, data = diab_df)
  Warning: Unknown or uninitialised column: `conf.low`.
  Warning: Unknown or uninitialised column: `conf.high`.
  Warning: Unknown or uninitialised column: `n`.
  Error in data.frame(variables = "Crude", estimate, conf_low, conf_high,  : 
    arguments imply differing number of rows: 1, 0
  Calls: all_cox -> data.frame
  Execution halted

In both

• checking dependencies in R code ... NOTE

  Namespaces in Imports field not imported from:
    ‘MASS’ ‘tibble’
    All declared Imports should be used.

• [x] arsenal

Results from deprecation of confint_tidy()--issue filed here.

* Version: 3.4.0 * Source code: https://github.com/cran/arsenal * URL: https://github.com/eheinzen/arsenal, https://cran.r-project.org/package=arsenal, https://eheinzen.github.io/arsenal/ * BugReports: https://github.com/eheinzen/arsenal/issues * Date/Publication: 2020-02-15 19:10:03 UTC * Number of recursive dependencies: 76 Run `revdep_details(,"arsenal")` for more info

Newly broken

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    'confint_tidy' is not an exported object from 'namespace:broom'
    Backtrace:
      1. testthat::expect_identical(...)
     11. arsenal::modelsum(...)
     12. arsenal:::modelsum_guts(...)
     13. broom::confint_tidy
     14. base::getExportedValue(pkg, name)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 426 | SKIPPED: 12 | WARNINGS: 12 | FAILED: 2 ]
    1. Error: ordinal works (@test_modelsum.R#213) 
    2. Error: 08/01/2017: Beth Atkinson's subset problem (@test_modelsum.R#359) 
  
    Error: testthat unit tests failed
    Execution halted

• checking dependencies in R code ... NOTE

  Missing or unexported object: ‘broom::confint_tidy’

• [x] biobroom

Results from deprecation of fix_data_frame()--issue filed here.

* Version: 1.18.0 * Source code: https://github.com/cran/biobroom * URL: https://github.com/StoreyLab/biobroom * BugReports: https://github.com/StoreyLab/biobroom/issues * Date/Publication: 2019-10-29 * Number of recursive dependencies: 141 Run `revdep_details(,"biobroom")` for more info

Newly broken

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    [1mBacktrace:[22m
    [90m 1. [39mgenerics::tidy(dds)
    [90m 2. [39mbiobroom::tidy.EList(dds)
    [90m 3. [39mbiobroom:::tidy_matrix(x$E)
    [90m 7. [39mbroom::fix_data_frame
    [90m 8. [39mbase::getExportedValue(pkg, name)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
    1. Error: limma tidier works as expected (@test-limma_tidiers.R#5) 
    2. Error: voom tidier adds weight column (@test-limma_tidiers.R#26) 
    3. Error: voomWithQualityWeights tidier adds weight and sample.weight columns (@test-limma_tidiers.R#49) 
  
    Error: testthat unit tests failed
    Execution halted

Newly fixed

• checking whether package ‘biobroom’ can be installed ... WARNING

  Found the following significant warnings:
    Warning: package ‘broom’ was built under R version 3.6.2
  See ‘/Users/max/github/broom/revdep/checks.noindex/biobroom/old/biobroom.Rcheck/00install.out’ for details.

In both

• checking dependencies in R code ... NOTE

  'library' or 'require' call to ‘DESeq2’ in package code.
    Please use :: or requireNamespace() instead.
    See section 'Suggested packages' in the 'Writing R Extensions' manual.
  Missing or unexported objects:
    ‘broom::fix_data_frame’ ‘dplyr::tbl_dt’

• checking R code for possible problems ... NOTE

  ...
    for ‘colData’
  tidy.deSet: no visible global function definition for ‘exprs<-’
  tidy.deSet: no visible binding for global variable ‘value’
  tidy.deSet: no visible binding for global variable ‘gene’
  tidy.deSet: no visible global function definition for ‘pData’
  tidy.qvalue: no visible binding for global variable ‘smoothed’
  tidy.qvalue: no visible binding for global variable ‘pi0’
  tidy.qvalue: no visible binding for global variable ‘lambda’
  tidy_matrix: no visible binding for global variable ‘value’
  tidy_matrix: no visible binding for global variable ‘gene’
  Undefined global functions or variables:
    . DGEList calcNormFactors colData counts design end estimate
    estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix
    p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames
    setNames smoothed start tbl_dt term value voom voomWithQualityWeights
  Consider adding
    importFrom("methods", "is")
    importFrom("stats", "end", "model.matrix", "p.adjust", "setNames",
               "start")
  to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
  contains 'methods').

• [x] breathtestcore

Results from deprecation of summary() tidiers--issue filed here.

* Version: 0.6.0 * Source code: https://github.com/cran/breathtestcore * URL: https://github.com/dmenne/breathtestcore * BugReports: https://github.com/dmenne/breathtestcore/issues * Date/Publication: 2020-03-22 02:50:02 UTC * Number of recursive dependencies: 88 Run `revdep_details(,"breathtestcore")` for more info

Newly broken

• checking examples ... ERROR

  ...
  > fit = nls_fit(data)
  > coef_by_group(fit)
  Error: `by` can't contain join column `lhs` which is missing from LHS
  Backtrace:
  [90m     [39m█
  [90m  1. [39m├─breathtestcore::coef_by_group(fit)
  [90m  2. [39m├─breathtestcore:::coef_by_group.breathtestfit(fit)
  [90m  3. [39m│ └─`%>%`(...)
  [90m  4. [39m│   ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  [90m  5. [39m│   └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  [90m  6. [39m│     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  [90m  7. [39m│       └─breathtestcore:::`_fseq`(`_lhs`)
  [90m  8. [39m│         └─magrittr::freduce(value, `_function_list`)
  [90m  9. [39m│           └─function_list[[i]](value)
  [90m 10. [39m│             ├─dplyr::do(...)
  [90m 11. [39m│             └─dplyr:::do.grouped_df(...)
  [90m 12. [39m│               └─rlang::eval_tidy(args[[j]], mask)
  [90m 13. [39m└─`%>%`(...)
  [90m 14. [39m  ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  [
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/test-all.R’ failed.
  Last 13 lines of output:
    [90m 24. [39mdplyr:::common_by.list(by, x, y)
    [90m 25. [39mdplyr:::bad_args(...)
    [90m 26. [39mdplyr:::glubort(fmt_args(args), ..., .envir = .envir)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 333 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 6 ]
    1. Error: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#13) 
    2. Error: Options digits is served (@test_coef_by_group.R#33) 
    3. Error: Result with default parameters is tbl_df with required columns (@test_coef_diff_by_group.R#13) 
    4. Error: Result with Dunnett contrast only returns 3 groups (@test_coef_diff_by_group.R#24) 
    5. Error: Correct Dunnett contrast when reference value is given (@test_coef_diff_by_group.R#45) 
    6. Error: Options digits is served (@test_coef_diff_by_group.R#67) 
  
    Error: testthat unit tests failed
    Execution halted

In both

• checking Rd cross-references ... NOTE

  Package unavailable to check Rd xrefs: ‘breathteststan’

• [x] CGPfunctions

* Version: 0.6.0 * Source code: https://github.com/cran/CGPfunctions * URL: https://github.com/ibecav/CGPfunctions * BugReports: https://github.com/ibecav/CGPfunctions/issues * Date/Publication: 2020-04-02 14:10:03 UTC * Number of recursive dependencies: 174 Run `revdep_details(,"CGPfunctions")` for more info

Newly broken

• checking examples ... ERROR

  ...
  > ### ** Examples
  > 
  > 
  > Plot2WayANOVA(mpg ~ am * cyl, mtcars, plottype = "line")
  
  Converting am to a factor --- check your results
  
  Converting cyl to a factor --- check your results
  Warning: Unknown or uninitialised column: `r.squared`.
  Warning: Unknown or uninitialised column: `r.squared`.
  Warning: Unknown or uninitialised column: `r.squared`.
  Warning: Unknown or uninitialised column: `r.squared`.
  Warning in max(limit1, limit2) :
    no non-missing arguments to max; returning -Inf
  Warning in min(limit1, limit2) :
    no non-missing arguments to min; returning Inf
  Warning: Unknown or uninitialised column: `r.squared`.
  Error in round(model_summary$r.squared, 3) : 
    non-numeric argument to mathematical function
  Calls: Plot2WayANOVA
  Execution halted

• [x] chest

Resulted from the removal of the n column in glance.coxph. Corrected.

* Version: 0.3.1 * Source code: https://github.com/cran/chest * Date/Publication: 2020-01-29 12:20:02 UTC * Number of recursive dependencies: 77 Run `revdep_details(,"chest")` for more info

Newly broken

• checking examples ... ERROR

  ...
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  Warning: Unknown or uninitialised column: `n`.
  
  Error in data.frame(out, p, n) : 
    arguments imply differing number of rows: 8, 0
  Calls: chest_clogit -> data.frame
  Execution halted

In both

• checking dependencies in R code ... NOTE

  Namespace in Imports field not imported from: ‘magrittr’
    All declared Imports should be used.

• [x] DeLorean

Not a broom issue.

* Version: 1.5.0 * Source code: https://github.com/cran/DeLorean * Date/Publication: 2018-10-17 22:30:16 UTC * Number of recursive dependencies: 118 Run `revdep_details(,"DeLorean")` for more info

Newly broken

• checking installed package size ... NOTE

    installed size is  7.7Mb
    sub-directories of 1Mb or more:
      libs   5.0Mb

• checking dependencies in R code ... NOTE

  Namespace in Imports field not imported from: ‘lattice’
    All declared Imports should be used.

• checking for GNU extensions in Makefiles ... NOTE

  GNU make is a SystemRequirements.

Newly fixed

• checking whether package ‘DeLorean’ can be installed ... ERROR

  Installation failed.
  See ‘/Users/max/github/broom/revdep/checks.noindex/DeLorean/old/DeLorean.Rcheck/00install.out’ for details.

• [x] disk.frame

Not a broom issue.

* Version: 0.3.5 * Source code: https://github.com/cran/disk.frame * URL: https://diskframe.com * BugReports: https://github.com/xiaodaigh/disk.frame/issues * Date/Publication: 2020-05-08 13:10:10 UTC * Number of recursive dependencies: 105 Run `revdep_details(,"disk.frame")` for more info

Newly broken

• checking examples ... ERROR

  ...
  +   # only run in interactive()
  +   setup_disk.frame(gui = TRUE)
  + }
  > 
  > # set the number workers to 2
  > setup_disk.frame(2)
  Warning in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE,  :
    port 37400 cannot be opened
  Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE,  : 
    Failed to launch and connect to R worker on local machine ‘localhost’ from local machine ‘imp.atlanticbb.net’.
   * The error produced by socketConnection() was: ‘cannot open the connection’
   * In addition, socketConnection() produced 1 warning(s):
     - Warning #1: ‘port 37400 cannot be opened’ (which suggests that this port is either already occupied by another process or blocked by the firewall on your local machine)
   * The localhost socket connection that failed to connect to the R worker used port 37400 using a communication timeout of 120 seconds and a connection timeout of 120 seconds.
   * Worker launch call: '/Library/Frameworks/R.framework/Resources/bin/Rscript' --default-packages=datasets,utils,grDevices,graphics,stats,methods -e '#label=UNKNOWN:56671:imp.atlanticbb.net:max' -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/lb/xhxqmcrd7gv302_b1pdfykh80000gn/T//RtmpqhMLhX/future.parent=56671.dd5f59ec707e.pid")), silent = TRUE)' -e 'parallel:::.slaveRSOCK()' MASTER=localhost PORT=37400 OUT=/dev/null TIMEOUT=120 XDR=TRUE.
   * Worker (PID 57088) was successfully killed: TRUE
   * Troubleshooting suggestions:
     - Suggestion #1: Set 'verbose=TRUE' to see more details.
     - Suggestion #2: Set 'outfile=NULL' to see output from worker.
  Calls: setup_disk.frame ... tryCatchList -> tryCatchOne -> <Anonymous> -> <Anonymous>
  Execution halted

In both

• checking whether package ‘disk.frame’ can be installed ... WARNING

  Found the following significant warnings:
    Warning: package ‘purrr’ was built under R version 3.6.2
  See ‘/Users/max/github/broom/revdep/checks.noindex/disk.frame/new/disk.frame.Rcheck/00install.out’ for details.

• [x] disto

Results from not exporting tidy.table(). Issue filed here.

* Version: 0.2.0 * Source code: https://github.com/cran/disto * URL: https://github.com/talegari/disto * BugReports: https://github.com/talegari/disto/issues * Date/Publication: 2018-08-02 12:50:02 UTC * Number of recursive dependencies: 122 Run `revdep_details(,"disto")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘disto-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: summary.disto
  > ### Title: Summary method for dist class
  > ### Aliases: summary.disto
  > 
  > ### ** Examples
  > 
  > temp <- stats::dist(iris[,1:4])
  > dio   <- disto(objectname = "temp")
  > dio
  disto with backend: dist
  size: 150
  > summary(dio)
  Warning: 'tidy.table' is deprecated.
  See help("Deprecated")
  Error in dimnames(x) <- dnx : 'dimnames' applied to non-array
  Calls: summary ... eval -> eval -> data.frame -> do.call -> provideDimnames
  Execution halted

In both

• checking dependencies in R code ... NOTE

  Namespaces in Imports field not imported from:
    ‘dplyr’ ‘proxy’
    All declared Imports should be used.

• [x] ERSA

Results from deprecation of summary() tidiers. Issue filed here.

* Version: 0.1.1 * Source code: https://github.com/cran/ERSA * Date/Publication: 2018-07-24 11:10:03 UTC * Number of recursive dependencies: 109 Run `revdep_details(,"ERSA")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘ERSA-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: plotSum
  > ### Title: Plots of model summaries
  > ### Aliases: plotSum plotAnovaStats plottStats plotCIStats
  > 
  > ### ** Examples
  > 
  > plotAnovaStats(lm(mpg ~ wt+hp+disp, data=mtcars))
  > plottStats(lm(mpg ~ wt+hp+disp, data=mtcars))
  Error: No tidy method for objects of class summary.lm
  Execution halted

• [x] eyetrackingR

This package is no longer maintained.

* Version: 0.1.8 * Source code: https://github.com/cran/eyetrackingR * URL: http://eyetracking-r.com * BugReports: https://github.com/jwdink/eyetrackingR/issues * Date/Publication: 2018-12-03 22:00:39 UTC * Number of recursive dependencies: 82 Run `revdep_details(,"eyetrackingR")` for more info

Newly broken

• checking examples ... ERROR

  ...
  > 
  > data(word_recognition)
  > data <- make_eyetrackingr_data(word_recognition, 
  +                                participant_column = "ParticipantName",
  +                                trial_column = "Trial",
  +                                time_column = "TimeFromTrialOnset",
  +                                trackloss_column = "TrackLoss",
  +                                aoi_columns = c('Animate','Inanimate'),
  +                                treat_non_aoi_looks_as_missing = TRUE )
  > response_window <- subset_by_window(data, window_start_time = 15500, window_end_time = 21000, 
  +                                     rezero = FALSE)
  Avg. window length in new data will be 5500
  > response_time <- make_time_sequence_data(response_window, time_bin_size = 500, aois = "Animate", 
  +                                          predictor_columns = "Sex")
  > 
  > time_cluster_data <- make_time_cluster_data(data = response_time, predictor_column = "SexM", 
  +                          aoi = "Animate", test = "lmer", 
  +                          threshold = 1.5, 
  +                          formula = LogitAdjusted ~ Sex + (1|Trial) + (1|ParticipantName))
  Error: No tidy method for objects of class lmerMod
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
  
    [31m──[39m [31m2. Error: (unknown) (@test_cluster_analysis.R#88) [39m [31m──────────────────────────[39m
    No tidy method for objects of class lmerMod
    [1mBacktrace:[22m
    [90m  1. [39meyetrackingR::make_time_cluster_data(...)
    [90m 16. [39meyetrackingR:::the_test(...)
    [90m 18. [39mbroom:::tidy.default(res_err_warn$res, effects = "fixed")
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 27 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
    1. Error: (unknown) (@test_analyze_time_bins.R#98) 
    2. Error: (unknown) (@test_cluster_analysis.R#88) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] GGally

Results from requiring the se_fit argument in augment.*() methods. Put in a PR here.

* Version: 1.5.0 * Source code: https://github.com/cran/GGally * URL: https://ggobi.github.io/ggally, https://github.com/ggobi/ggally * BugReports: https://github.com/ggobi/ggally/issues * Date/Publication: 2020-03-25 18:20:15 UTC * Number of recursive dependencies: 133 Run `revdep_details(,"GGally")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘GGally-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: ggally_nostic_se_fit
  > ### Title: ggnostic - fitted value standard error
  > ### Aliases: ggally_nostic_se_fit
  > 
  > ### ** Examples
  > 
  > dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
  > ggally_nostic_se_fit(dt, ggplot2::aes(wt, .se.fit))
  Error in FUN(X[[i]], ...) : object '.se.fit' not found
  Calls: <Anonymous> ... <Anonymous> -> f -> scales_add_defaults -> lapply -> FUN
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    > 
    > test_check("GGally")
    [31m──[39m [31m1. Error: ggnostic mtcars (@test-ggnostic.R#64) [39m [31m────────────────────────────[39m
    Columns in 'columnsY' not found in data: c('.se.fit'). Choices: c('.rownames', 'mpg', 'wt', 'qsec', 'am', '.fitted', '.resid', '.std.resid', '.hat', '.sigma', '.cooksd')
    [1mBacktrace:[22m
    [90m 1. [39mGGally::ggnostic(...)
    [90m 2. [39mGGally::ggduo(...)
    [90m 3. [39mGGally:::fix_column_values(...)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 757 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
    1. Error: ggnostic mtcars (@test-ggnostic.R#64) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] ggasym

Results from warning -> error switch -- unit tests reflected broom functionality. Issue filed here.

* Version: 0.1.3 * Source code: https://github.com/cran/ggasym * URL: https://github.com/jhrcook/ggasym https://jhrcook.github.io/ggasym/ * BugReports: https://github.com/jhrcook/ggasym/issues * Date/Publication: 2020-04-03 20:10:02 UTC * Number of recursive dependencies: 101 Run `revdep_details(,"ggasym")` for more info

Newly broken

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    > 
    > test_check("ggasym")
    Error : No tidy method for objects of class character
    [31m──[39m [31m1. Error: stats asymmetrization works (@test-asymmetrise_stats.R#13) [39m [31m───────[39m
    Could not handle input data; try turning into a tibble using the broom package
    [1mBacktrace:[22m
    [90m 1. [39mtestthat::expect_warning(prepare_data(grps))
    [90m 6. [39mggasym::prepare_data(grps)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 260 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
    1. Error: stats asymmetrization works (@test-asymmetrise_stats.R#13) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] glmmfields

Results from planned deprecation of mixed model tidiers to broom.mixed. Issue filed here.

* Version: 0.1.3 * Source code: https://github.com/cran/glmmfields * URL: https://github.com/seananderson/glmmfields * BugReports: https://github.com/seananderson/glmmfields/issues * Date/Publication: 2019-05-18 04:40:03 UTC * Number of recursive dependencies: 85 Run `revdep_details(,"glmmfields")` for more info

Newly broken

• checking dependencies in R code ... NOTE

  Missing or unexported object: ‘broom::tidyMCMC’

In both

• checking for GNU extensions in Makefiles ... NOTE

  GNU make is a SystemRequirements.

• [x] gtsummary

Resulted from deprecation of confint_tidy(). Issue filed here.

* Version: 1.3.0 * Source code: https://github.com/cran/gtsummary * URL: https://github.com/ddsjoberg/gtsummary, http://www.danieldsjoberg.com/gtsummary/ * BugReports: https://github.com/ddsjoberg/gtsummary/issues * Date/Publication: 2020-04-17 08:00:02 UTC * Number of recursive dependencies: 151 Run `revdep_details(,"gtsummary")` for more info

Newly broken

• checking examples ... ERROR

  ...
  > ### Title: Vetted tidy models
  > ### Aliases: vetted_models
  > ### Keywords: internal
  > 
  > ### ** Examples
  > 
  > my_tidy <- function(x, exponentiate =  FALSE, conf.level = 0.95, ...) {
  +   tidy <-
  +     dplyr::bind_cols(
  +       broom::tidy(x, conf.int = FALSE),
  +       broom::confint_tidy(x, func = stats::confint.default, conf.level = conf.level)
  +     )
  +   # exponentiating, if requested
  +   if (exponentiate == TRUE)
  +     tidy <- dplyr::mutate_at(vars(estimate, conf.low, conf.high), exp)
  + }
  > 
  > lm(age ~ grade + response, trial) %>%
  +   my_tidy()
  Error: 'confint_tidy' is not an exported object from 'namespace:broom'
  Execution halted

• [x] jtools

Related to use of previously unexported svyglm tidier methods. Issue filed here.

* Version: 2.0.5 * Source code: https://github.com/cran/jtools * URL: https://jtools.jacob-long.com * BugReports: https://github.com/jacob-long/jtools/issues * Date/Publication: 2020-04-21 12:20:12 UTC * Number of recursive dependencies: 125 Run `revdep_details(,"jtools")` for more info

Newly broken

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    [90m  4. [39mjtools::plot_summs(regmodel, scale = T)
    [90m  6. [39mjtools::plot_coefs(...)
    [90m  7. [39mjtools:::make_tidies(...)
    [90m 10. [39mjtools:::tidy.summ(...)
    [90m 14. [39mbroom:::tidy.svyglm(...)
    [90m 15. [39mbroom:::broom_confint_terms(x, level = conf.level, ...)
    [90m 17. [39mellipsis:::action_dots(...)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 358 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 2 ]
    1. Error: plot_summs works with svyglm (@test-export-summs.R#211) 
    2. Error: plot_summs accepts summ args with svyglm (@test-export-summs.R#216) 
  
    Error: testthat unit tests failed
    Execution halted

In both

• checking Rd cross-references ... NOTE

  Packages unavailable to check Rd xrefs: ‘wec’, ‘interactions’, ‘piecewiseSEM’

• [x] konfound

Results from planned deprecation of mixed model tidiers to broom.mixed. Issue filed here.

* Version: 0.2.1 * Source code: https://github.com/cran/konfound * URL: https://github.com/jrosen48/konfound * BugReports: https://github.com/jrosen48/konfound/issues * Date/Publication: 2020-02-26 14:50:02 UTC * Number of recursive dependencies: 113 Run `revdep_details(,"konfound")` for more info

Newly broken

• checking examples ... ERROR

  ...
  To sustain an inference, 17334 of the cases with 0 effect would have to be replaced with cases at the threshold of inference.
  See Frank et al. (2013) for a description of the method
  [4mCitation:[24m Frank, K.A., Maroulis, S., Duong, M., and Kelcey, B. 2013. What would it take to change an inference? Using Rubin's causal model to interpret the robustness of causal inferences. [3mEducation, Evaluation and Policy Analysis, 35[23m 437-460.
  [1mImpact Threshold for a Confounding Variable:
  [22mThe minimum impact to invalidate an inference for a null hypothesis of 0 effect is based on a correlation of 5.535 with the outcome and at 5.535 with the predictor of interest (conditioning on observed covariates) based on a threshold of 1.003 for statistical significance (alpha = 0.05).
  Correspondingly the impact of an omitted variable (as defined in Frank 2000) must be 5.535 X 5.535 = 30.636 to invalidate an inference for a null hypothesis of 0 effect.
  See Frank (2000) for a description of the method
  [4mCitation:[24m Frank, K. 2000. Impact of a confounding variable on the inference of a regression coefficient. [3mSociological Methods and Research, 29[23m (2), 147-194
  NULL
  > 
  > # using lme4 for mixed effects (or multi-level) models
  > if (requireNamespace("lme4")) {
  +   library(lme4)
  +   m3 <- fm1 <- lme4::lmer(Reaction ~ Days + (1 | Subject), sleepstudy)
  +   konfound(m3, Days)
  + }
  Loading required namespace: lme4
  Warning: package ‘lme4’ was built under R version 3.6.2
  Loading required package: Matrix
  Error: No tidy method for objects of class lmerMod
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
  
    [31m──[39m [31m2. Error: (unknown) (@test-pkonfound.R#11) [39m [31m─────────────────────────────────[39m
    No tidy method for objects of class lmerMod
    [1mBacktrace:[22m
    [90m 1. [39mkonfound::konfound(testmod2, texp, test_all = TRUE, to_return = "raw_output")
    [90m 2. [39mkonfound:::konfound_lmer(...)
    [90m 4. [39mbroom:::tidy.default(model_object)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 0 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ]
    1. Error: (unknown) (@test-mkonfound.r#12) 
    2. Error: (unknown) (@test-pkonfound.R#11) 
  
    Error: testthat unit tests failed
    Execution halted

In both

• checking dependencies in R code ... NOTE

  Namespace in Imports field not imported from: ‘mice’
    All declared Imports should be used.

• [x] merTools

Results from planned deprecation of mixed model tidiers to broom.mixed. Issue filed here.

* Version: 0.5.0 * Source code: https://github.com/cran/merTools * BugReports: https://www.github.com/jknowles/merTools * Date/Publication: 2019-05-13 12:30:06 UTC * Number of recursive dependencies: 131 Run `revdep_details(,"merTools")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘merTools-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: lmerModList
  > ### Title: Apply a multilevel model to a list of data frames
  > ### Aliases: lmerModList blmerModList glmerModList bglmerModList
  > 
  > ### ** Examples
  > 
  > sim_list <- replicate(n = 10,
  +         expr = sleepstudy[sample(row.names(sleepstudy), 180),],
  +         simplify=FALSE)
  > fml <- "Reaction ~ Days + (Days | Subject)"
  > mod <- lmerModList(fml, data = sim_list)
  > summary(mod)
  Error: No tidy method for objects of class lmerMod
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat-a_p.R’ failed.
  Last 13 lines of output:
    [31m──[39m [31m1. Error: print methods work for merModList (@test-merModList.R#58) [39m [31m────────[39m
    No tidy method for objects of class lmerMod
    [1mBacktrace:[22m
    [90m 1. [39mbase::summary(g1)
    [90m 2. [39mmerTools:::summary.merModList(g1)
    [90m 3. [39mmerTools::modelFixedEff(modList)
    [90m 4. [39mbase::lapply(modList, tidy, effects = "fixed", ...)
    [90m 6. [39mbroom:::tidy.default(X[[i]], ...)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 285 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
    1. Error: print methods work for merModList (@test-merModList.R#58) 
  
    Error: testthat unit tests failed
    Execution halted

In both

• checking whether package ‘merTools’ can be installed ... WARNING

  Found the following significant warnings:
    Warning: package ‘arm’ was built under R version 3.6.2
    Warning: package ‘MASS’ was built under R version 3.6.2
    Warning: package ‘lme4’ was built under R version 3.6.2
  See ‘/Users/max/github/broom/revdep/checks.noindex/merTools/new/merTools.Rcheck/00install.out’ for details.

• [x] mice

Relevant to changes in glance.*() methods for lm and aov objects. Issue filed here/

* Version: 3.9.0 * Source code: https://github.com/cran/mice * URL: https://github.com/stefvanbuuren/mice, https://stefvanbuuren.name/mice/, https://stefvanbuuren.name/fimd/ * BugReports: https://github.com/stefvanbuuren/mice/issues * Date/Publication: 2020-05-14 15:20:03 UTC * Number of recursive dependencies: 85 Run `revdep_details(,"mice")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘mice-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: D3
  > ### Title: Compare two nested models using D3-statistic
  > ### Aliases: D3
  > 
  > ### ** Examples
  > 
  > # Compare two linear models:
  > imp <- mice(nhanes2, seed = 51009, print = FALSE)
  > mi1 <- with(data = imp, expr = lm(bmi ~ age + hyp + chl))
  > mi0 <- with(data = imp, expr = lm(bmi ~ age + hyp))
  > D3(mi1, mi0)
  Error in eval_tidy(xs[[j]], mask) : object 'fstatistic' not found
  Calls: D3 ... with.default -> eval -> eval -> tibble -> tibble_quos -> eval_tidy
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    [90m 19. [39mbroom:::glance.lm(X[[i]], ...)
    [90m 21. [39mbase::with.default(...)
    [90m 22. [39m[ base::eval(...) ][90m with 1 more call[39m
    [90m 24. [39mtibble::tibble(...)
    [90m 25. [39mtibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
    [90m 26. [39mrlang::eval_tidy(xs[[j]], mask)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 280 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 3 ]
    1. Error: (unknown) (@test-D3.R#10) 
    2. Error: anova.mira() produces silent D1 and D3 (@test-anova.R#9) 
    3. Error: anova.mira() produces warnings on D2 (@test-anova.R#14) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] moderndive

False positive. master works fine, which will be submitted soon.

* Version: 0.4.0 * Source code: https://github.com/cran/moderndive * URL: https://github.com/ModernDive/moderndive_package * BugReports: https://github.com/ModernDive/moderndive_package/issues * Date/Publication: 2019-11-04 05:40:02 UTC * Number of recursive dependencies: 120 Run `revdep_details(,"moderndive")` for more info

Newly broken

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(moderndive)
    > 
    > test_check("moderndive")
    [31m──[39m [31m1. Failure: README code works (@test-get_regression_functions.R#91) [39m [31m────────[39m
    `get_regression_points(mpg_mlr_model2, newdata = newcars)` produced warnings.
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 33 | SKIPPED: 11 | WARNINGS: 3 | FAILED: 1 ]
    1. Failure: README code works (@test-get_regression_functions.R#91) 
  
    Error: testthat unit tests failed
    Execution halted

In both

• checking Rd cross-references ... NOTE

  Package unavailable to check Rd xrefs: ‘openintro’

• [x] NetworkExtinction

Uncovered a bug where the augment.nls() method didn't return .resid. Fixed on 0-7-0-9000-revdeps branch.

* Version: 0.1.1 * Source code: https://github.com/cran/NetworkExtinction * URL: https://derek-corcoran-barrios.github.io/NetworkExtintion/ * Date/Publication: 2019-10-27 22:20:02 UTC * Number of recursive dependencies: 85 Run `revdep_details(,"NetworkExtinction")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘NetworkExtinction-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: degree_distribution
  > ### Title: Degree distribution of the network
  > ### Aliases: degree_distribution
  > 
  > ### ** Examples
  > 
  > library(NetworkExtinction)
  > data("net")
  > degree_distribution(net, name = "Test")
  Warning: Unknown or uninitialised column: `.resid`.
  Error in ks.test(augment(exp.model)$.resid, y = "pnorm", alternative = "two.sided") : 
    not enough 'x' data
  Calls: degree_distribution -> ifelse -> tidy -> ks.test
  Execution halted

• [x] nlstimedist

Same bug as for NetworkExtinction. Fixed.

* Version: 1.1.4 * Source code: https://github.com/cran/nlstimedist * URL: https://github.com/nathaneastwood/nlstimedist * BugReports: https://github.com/nathaneastwood/nlstimedist/issues * Date/Publication: 2019-05-15 21:40:03 UTC * Number of recursive dependencies: 72 Run `revdep_details(,"nlstimedist")` for more info

Newly broken

• checking examples ... ERROR

  ...
  > tdTilia <- tdData(tilia, x = "Day", y = "Trees")
  > model <- timedist(data = tdTilia, x = "Day", y = "propMax", r = 0.1, c = 0.5,
  +                   t = 120)
  > tdCdfPlot(model)
  Error: Can't subset columns that don't exist.
  [31m✖[39m Column `.resid` doesn't exist.
  Backtrace:
  [90m     [39m█
  [90m  1. [39m├─nlstimedist::tdCdfPlot(model)
  [90m  2. [39m│ ├─data[, c(nameMod, ".fitted", ".resid")]
  [90m  3. [39m│ └─tibble:::`[.tbl_df`(data, , c(nameMod, ".fitted", ".resid"))
  [90m  4. [39m│   └─tibble:::tbl_subset_col(x, j = j, j_arg)
  [90m  5. [39m│     └─tibble:::vectbl_as_col_index(j, x, j_arg = j_arg)
  [90m  6. [39m│       └─tibble:::vectbl_as_col_location(...)
  [90m  7. [39m│         ├─tibble:::subclass_col_index_errors(...)
  [90m  8. [39m│         │ ├─base::tryCatch(...)
  [90m  9. [39m│         │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
  [90m 10. [39m│         │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  [90m 11. [39m│         │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
  [90m 12. [39m│         
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    > library(nlstimedist)
    > 
    > test_check("nlstimedist")
    [31m──[39m [31m1. Failure: Ensure the glance method is returning expected values (@test-glan[39m
    `out` not equal to `expect`.
    Names: 1 string mismatch
    Length mismatch: comparison on first 9 components
    Component 9: Mean relative difference: 0.9308432
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
    1. Failure: Ensure the glance method is returning expected values (@test-glance.timedist.R#17) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] panelr

Results from planned deprecation of mixed model tidiers to broom.mixed. Issue filed here.

* Version: 0.7.2 * Source code: https://github.com/cran/panelr * URL: https://panelr.jacob-long.com * BugReports: https://github.com/jacob-long/panelr * Date/Publication: 2020-03-08 22:10:02 UTC * Number of recursive dependencies: 168 Run `revdep_details(,"panelr")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘panelr-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: tidy.wbm
  > ### Title: Tidy methods for 'wbm' models
  > ### Aliases: tidy.wbm glance.wbm glance.summ.wbm tidy.summ.wbm
  > 
  > ### ** Examples
  > 
  > data("WageData")
  > wages <- panel_data(WageData, id = id, wave = t)
  > model <- wbm(lwage ~ lag(union) + wks, data = wages)
  > if (requireNamespace("broom")) {
  +   broom::tidy(model)
  + }
  Error: No tidy method for objects of class lmerMod
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    > 
    > test_check("panelr")
    [31m──[39m [31m1. Error: tidy works (@test-utils.R#341) [39m [31m───────────────────────────────────[39m
    No tidy method for objects of class lmerMod
    [1mBacktrace:[22m
    [90m 1. [39mtestthat::expect_is(tidy.wbm(wb), "tbl_df")
    [90m 4. [39mpanelr:::tidy.wbm(wb)
    [90m 6. [39mbroom:::tidy.default(...)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 291 | SKIPPED: 0 | WARNINGS: 2436 | FAILED: 1 ]
    1. Error: tidy works (@test-utils.R#341) 
  
    Error: testthat unit tests failed
    Execution halted

In both

• checking whether package ‘panelr’ can be installed ... WARNING

  Found the following significant warnings:
    Warning: package ‘lme4’ was built under R version 3.6.2
  See ‘/Users/max/github/broom/revdep/checks.noindex/panelr/new/panelr.Rcheck/00install.out’ for details.

• [x] pixiedust

Results from testing a broom warning that is now an error. Issue filed here.

* Version: 0.9.0 * Source code: https://github.com/cran/pixiedust * URL: https://github.com/nutterb/pixiedust * BugReports: https://github.com/nutterb/pixiedust/issues * Date/Publication: 2020-05-15 05:50:10 UTC * Number of recursive dependencies: 65 Run `revdep_details(,"pixiedust")` for more info

Newly broken

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    > 
    > test_check("pixiedust")
    [31m──[39m [31m1. Error: dust runs when passed a data frame with tidy_df = TRUE (@test-dust.[39m
    No tidy method for objects of class data.frame
    [1mBacktrace:[22m
    [90m  1. [39mtestthat::expect_warning(dust(mtcars, tidy_df = TRUE))
    [90m  7. [39mpixiedust:::dust.default(mtcars, tidy_df = TRUE)
    [90m 10. [39mbroom:::tidy.default(object, ...)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 512 | SKIPPED: 120 | WARNINGS: 0 | FAILED: 1 ]
    1. Error: dust runs when passed a data frame with tidy_df = TRUE (@test-dust.R#52) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] qgcomp

Results from deprecation of finish_glance(). Issued filed here.

* Version: 2.3.0 * Source code: https://github.com/cran/qgcomp * Date/Publication: 2020-04-08 05:50:02 UTC * Number of recursive dependencies: 116 Run `revdep_details(,"qgcomp")` for more info

Newly broken

• checking dependencies in R code ... NOTE

  Missing or unexported object: ‘broom::finish_glance’

• [x] radiant.model

Resulted from the augment() rewrite. Issue filed here.

* Version: 1.3.10 * Source code: https://github.com/cran/radiant.model * URL: https://github.com/radiant-rstats/radiant.model, https://radiant-rstats.github.io/radiant.model, https://radiant-rstats.github.io/docs * BugReports: https://github.com/radiant-rstats/radiant.model/issues * Date/Publication: 2020-03-24 09:50:03 UTC * Number of recursive dependencies: 155 Run `revdep_details(,"radiant.model")` for more info

Newly broken

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
  
    SI1     9 114304.420 104924.680 123684.159  9379.739
    sex|male    0.080 -92.0%      -2.522     0.163 -15.447  < .001 ***
    2nd female      0.779 0.712 0.833
    1st female      0.896 0.856 0.926
    1st female 29.000      0.919 0.880 0.945
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 24 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
    1. Failure: regress (@test_stats.R#23) 
  
    Error: testthat unit tests failed
    In addition: Warning messages:
    1: package 'lubridate' was built under R version 3.6.2 
    2: package 'tidyr' was built under R version 3.6.2 
    Execution halted

In both

• checking whether package ‘radiant.model’ can be installed ... WARNING

  Found the following significant warnings:
    Warning: package ‘lubridate’ was built under R version 3.6.2
    Warning: package ‘tidyr’ was built under R version 3.6.2
  See ‘/Users/max/github/broom/revdep/checks.noindex/radiant.model/new/radiant.model.Rcheck/00install.out’ for details.

• [x] RCT

Not a broom problem.

* Version: 1.0.2 * Source code: https://github.com/cran/RCT * Date/Publication: 2020-05-13 06:20:10 UTC * Number of recursive dependencies: 80 Run `revdep_details(,"RCT")` for more info

Newly broken

• checking examples ... ERROR

  ...
  > ### Title: Impact Evaluation of Treatment Effects
  > ### Aliases: impact_eval
  > 
  > ### ** Examples
  > 
  > data <- data.frame(y_1 = rnorm(n = 100, mean = 100, sd = 15), 
  +                   y_2 = rnorm(n = 100, mean = 8, sd = 2), 
  +                   treat = rep(c(0,1,2,3), each = 25), 
  +                   heterogenous_var1 = rep(c("X_Q1", "X_Q2", "X_Q3", "X_Q4"), times = 25),
  +                   cluster_var1 = rep(c(1:5), times = 20), 
  +                   fixed_effect_var1 = rep(c(1,2), times = 50),
  +                   control_var1 = rnorm(n = 100, mean = 20, sd = 1))
  > 
  > evaluation<-impact_eval(data = data, 
  +                        endogenous_vars = c("y_1", "y_2"), 
  +                        treatment = "treat", 
  +                        heterogenous_vars = c("heterogenous_var1"), 
  +                        cluster_vars = "cluster_var1", fixed_effect_vars = c("fixed_effect_var1"), 
  +                        control_vars = c("control_var1"))
  Error: No tidy method for objects of class rowwise_df
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    No tidy method for objects of class rowwise_df
    [1mBacktrace:[22m
    [90m  1. [39mRCT::impact_eval(...)
    [90m  2. [39mpurrr::map2(...)
    [90m  3. [39mRCT:::.f(.x[[1L]], .y[[1L]], ...)
    [90m  4. [39mdplyr::group_by(., !!rlang::sym(x))
    [90m  4. [39mdplyr::do(., fit = lfe::felm(stats::as.formula(y), data = .))
    [90m 12. [39mbroom::tidy(., fit)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 79 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
    1. Error: (unknown) (@test_impact_eval.R#64) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] rstatix

Results from deprecation of summary().* tidiers. Issue filed here.

* Version: 0.5.0 * Source code: https://github.com/cran/rstatix * URL: https://rpkgs.datanovia.com/rstatix/ * BugReports: https://github.com/kassambara/rstatix/issues * Date/Publication: 2020-04-28 10:40:02 UTC * Number of recursive dependencies: 127 Run `revdep_details(,"rstatix")` for more info

Newly broken

• checking examples ... ERROR

  ...
  Running examples in ‘rstatix-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: emmeans_test
  > ### Title: Pairwise Comparisons of Estimated Marginal Means
  > ### Aliases: emmeans_test get_emmeans
  > 
  > ### ** Examples
  > 
  > # Data preparation
  > df <- ToothGrowth
  > df$dose <- as.factor(df$dose)
  > 
  > # Pairwise comparisons
  > res <- df %>%
  +  group_by(supp) %>%
  +  emmeans_test(len ~ dose, p.adjust.method = "bonferroni")
  Error in summary.emmGrid(x, ...) : 
    formal argument "infer" matched by multiple actual arguments
  Calls: %>% ... <Anonymous> -> tidy -> tidy.emmGrid -> tidy_emmeans -> summary
  Execution halted

• [x] simglm

Results from planned deprecation of mixed model tidiers to broom.mixed. Issue filed here.

* Version: 0.7.4 * Source code: https://github.com/cran/simglm * Date/Publication: 2019-05-31 17:10:03 UTC * Number of recursive dependencies: 90 Run `revdep_details(,"simglm")` for more info

Newly broken

• checking examples ... ERROR

  ...
  > with_err_gen <- 'rnorm'
  > data_str <- "long"
  > pow_param <- c('time', 'diff', 'act', 'actClust')
  > alpha <- .01
  > pow_dist <- "z"
  > pow_tail <- 2
  > replicates <- 1
  > power_out <- sim_pow(fixed = fixed, random = random, random3 = random3,
  +                      fixed_param = fixed_param, 
  +                      random_param = random_param, 
  +                      random_param3 = random_param3, 
  +                      cov_param = cov_param, 
  +                      k = k, n = n, p = p,
  +                      error_var = error_var, with_err_gen = "rnorm",
  +                      data_str = data_str, 
  +                      unbal = list(level3 = FALSE, level2 = FALSE), 
  +                      pow_param = pow_param, alpha = alpha,
  +                      pow_dist = pow_dist, pow_tail = pow_tail, 
  +                      replicates = replicates, raw_power = FALSE)
  Error: No tidy method for objects of class lmerMod
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    [90m  7. [39msimglm:::FUN(X[[i]], ...)
    [90m 10. [39msimglm::sim_pow_glm_nested3(...)
    [90m 12. [39mbroom:::tidy.default(temp_mod, effects = "fixed")
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 125 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 6 ]
    1. Error: three level power continuous (@test_power_struc.r#169) 
    2. Error: two level power dich (@test_power_struc.r#203) 
    3. Error: three level power dich (@test_power_struc.r#238) 
    4. Error: three level power continuous (@test_power_vary.r#91) 
    5. Error: two level power dich (@test_power_vary.r#128) 
    6. Error: three level power dich (@test_power_vary.r#166) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] survminer

This is an issue that is unrelated to broom and is addressed on 472 of that package.

* Version: 0.4.6 * Source code: https://github.com/cran/survminer * URL: http://www.sthda.com/english/rpkgs/survminer/ * BugReports: https://github.com/kassambara/survminer/issues * Date/Publication: 2019-09-03 23:00:02 UTC * Number of recursive dependencies: 119 Run `revdep_details(,"survminer")` for more info

Newly broken

• checking examples ... ERROR

  ...
  Running examples in ‘survminer-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: ggforest
  > ### Title: Forest Plot for Cox Proportional Hazards Model
  > ### Aliases: ggforest
  > 
  > ### ** Examples
  > 
  > require("survival")
  Loading required package: survival
  Warning: package ‘survival’ was built under R version 3.6.2
  > model <- coxph( Surv(time, status) ~ sex + rx + adhere,
  +                 data = colon )
  > ggforest(model)
  Warning in .get_data(model, data = data) :
    The `data` argument is not provided. Data will be extracted from model fit.
  Error in `[.data.frame`(cbind(allTermsDF, coef[inds, ]), , c("var", "level",  : 
    undefined columns selected
  Calls: ggforest -> [ -> [.data.frame
  Execution halted

In both

• checking whether package ‘survminer’ can be installed ... WARNING

  Found the following significant warnings:
    Warning: package ‘ggpubr’ was built under R version 3.6.2
  See ‘/Users/max/github/broom/revdep/checks.noindex/survminer/new/survminer.Rcheck/00install.out’ for details.

• checking installed package size ... NOTE

    installed size is  5.6Mb
    sub-directories of 1Mb or more:
      doc   5.1Mb

• [x] survutils

Results from new conf.int = FALSE default. Issue filed here.

* Version: 1.0.2 * Source code: https://github.com/cran/survutils * URL: https://github.com/tinyheero/survutils * BugReports: https://github.com/tinyheero/survutils/issues * Date/Publication: 2018-07-22 17:50:02 UTC * Number of recursive dependencies: 61 Run `revdep_details(,"survutils")` for more info

Newly broken

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    > 
    > test_check("survutils")
    [31m──[39m [31m1. Failure: get_cox_res runs univariate Cox regression on a single feature (@[39m
    as.data.frame(out_df) not equal to as.data.frame(expected_out_df).
    Names: 1 string mismatch
    Length mismatch: comparison on first 6 components
    Component 6: Modes: character, numeric
    Component 6: target is character, current is numeric
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
    1. Failure: get_cox_res runs univariate Cox regression on a single feature (@test_get_cox_res.R#48) 
  
    Error: testthat unit tests failed
    Execution halted

• [x] sweep

Resulted from finish_glance() and rowwise DF tidier deprecations. Issue filed here.

* Version: 0.2.2 * Source code: https://github.com/cran/sweep * URL: https://github.com/business-science/sweep * BugReports: https://github.com/business-science/sweep/issues * Date/Publication: 2019-10-08 13:50:02 UTC * Number of recursive dependencies: 142 Run `revdep_details(,"sweep")` for more info

Newly broken

• checking examples ... ERROR

  ...
  
  The following objects are masked from ‘package:base’:
  
      intersect, setdiff, setequal, union
  
  > library(forecast)
  Warning: package ‘forecast’ was built under R version 3.6.2
  > library(sweep)
  > 
  > fit_arima <- WWWusage %>%
  +     auto.arima()
  > 
  > sw_tidy(fit_arima)
  [90m# A tibble: 2 x 2[39m
    term  estimate
    [3m[90m<chr>[39m[23m    [3m[90m<dbl>[39m[23m
  [90m1[39m ar1      0.650
  [90m2[39m ma1      0.526
  > sw_glance(fit_arima)
  Error: 'finish_glance' is not an exported object from 'namespace:broom'
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    [90m 2. [39msweep:::sw_glance.robets(fit_robets)
    [90m 6. [39mbroom::finish_glance
    [90m 7. [39mbase::getExportedValue(pkg, name)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 143 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 6 ]
    1. Error: sw_sweep test returns tibble with correct rows and columns. (@test_sw_sweep.R#156) 
    2. Error: sw_*.Arima test returns tibble with correct rows and columns. (@test_tidiers_arima.R#19) 
    3. Error: sw_*.ets test returns tibble with correct rows and columns. (@test_tidiers_ets.R#19) 
    4. Failure: sw_*.default test returns tibble with correct rows and columns. (@test_tidiers_lm.R#22) 
    5. Failure: sw_*.default test returns tibble with correct rows and columns. (@test_tidiers_lm.R#32) 
    6. Error: sw_*.robets test returns tibble with correct rows and columns. (@test_tidiers_robets.R#19) 
  
    Error: testthat unit tests failed
    Execution halted

• checking Rd cross-references ... WARNING

  Missing link or links in documentation object 'sw_augment.Rd':
    ‘rowwise_df_tidiers’
  
  See section 'Cross-references' in the 'Writing R Extensions' manual.

In both

• checking dependencies in R code ... NOTE

  Namespaces in Imports field not imported from:
    ‘lazyeval’ ‘lubridate’ ‘tidyr’
    All declared Imports should be used.
  Missing or unexported object: ‘broom::finish_glance’

• [x] SWMPrExtension

Resulted from rowwise DF tidier deprecations. Issue filed here.

* Version: 1.1.4 * Source code: https://github.com/cran/SWMPrExtension * BugReports: https://github.com/NOAA-OCM/SWMPrExtension/issues * Date/Publication: 2020-05-04 15:10:11 UTC * Number of recursive dependencies: 120 Run `revdep_details(,"SWMPrExtension")` for more info

Newly broken

• checking examples ... ERROR

  Running examples in ‘SWMPrExtension-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: seasonal_dot
  > ### Title: Seasonal Dot Plot
  > ### Aliases: seasonal_dot seasonal_dot.swmpr
  > 
  > ### ** Examples
  > 
  > dat_wq <- elksmwq
  > #dat_wq <- subset(dat_wq, subset = c('2010-01-01 0:00', '2017-01-01 0:00'))
  > dat_wq <- qaqc(dat_wq, qaqc_keep = c(0, 3, 5))
  > 
  > x <-
  +   seasonal_dot(dat_wq, param = 'do_mgl'
  +                , lm_trend = TRUE
  +                , lm_lab = TRUE
  +                , plot_title = TRUE)
  Error: No tidy method for objects of class rowwise_df
  Execution halted

In both

• checking whether package ‘SWMPrExtension’ can be installed ... WARNING

  Found the following significant warnings:
    Warning: package ‘zoo’ was built under R version 3.6.2
  See ‘/Users/max/github/broom/revdep/checks.noindex/SWMPrExtension/new/SWMPrExtension.Rcheck/00install.out’ for details.

• checking dependencies in R code ... NOTE

  Namespace in Imports field not imported from: ‘rgeos’
    All declared Imports should be used.

• [x] tadaatoolbox

Results from changes to tukeyHSD tidier methods. Issue filed here.

* Version: 0.16.1 * Source code: https://github.com/cran/tadaatoolbox * URL: https://github.com/tadaadata/tadaatoolbox * BugReports: https://github.com/tadaadata/tadaatoolbox/issues * Date/Publication: 2018-11-23 11:20:04 UTC * Number of recursive dependencies: 118 Run `revdep_details(,"tadaatoolbox")` for more info

Newly broken

• checking examples ... ERROR

  ...
  [90m 6[39m jahrgang:… 13:Männlich-11…          0   1.16    -[31m0[39m[31m.[39m[31m190[39m      2.51  0.138      
  [90m 7[39m jahrgang:… 11:Weiblich-11…          0   1.58     0.478      2.68  0.000[4m7[24m[4m3[24m[4m6[24m   
  [90m 8[39m jahrgang:… 12:Weiblich-11…          0   0.940   -[31m0[39m[31m.[39m[31m162[39m      2.04  0.143      
  [90m 9[39m jahrgang:… 13:Weiblich-11…          0   2.76     1.41       4.11  0.000[4m0[24m[4m0[24m[4m0[24m207
  [90m10[39m jahrgang:… 13:Männlich-12…          0   0.420   -[31m0[39m[31m.[39m[31m930[39m      1.77  0.948      
  [90m11[39m jahrgang:… 11:Weiblich-12…          0   0.840   -[31m0[39m[31m.[39m[31m262[39m      1.94  0.246      
  [90m12[39m jahrgang:… 12:Weiblich-12…          0   0.200   -[31m0[39m[31m.[39m[31m902[39m      1.30  0.995      
  [90m13[39m jahrgang:… 13:Weiblich-12…          0   2.02     0.670      3.37  0.000[4m3[24m[4m5[24m[4m4[24m   
  [90m14[39m jahrgang:… 11:Weiblich-13…          0   0.420   -[31m0[39m[31m.[39m[31m930[39m      1.77  0.948      
  [90m15[39m jahrgang:… 12:Weiblich-13…          0  -[31m0[39m[31m.[39m[31m220[39m   -[31m1[39m[31m.[39m[31m57[39m       1.13  0.997      
  [90m16[39m jahrgang:… 13:Weiblich-13…          0   1.60     0.041[4m5[24m     3.16  0.040[4m4[24m     
  [90m17[39m jahrgang:… 12:Weiblich-11…          0  -[31m0[39m[31m.[39m[31m640[39m   -[31m1[39m[31m.[39m[31m74[39m       0.462 0.554      
  [90m18[39m jahrgang:… 13:Weiblich-11…          0   1.18    -[31m0[39m[31m.[39m[31m170[39m      2.53  0.125      
  [90m19[39m jahrgang:… 13:Weiblich-12…          0   1.82     0.470      3.17  0.001[4m9[24m[4m0[24m    
  > tadaa_pairwise_tukey(data = ngo, deutsch, jahrgang, print = "console")
  Error in tadaa_pairwise_tukey(data = ngo, deutsch, jahrgang, print = "console") : 
    1 assertions failed:
   * The following variable names are not found in the dust table:
   * comparison
  Calls: tadaa_pairwise_tukey ... <Anonymous> -> sprinkle_colnames.default -> <Anonymous>
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    [90m  6. [39mtibble:::`$<-.tbl_df`(...)
    [90m  7. [39mtibble:::tbl_subassign(...)
    [90m  8. [39mtibble:::vectbl_recycle_rhs(...)
    [90m  9. [39mbase::tryCatch(...)
    [90m 10. [39mbase:::tryCatchList(expr, classes, parentenv, handlers)
    [90m 11. [39mbase:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
    [90m 12. [39mvalue[[3L]](cond)
  
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 153 | SKIPPED: 1 | WARNINGS: 32 | FAILED: 2 ]
    1. Error: Pairwise tukey returns correct data structure (@test-pairwise_tests.R#50) 
    2. Error: tadaa_pairwise_tukey produces plot (@test-plots.R#27) 
  
    Error: testthat unit tests failed
    Execution halted

In both

• checking data for non-ASCII characters ... NOTE

    Note: found 3 marked UTF-8 strings

• [x] timetk

Results from deprecation of tidy.table(). Issue filed here.

* Version: 1.0.0 * Source code: https://github.com/cran/timetk * URL: https://github.com/business-science/timetk * BugReports: https://github.com/business-science/timetk/issues * Date/Publication: 2020-04-19 17:50:02 UTC * Number of recursive dependencies: 150 Run `revdep_details(,"timetk")` for more info

Newly broken

• checking examples ... ERROR

  ...
  Business Science offers a 1-hour course - Learning Lab #9: Performance Analysis & Portfolio Optimization with tidyquant!
  [39m[34m</> Learn more at: https://university.business-science.io/p/learning-labs-pro </>[39m
  
  Attaching package: ‘tidyquant’
  
  The following objects are masked from ‘package:timetk’:
  
      summarise_by_time, summarize_by_time
  
  > library(timetk)
  > 
  > # Filter values in January 1st through end of February, 2013
  > FANG %>%
  +     group_by(symbol) %>%
  +     filter_by_time(date, "start", "2013-02") %>%
  +     plot_time_series(date, adjusted, .facet_ncol = 2, .interactive = FALSE)
  Warning: 'tidy.table' is deprecated.
  See help("Deprecated")
  Error in dimnames(x) <- dnx : 'dimnames' applied to non-array
  Calls: %>% ... eval -> eval -> data.frame -> do.call -> provideDimnames
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 233 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 10 ]
    1.  Error: tk_get_timeseries_summary(datetime) test returns correct format. (@test_tk_get_timeseries.R#79) 
    2.  Error: tk_get_timeseries_summary(date) test returns correct format. (@test_tk_get_timeseries.R#91) 
    3.  Error: tk_get_timeseries_summary(yearmon) test returns correct format. (@test_tk_get_timeseries.R#103) 
    4.  Error: tk_get_timeseries_summary(yearqtr) test returns correct format. (@test_tk_get_timeseries.R#116) 
    5.  Error: tk_make_future_timeseries(datetime) test returns correct format. (@test_tk_make_future_timeseries.R#12) 
    6.  Error: tk_make_future_timeseries(date) test returns correct format. (@test_tk_make_future_timeseries.R#53) 
    7.  Error: tk_make_future_timeseries(predict_every_two) test returns correct format. (@test_tk_make_future_timeseries.R#309) 
    8.  Error: tk_make_future_timeseries(predict_every_three) test returns correct format. (@test_tk_make_future_timeseries.R#348) 
    9.  Error: tk_make_future_timeseries(predict_every_four) test returns correct format. (@test_tk_make_future_timeseries.R#386) 
    10. Error: tk_make_future_timeseries(predict_random) test returns correct format. (@test_tk_make_future_timeseries.R#430) 
  
    Error: testthat unit tests failed
    Execution halted

In both

• checking installed package size ... NOTE

    installed size is  6.5Mb
    sub-directories of 1Mb or more:
      doc   5.1Mb

• checking data for non-ASCII characters ... NOTE

    Note: found 2750 marked UTF-8 strings

• [x] widyr

Results from deprecation of sparse matrix tidiers, which needs to be undone. Fixing now.

* Version: 0.1.3 * Source code: https://github.com/cran/widyr * URL: http://github.com/dgrtwo/widyr * BugReports: http://github.com/dgrtwo/widyr/issues * Date/Publication: 2020-04-12 06:00:02 UTC * Number of recursive dependencies: 113 Run `revdep_details(,"widyr")` for more info

Newly broken

• checking examples ... ERROR

  ...
  The following objects are masked from ‘package:stats’:
  
      filter, lag
  
  The following objects are masked from ‘package:base’:
  
      intersect, setdiff, setequal, union
  
  > dat <- tibble(group = rep(1:5, each = 2),
  +               letter = c("a", "b",
  +                          "a", "c",
  +                          "a", "c",
  +                          "b", "e",
  +                          "b", "f"))
  > 
  > # count the number of times two letters appear together
  > pairwise_count(dat, letter, group)
  Error in `colnames<-`(`*tmp*`, value = c("item1", "item2", "value")) : 
    attempt to set 'colnames' on an object with less than two dimensions
  Calls: pairwise_count ... freduce -> <Anonymous> -> custom_melt -> colnames<-
  Execution halted

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 38 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 10 ]
    1.  Error: pairing and counting works (@test-pairwise-count.R#16) 
    2.  Error: We can count with a weight column (@test-pairwise-count.R#63) 
    3.  Error: Counts co-occurrences of words in Pride & Prejudice (@test-pairwise-count.R#79) 
    4.  Error: Can count within groups (@test-pairwise-count.R#104) 
    5.  Error: Can count within groups (@test-pairwise-count.R#103) 
    6.  Error: (unknown) (@test-pairwise-count.R#103) 
    7.  Error: pairwise_similarity computes pairwise cosine similarity (@test-pairwise-similarity.R#14) 
    8.  Error: pairwise_similarity retains factor levels (@test-pairwise-similarity.R#29) 
    9.  Failure: Can perform 'squarely' operations on pairs of items (@test-squarely.R#14) 
    10. Failure: Can perform 'squarely' within groups (@test-squarely.R#25) 
  
    Error: testthat unit tests failed
    Execution halted

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