reverse dependency checks for 0.7.0 #862

simonpcouch · 2020-05-26T18:04:56Z

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.

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.

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’

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').

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’

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

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.

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.

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.

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.

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

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

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

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

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.
```

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

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’

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.

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.

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

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’

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

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

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.

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

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’

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.

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

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

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

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

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

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’

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.

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
```

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
```

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

The text was updated successfully, but these errors were encountered:

github-actions · 2021-03-08T00:25:34Z

This issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with a reprex: https://reprex.tidyverse.org) and link to this issue.

simonpcouch added a commit that referenced this issue May 26, 2020

note deprecation of fix_data_frame() (#806, #862)

f12396c

simonpcouch added a commit that referenced this issue May 26, 2020

restore n column re: chest revdepcheck (#862)

f6d1b99

This was referenced May 27, 2020

remove finish_glance and add nobs #597

Merged

Changes re: revdepcheck for 0.7.0 (closes #862) #863

Merged

simonpcouch closed this as completed May 27, 2020

simonpcouch mentioned this issue May 27, 2020

Removed columns in glance.aov() #864

Closed

simonpcouch mentioned this issue Jun 24, 2020

reverse dependency checks for 0.7.0, round 3 #885

Closed

simonpcouch mentioned this issue Jul 8, 2020

Fixes for 0.7.0 revdepchecks #890

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reverse dependency checks for 0.7.0 #862

reverse dependency checks for 0.7.0 #862

simonpcouch commented May 26, 2020 •

edited

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github-actions bot commented Mar 8, 2021

reverse dependency checks for 0.7.0 #862

reverse dependency checks for 0.7.0 #862

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simonpcouch commented May 26, 2020 • edited Loading

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github-actions bot commented Mar 8, 2021

simonpcouch commented May 26, 2020 •

edited

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