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
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
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
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
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
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
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
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
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.
A thread to document working through reverse dependency checks for 0.7.0.
broom
changes will be pushed to the0-7-0-9000-revdeps
branch and I'll link out to issues/PRs on other repositories when relevant.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.
Newly broken
checking examples ... ERROR
In both
checking dependencies in R code ... NOTE
[x] arsenal
Results from deprecation of
confint_tidy()
--issue filed here.Newly broken
checking tests ...
checking dependencies in R code ... NOTE
[x] biobroom
Results from deprecation of
fix_data_frame()
--issue filed here.Newly broken
checking tests ...
Newly fixed
In both
checking dependencies in R code ... NOTE
checking R code for possible problems ... NOTE
[x] breathtestcore
Results from deprecation of
summary()
tidiers--issue filed here.Newly broken
checking examples ... ERROR
checking tests ...
In both
checking Rd cross-references ... NOTE
[x] CGPfunctions
Newly broken
checking examples ... ERROR
[x] chest
Resulted from the removal of the
n
column inglance.coxph
. Corrected.Newly broken
checking examples ... ERROR
In both
checking dependencies in R code ... NOTE
[x] DeLorean
Not a broom issue.
Newly broken
checking installed package size ... NOTE
checking dependencies in R code ... NOTE
checking for GNU extensions in Makefiles ... NOTE
Newly fixed
checking whether package ‘DeLorean’ can be installed ... ERROR
[x] disk.frame
Not a broom issue.
Newly broken
In both
checking whether package ‘disk.frame’ can be installed ... WARNING
[x] disto
Results from not exporting
tidy.table()
. Issue filed here.Newly broken
checking examples ... ERROR
In both
checking dependencies in R code ... NOTE
[x] ERSA
Results from deprecation of
summary()
tidiers. Issue filed here.Newly broken
checking examples ... ERROR
[x] eyetrackingR
This package is no longer maintained.
Newly broken
checking examples ... ERROR
checking tests ...
[x] GGally
Results from requiring the
se_fit
argument inaugment.*()
methods. Put in a PR here.Newly broken
checking examples ... ERROR
checking tests ...
[x] ggasym
Results from warning -> error switch -- unit tests reflected broom functionality. Issue filed here.
Newly broken
checking tests ...
[x] glmmfields
Results from planned deprecation of mixed model tidiers to
broom.mixed
. Issue filed here.Newly broken
In both
checking for GNU extensions in Makefiles ... NOTE
[x] gtsummary
Resulted from deprecation of
confint_tidy()
. Issue filed here.Newly broken
checking examples ... ERROR
[x] jtools
Related to use of previously unexported
svyglm
tidier methods. Issue filed here.Newly broken
checking tests ...
In both
checking Rd cross-references ... NOTE
[x] konfound
Results from planned deprecation of mixed model tidiers to
broom.mixed
. Issue filed here.Newly broken
checking examples ... ERROR
checking tests ...
In both
checking dependencies in R code ... NOTE
[x] merTools
Results from planned deprecation of mixed model tidiers to
broom.mixed
. Issue filed here.Newly broken
checking examples ... ERROR
checking tests ...
In both
checking whether package ‘merTools’ can be installed ... WARNING
[x] mice
Relevant to changes in
glance.*()
methods forlm
andaov
objects. Issue filed here/Newly broken
checking examples ... ERROR
checking tests ...
[x] moderndive
False positive.
master
works fine, which will be submitted soon.Newly broken
checking tests ...
In both
checking Rd cross-references ... NOTE
[x] NetworkExtinction
Uncovered a bug where the
augment.nls()
method didn't return.resid
. Fixed on0-7-0-9000-revdeps
branch.Newly broken
checking examples ... ERROR
[x] nlstimedist
Same bug as for NetworkExtinction. Fixed.
Newly broken
checking examples ... ERROR
checking tests ...
[x] panelr
Results from planned deprecation of mixed model tidiers to
broom.mixed
. Issue filed here.Newly broken
checking examples ... ERROR
checking tests ...
In both
checking whether package ‘panelr’ can be installed ... WARNING
[x] pixiedust
Results from testing a broom warning that is now an error. Issue filed here.
Newly broken
checking tests ...
[x] qgcomp
Results from deprecation of
finish_glance()
. Issued filed here.Newly broken
checking dependencies in R code ... NOTE
[x] radiant.model
Resulted from the
augment()
rewrite. Issue filed here.Newly broken
checking tests ...
In both
checking whether package ‘radiant.model’ can be installed ... WARNING
[x] RCT
Not a broom problem.
Newly broken
checking examples ... ERROR
checking tests ...
[x] rstatix
Results from deprecation of
summary().*
tidiers. Issue filed here.Newly broken
checking examples ... ERROR
[x] simglm
Results from planned deprecation of mixed model tidiers to
broom.mixed
. Issue filed here.Newly broken
checking examples ... ERROR
checking tests ...
[x] survminer
This is an issue that is unrelated to broom and is addressed on 472 of that package.
Newly broken
checking examples ... ERROR
In both
checking whether package ‘survminer’ can be installed ... WARNING
checking installed package size ... NOTE
[x] survutils
Results from new
conf.int = FALSE
default. Issue filed here.Newly broken
checking tests ...
[x] sweep
Resulted from
finish_glance()
and rowwise DF tidier deprecations. Issue filed here.Newly broken
checking examples ... ERROR
checking tests ...
checking Rd cross-references ... WARNING
In both
checking dependencies in R code ... NOTE
[x] SWMPrExtension
Resulted from rowwise DF tidier deprecations. Issue filed here.
Newly broken
checking examples ... ERROR
In both
checking whether package ‘SWMPrExtension’ can be installed ... WARNING
checking dependencies in R code ... NOTE
[x] tadaatoolbox
Results from changes to
tukeyHSD
tidier methods. Issue filed here.Newly broken
checking examples ... ERROR
checking tests ...
In both
checking data for non-ASCII characters ... NOTE
[x] timetk
Results from deprecation of
tidy.table()
. Issue filed here.Newly broken
checking examples ... ERROR
checking tests ...
In both
checking installed package size ... NOTE
checking data for non-ASCII characters ... NOTE
[x] widyr
Results from deprecation of sparse matrix tidiers, which needs to be undone. Fixing now.
Newly broken
checking examples ... ERROR
checking tests ...