fwildclusterboot submission

[s3alfisc]

Submitting Author Name: Alexander Fischer Submitting Author Github Handle: @s3alfisc Other Package Authors Github handles: (comma separated, delete if none) @droodman Repository: https://github.com/s3alfisc/fwildclusterboot/tree/master Version submitted: 0.9.1 (in ropensci branch) Submission type: Stats Badge grade: silver Editor: @helske Reviewers: @meghapsimatrix, @markean

Due date for @meghapsimatrix: 2023-04-17

Due date for @markean: 2023-05-29 Archive: TBD Version accepted: TBD Language: en

• Paste the full DESCRIPTION file inside a code block below:

Package: fwildclusterboot
Title: Fast Wild Cluster Bootstrap Inference for Linear Models
Version: 0.13.2
Authors@R: c(
    person("Alexander", "Fischer", , "[email protected]", role = c("aut", "cre")),
    person("David", "Roodman", role = "aut"),
    person("Achim", "Zeileis", role = "ctb",
           comment = "Author of included sandwich fragments"),
    person("Nathaniel", "Graham", role = "ctb",
           comment = "Contributor to included sandwich fragments"),
    person("Susanne", "Koell", role = "ctb",
           comment = "Contributor to included sandwich fragments"),
    person("Laurent", "Berge", role = "ctb",
           comment = "Author of included fixest fragments"),
    person("Sebastian", "Krantz", role = "ctb")
  )
Description: Implementation of fast algorithms for wild cluster bootstrap
    inference developed in 'Roodman et al' (2019, 'STATA' Journal,
    <doi:10.1177/1536867X19830877>) and 'MacKinnon et al' (2022), which
    makes it feasible to quickly calculate bootstrap test statistics based
    on a large number of bootstrap draws even for large samples.  Multiple
    bootstrap types as described in 'MacKinnon, Nielsen & Webb' (2022) are
    supported.  Further, 'multiway' clustering, regression weights,
    bootstrap weights, fixed effects and 'subcluster' bootstrapping are
    supported. Further, both restricted ('WCR') and unrestricted ('WCU')
    bootstrap are supported. Methods are provided for a variety of fitted
    models, including 'lm()', 'feols()' (from package 'fixest') and
    'felm()' (from package 'lfe').  Additionally implements a
    'heteroskedasticity-robust' ('HC1') wild bootstrap.  Last, the package
    provides an R binding to 'WildBootTests.jl', which provides additional
    speed gains and functionality, including the 'WRE' bootstrap for
    instrumental variable models (based on models of type 'ivreg()' from
    package 'ivreg') and hypotheses with q > 1.
License: GPL-3
URL: https://s3alfisc.github.io/fwildclusterboot/
BugReports: https://github.com/s3alfisc/fwildclusterboot/issues/
Imports:
    collapse,
    dqrng,
    dreamerr,
    Formula,
    generics,
    gtools,
    JuliaConnectoR,
    MASS,
    Matrix,
    Rcpp,
    rlang,
    summclust
Suggests:
    bench,
    broom,
    clubSandwich,
    covr,
    data.table,
    fabricatr,
    fixest,
    gt,
    ivreg,
    knitr,
    lfe,
    lmtest,
    modelsummary,
    rmarkdown,
    sandwich,
    testthat (>= 3.0.0),
    tibble
LinkingTo:
    Rcpp,
    RcppArmadillo,
    RcppEigen
VignetteBuilder:
    knitr
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE, roclets = c ("namespace", "rd",
    "srr::srr_stats_roclet"))
RoxygenNote: 7.2.1
SystemRequirements: Version Requirements to run the wild bootstrap through
    Julia - Julia (>= 1.8), WildBootTests.jl (>=0.9).  Julia is
    downloadable via the official Julia website
    (https://julialang.org/downloads/), WildBootTests.jl via Julia's
    package manager (https://docs.julialang.org/en/v1/stdlib/Pkg/) or its
    github repository (https://github.com/droodman/WildBootTests.jl)

Pre-submission Inquiry

• [x] A pre-submission inquiry has been approved in #542

General Information

• Who is the target audience and what are scientific applications of this package? The target audience is academic social scientists (economics, political science, sociology). fwildclusterboot should be used whenever regression errors are "clustered" into few groups, in which case inference based on asymptotic approximations might fail.

• Paste your responses to our General Standard G1.1 here, describing whether your software is:

  • The first implementation of a novel algorithm; or
  • The first implementation within R of an algorithm which has previously been implemented in other languages or contexts; or
  • An improvement on other implementations of similar algorithms in R.

fwildclusterboot is the first R-implementation of the 'fast' wild cluster bootstrap algorithm outlined in Roodman et al (2019, Stata Journal) and implemented in Stata via the boottest package. Recently, @droodman has also ported the algorithm to Julia. Besides implementing the "fast & wild" algorithm in native R, fwildclusterboot also allows to call WildBootTests.jl via the JuliaConnectoR package. The "fast" algorithm is significantly faster than any other R-implementations of the wild cluster bootstrap to date (e.g. see here).

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

Yes.

Badging

• What grade of badge are you aiming for? (bronze, silver, gold)

At a minimal level, I strive for a silver badge.

• If aiming for silver or gold, describe which of the four aspects listed in the Guide for Authors chapter the package fulfils (at least one aspect for silver; three for gold)

1. Compliance with a good number of standards; 2) I strive for compliance with all standards regarding a) documentation and b) testing.

Technical checks

Confirm each of the following by checking the box.

• [x] I have read the rOpenSci packaging guide.
• [x] I have read the author guide and I expect to maintain this package for at least 2 years or have another maintainer identified.
• [x] I/we have read the Statistical Software Peer Review Guide for Authors.
• [x] I/we have run autotest checks on the package, and ensured no tests fail.
• [x] The srr_stats_pre_submit() function confirms this package may be submitted.
• [ ] The pkgcheck() function confirms this package may be submitted - alternatively, please explain reasons for any checks which your package is unable to pass.

pkgcheck::pkgcheck() currently fails on my machine with the following error message: "Error in normalizePath(path.expand(path), winslash, mustWork).: path[1]="C:/.../fwildclusterboot/NA" The system cannot find the specified file. It also fails on github-actions on the ropensci branch.

Also, note that the CMD checks currently fail on github actions as the gtools package has been orphaned - I am monitoring the situation, but it looks like the package will not be removed from CRAN.

This package:

• [x] does not violate the Terms of Service of any service it interacts with.
• [x] has a CRAN and OSI accepted license.
• [x] contains a README with instructions for installing the development version.

Publication options

• [x] Do you intend for this package to go on CRAN? The package is already on CRAN. In case major changes are suggested during the review, I would consider integrating them into a successor package (e.g. 'fwildclusterboot2').
• [ ] Do you intend for this package to go on Bioconductor?

Code of conduct

• [x] I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

[ropensci-review-bot]

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

[ropensci-review-bot]

Error (500). The editorcheck service is currently unavailable

[emilyriederer]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

Error (500). The editorcheck service is currently unavailable

[s3alfisc]

Hi @emilyriederer, is it possible that the editor check bot fails because I have submitted the package via a side-branch? @mpadge mentioned in the pre-submission that some of the automated tools might fail in this case, but suggested to nevertheless submit via a non default branch for testing purposes.

[emilyriederer]

Looks like @mpadge beat me to this but it appears we have our answer. Marc, I assume we shall wait to proceed until this issue is closed? Thanks!

[mpadge]

Thanks @emilyriederer, because of this submission we now have an ability to process packages with non-default review branches. You (or indeed @s3alfisc) may call check package at any time. (But I've noted to @s3alfisc elsewhere that R CMD check currently fails on his package because our check systems don't have Julia installed.)

[s3alfisc]

Thanks @mpadge - it looks like I have some work to do :) I will trigger check page once I believe I have managed to align the package with all pkgcheck requirements!

[s3alfisc]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

:rocket:

Editor check started

:wave:

[ropensci-review-bot]

Checks for fwildclusterboot (v0.10)

git hash: 274030f8

• :heavy_check_mark: Package is already on CRAN.
• :heavy_check_mark: has a 'codemeta.json' file.
• :heavy_check_mark: has a 'contributing' file.
• :heavy_check_mark: uses 'roxygen2'.
• :heavy_check_mark: 'DESCRIPTION' has a URL field.
• :heavy_check_mark: 'DESCRIPTION' has a BugReports field.
• :heavy_check_mark: Package has at least one HTML vignette
• :heavy_multiplication_x: These functions do not have examples: [check_mboottest_args_plus, check_r_lean, cpp_get_nb_threads, eigenMapMatMult, model_matrix, nobs.boottest, teststat].
• :heavy_multiplication_x: Function names are duplicated in other packages
• :heavy_check_mark: Package has continuous integration checks.
• :heavy_multiplication_x: Package coverage failed
• :heavy_multiplication_x: R CMD check found 1 error.
• :heavy_check_mark: R CMD check found no warnings.

Important: All failing checks above must be addressed prior to proceeding

Package License: GPL-3

---

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

• Regression and Supervised Learning

:heavy_check_mark: All applicable standards [v0.1.0] have been documented in this package (70 complied with; 46 N/A standards)

Click to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

---

2. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	385
internal	fwildclusterboot	104
internal	stats	80
internal	utils	8
internal	graphics	3
internal	compiler	1
imports	collapse	14
imports	dreamerr	10
imports	generics	5
imports	dqrng	5
imports	Matrix	3
imports	Matrix.utils	3
imports	JuliaConnectoR	1
imports	Formula	NA
imports	Rcpp	NA
suggests	fabricatr	6
suggests	fixest	NA
suggests	lfe	NA
suggests	ivreg	NA
suggests	clubSandwich	NA
suggests	sandwich	NA
suggests	lmtest	NA
suggests	data.table	NA
suggests	covr	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	broom	NA
suggests	modelsummary	NA
suggests	bench	NA
suggests	testthat	NA
suggests	tibble	NA
linking_to	Rcpp	NA
linking_to	RcppArmadillo	NA
linking_to	RcppEigen	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

length (36), call (31), list (28), c (16), lapply (13), vapply (13), as.vector (11), names (11), t (11), drop (10), stop (10), unique (10), rep (9), ifelse (8), paste0 (8), data.frame (7), match.call (7), which (7), as.matrix (6), ncol (6), nrow (6), replace (6), sqrt (6), mode (5), seq_along (5), vector (5), as.numeric (4), for (4), is.null (4), mean (4), Reduce (4), sample (4), sum (4), switch (4), tcrossprod (4), abs (3), col (3), colnames (3), environment (3), q (3), as.integer (2), attr (2), crossprod (2), getOption (2), if (2), loadedNamespaces (2), min (2), norm (2), paste (2), Recall (2), solve (2), suppressWarnings (2), append (1), as.character (1), as.factor (1), cbind (1), class (1), do.call (1), exp (1), integer (1), is.na (1), is.numeric (1), logical (1), max (1), message (1), sample.int (1), seq (1), sort (1), Sys.getenv (1), try (1), unlist (1)

fwildclusterboot

get_ssc_julia (8), check_set_full_enumeration (7), set_seed (7), teststat (6), boot_algo_julia (5), crosstab (4), get_cluster (4), model_matrix (4), boot_algo2 (3), cpp_get_nb_threads (3), eigenMapMatMult (3), get_bootstrap_pvalue (3), get_ssc (3), demean_fe (2), gtools_permutations (2), preprocess2.felm (2), preprocess2.fixest (2), preprocess2.lm (2), transform_fe (2), boottest (1), boottest.felm (1), boottest.fixest (1), boottest.ivreg (1), boottest.lm (1), check_boottest_args_plus (1), check_mboottest_args_plus (1), check_params_in_model (1), check_r_lean (1), check_set_nthreads (1), confint.boottest (1), crosstab4 (1), get_seed (1), get_start_vals (1), getBoottest_boot_algo (1), getBoottest_nthreads (1), glance.boottest (1), invert_p_val (1), mboottest (1), mboottest.felm (1), mboottest.fixest (1), mboottest.lm (1), model_matrix.felm (1), model_matrix.lm (1), nobs.boottest (1), nobs.mboottest (1), p_val_null2 (1), p_val_null2_x (1), p_val_null2_x_sign_level (1), preprocess2.ivreg (1), to_integer (1), wildboottestHC (1)

stats

weights (24), model.matrix (12), formula (8), coef (6), na.omit (6), model.frame (5), nobs (4), aggregate (3), model.response (3), na.exclude (3), reformulate (2), na.action (1), na.pass (1), rlnorm (1), update (1)

collapse

fsum (7), GRP (4), qF (3)

dreamerr

validate_dots (10)

utils

data (7), combn (1)

fabricatr

draw_binary (2), draw_normal_icc (2), draw_ordered (1), fabricate (1)

dqrng

dqsample (4), dqset.seed (1)

generics

tidy (4), glance (1)

graphics

abline (3)

Matrix

t (2), Diagonal (1)

Matrix.utils

aggregate.Matrix (3)

compiler

cmpfun (1)

JuliaConnectoR

juliaImport (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

---

3. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in C++ (8% in 2 files) and R (92% in 28 files)
• 2 authors
• 2 vignettes
• 1 internal data file
• 9 imported packages
• 33 exported functions (median 8 lines of code)
• 121 non-exported functions in R (median 26 lines of code)
• 13 R functions (median 17 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	28	88.2
files_src	2	79.1
files_vignettes	2	85.7
files_tests	17	95.3
loc_R	3873	93.2
loc_src	325	37.1
loc_vignettes	436	74.7
loc_tests	5291	98.3	TRUE
num_vignettes	2	89.2
data_size_total	14024	72.7
data_size_median	14024	81.0
n_fns_r	154	85.7
n_fns_r_exported	33	80.4
n_fns_r_not_exported	121	87.1
n_fns_src	13	35.0
n_fns_per_file_r	3	55.2
n_fns_per_file_src	6	61.3
num_params_per_fn	2	11.9
loc_per_fn_r	23	66.0
loc_per_fn_r_exp	8	16.3
loc_per_fn_r_not_exp	26	73.5
loc_per_fn_src	17	59.6
rel_whitespace_R	18	92.7
rel_whitespace_src	30	48.8
rel_whitespace_vignettes	43	83.2
rel_whitespace_tests	11	96.1	TRUE
doclines_per_fn_exp	29	31.0
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	132	83.4

---

3a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

---

4. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
2828472276	pages build and deployment	success	b71a32	155	2022-08-09
2827237407	pkgcheck	failure	274030	24	2022-08-09
2862000970	pkgdown	failure	85eba8	101	2022-08-15
2862000975	R-CMD-check	failure	85eba8	458	2022-08-15
2862000968	test-coverage	failure	85eba8	435	2022-08-15

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following error:

1. checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ▆
   1. ├─fwildclusterboot::boottest(...) at test_fixest_sugar.R:44:2
   2. └─fwildclusterboot:::boottest.fixest(...)
   3. └─fwildclusterboot:::preprocess2.fixest(...)

   4. └─fwildclusterboot:::get_cluster(...)
      

   5.   ├─stats::model.frame(clustid_fml, cluster_tmp, na.action = na.pass)
      

   6.   └─stats::model.frame.default(clustid_fml, cluster_tmp, na.action = na.pass)
      

   7.     ├─base::as.data.frame(data)
      

   8.     └─base::as.data.frame.default(data)
      

── Error (test_multicollinearity.R:16:3): test multicollinearity ─────────────── Error in feols(Y ~ X1 + X2, data = data): could not find function "feols"

[ FAIL 2 | WARN 4 | SKIP 15 | PASS 59 ] Error: Test failures Execution halted

R CMD check generated the following notes:

1. checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: libs 5.9Mb
2. checking R code for possible problems ... NOTE mboottest.lm: no visible binding for global variable ‘teststat_boot’ Undefined global functions or variables: teststat_boot

R CMD check generated the following test_fail:

1. library(testthat)

library(fwildclusterboot)

test_check("fwildclusterboot") The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
Error in i(treatment, ideology1) : could not find function "i" test_tidy.R, q = 1 skipped as 'JULIA_BINDIR' not found. test_tidy.R, q > 1 skipped as 'JULIA_BINDIR' not found. Loading required namespace: data.table test-error_warning.R with q = 1 skipped as JULIA_BINDIR not found. test-error_warning.R with q > 1 skipped as JULIA_BINDIR not found. Loading required package: Matrix Error in post1 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | 0 | 0 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | Utility_state : operations are possible only for numeric, logical or complex types Error in post1 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | 0 | 0 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | Utility_state : operations are possible only for numeric, logical or complex types Error in post1 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | 0 | 0 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | Utility_state : operations are possible only for numeric, logical or complex types test-global_vars.R skipped as JULIA_BINDR not found. test-method_equivalence.R I skipped as JULIA_BINDR not found. test-method_equivalence.R II skipped as JULIA_BINDR not found. test-r-vs-julia.R skipped as JULIA_BINDIR not found. test-seed.R skipped as JULIA_BINDR not found. test-tstat_equivalence.R I skipped as JULIA_BINDR not found. test-tstat_equivalence.R II skipped as JULIA_BINDR not found. test-stat_equivalence.R III skipped as JULIA_BINDR not found. Error in Q1_immigration + Q2_defense : non-numeric argument to binary operator Error in Q1_immigration + Q2_defense : non-numeric argument to binary operator [ FAIL 2 | WARN 4 | SKIP 15 | PASS 59 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (15)

══ Warnings ════════════════════════════════════════════════════════════════════ ── Warning (test-uncategorized.R:44:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:

1. fwildclusterboot::boottest(...) at test-uncategorized.R:44:2
2. fwildclusterboot:::boottest.fixest(...)
3. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:52:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
4. fwildclusterboot::boottest(...) at test-uncategorized.R:52:2
5. fwildclusterboot:::boottest.fixest(...)
6. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:60:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
7. fwildclusterboot::boottest(...) at test-uncategorized.R:60:2
8. fwildclusterboot:::boottest.fixest(...)
9. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:68:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
10. fwildclusterboot::boottest(...) at test-uncategorized.R:68:2
11. fwildclusterboot:::boottest.fixest(...)
12. fwildclusterboot:::check_set_full_enumeration(...)

══ Failed tests ════════════════════════════════════════════════════════════════ ── Error (test_fixest_sugar.R:44:3): test fixest formula sugar ───────────────── Error in as.data.frame.default(data): cannot coerce class '"try-error"' to a data.frame Backtrace: ▆

1. ├─fwildclusterboot::boottest(...) at test_fixest_sugar.R:44:2
2. └─fwildclusterboot:::boottest.fixest(...)
3. └─fwildclusterboot:::preprocess2.fixest(...)

4. └─fwildclusterboot:::get_cluster(...)
   

5.   ├─stats::model.frame(clustid_fml, cluster_tmp, na.action = na.pass)
   

6.   └─stats::model.frame.default(clustid_fml, cluster_tmp, na.action = na.pass)
   

7.     ├─base::as.data.frame(data)
   

8.     └─base::as.data.frame.default(data)
   

── Error (test_multicollinearity.R:16:3): test multicollinearity ─────────────── Error in feols(Y ~ X1 + X2, data = data): could not find function "feols"

[ FAIL 2 | WARN 4 | SKIP 15 | PASS 59 ] Error: Test failures Execution halted

R CMD check generated the following check_fails:

1. rcmdcheck_undefined_globals
2. rcmdcheck_tests_pass
3. rcmdcheck_reasonable_installed_size

Test coverage with covr

ERROR: Test Coverage Failed

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
get_cluster	45
gtools_permutations	34
boot_algo_julia	20
boot_algo2	17
getBoottest_nthreads	16
check_boottest_args_plus	15

Static code analyses with lintr

lintr found the following 35 potential issues:

message	number of times
Avoid library() and require() calls in packages	12
Lines should not be more than 80 characters.	23

---

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 2 function names are duplicated in other packages:

• • model_matrix from bayesbr, hardhat, mcmcsae, modelr, ZIprop
• • pval from CIPerm, dostats, dostats, GUIDE, learnstats, molic, mosaic, overlapptest, RPtests, timereg

---

Package Versions

package	version
pkgstats	0.1.1.20
pkgcheck	0.1.0.3
srr	0.0.1.176

---

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.

[s3alfisc]

Hi, I wanted to give some feedback on the state of the package:

• Over the last weeks, I have integrated new bootstrap variants to the package as recently suggested in MacKinnon, Nielsen & Webb. The new variants seem to perform even better than "old" variants implemented in fwildclusterboot and are also relatively fast to compute.
• I have spent quite some time on trying to make the package compliant with all pkgchecks - unfortunately, I still fail to run the entire process locally, so please apologize if it will take me one or two more attempts to fully align the package. When running pkgcheck::pkgcheck(), I usually get the following error Error in normalizePath(path.expand(path), winslash, mustWork) : path[1]="C:\Users\...\fwildclusterboot/NA": The system cannot find the file specified. I also cannot get the pkgcheck github action to run with fwildclusterboot. For another package of mine, the pkgcheck action runs flawlessly .
• As suggested by @mpadge , I have added a clause that will prohibit that unit tests will run if Julia is not installed. Unfortunately, this has affected the CI statistics of the package by disabling any Julia based testing on CI. I am currently investigating this - the computed coverage of 56% does not look very good & is quite a bit higher when adding all tests against Julia (it should be around 85%).

[s3alfisc]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

:rocket:

Editor check started

:wave:

[ropensci-review-bot]

Checks for fwildclusterboot (v0.11)

git hash: 00c38b8d

• :heavy_check_mark: Package is already on CRAN.
• :heavy_check_mark: has a 'codemeta.json' file.
• :heavy_check_mark: has a 'contributing' file.
• :heavy_multiplication_x: The following functions have no documented return values: [boot_ssc, pval, teststat]
• :heavy_check_mark: uses 'roxygen2'.
• :heavy_check_mark: 'DESCRIPTION' has a URL field.
• :heavy_check_mark: 'DESCRIPTION' has a BugReports field.
• :heavy_check_mark: Package has at least one HTML vignette
• :heavy_check_mark: All functions have examples.
• :heavy_multiplication_x: Function names are duplicated in other packages
• :heavy_check_mark: Package has continuous integration checks.
• :heavy_multiplication_x: Package coverage failed
• :heavy_multiplication_x: R CMD check found 1 error.
• :heavy_check_mark: R CMD check found no warnings.

Important: All failing checks above must be addressed prior to proceeding

Package License: GPL-3

---

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

• Regression and Supervised Learning

:heavy_check_mark: All applicable standards [v0.1.0] have been documented in this package (70 complied with; 46 N/A standards)

Click to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

---

2. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	441
internal	fwildclusterboot	113
internal	stats	83
internal	utils	8
internal	graphics	3
internal	compiler	1
imports	collapse	14
imports	dreamerr	10
imports	generics	5
imports	dqrng	5
imports	MASS	4
imports	Matrix	3
imports	Matrix.utils	3
imports	JuliaConnectoR	1
imports	summclust	1
imports	sandwich	1
imports	Formula	NA
imports	Rcpp	NA
suggests	fabricatr	6
suggests	fixest	NA
suggests	lfe	NA
suggests	ivreg	NA
suggests	clubSandwich	NA
suggests	lmtest	NA
suggests	data.table	NA
suggests	covr	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	broom	NA
suggests	modelsummary	NA
suggests	bench	NA
suggests	testthat	NA
suggests	tibble	NA
linking_to	Rcpp	NA
linking_to	RcppArmadillo	NA
linking_to	RcppEigen	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

length (40), call (31), list (30), lapply (20), c (16), t (15), vapply (13), as.vector (12), drop (12), names (12), unique (12), stop (10), ifelse (9), Reduce (9), rep (9), paste0 (8), which (8), data.frame (7), match.call (7), mode (7), nrow (7), sqrt (7), vector (7), as.matrix (6), for (6), ncol (6), replace (6), switch (6), seq_along (5), as.numeric (4), crossprod (4), is.null (4), mean (4), sample (4), solve (4), sum (4), tcrossprod (4), abs (3), col (3), colnames (3), environment (3), q (3), as.factor (2), as.integer (2), attr (2), dim (2), getOption (2), if (2), loadedNamespaces (2), matrix (2), min (2), norm (2), paste (2), Recall (2), split (2), suppressWarnings (2), append (1), as.character (1), cbind (1), class (1), colSums (1), diag (1), do.call (1), eval (1), exp (1), integer (1), is.na (1), is.numeric (1), logical (1), max (1), message (1), row (1), sample.int (1), seq (1), sort (1), Sys.getenv (1), try (1), tryCatch (1), unlist (1)

fwildclusterboot

get_ssc_julia (8), check_set_full_enumeration (7), set_seed (7), teststat (6), boot_algo_julia (5), crosstab (4), get_bootstrap_pvalue (4), get_cluster (4), model_matrix (4), boot_algo2 (3), cpp_get_nb_threads (3), eigenMapMatMult (3), get_ssc (3), get_weights (3), matrix_split (3), demean_fe (2), get_scores (2), gtools_permutations (2), preprocess2.felm (2), preprocess2.fixest (2), preprocess2.lm (2), transform_fe (2), boot_algo3 (1), boottest (1), boottest.felm (1), boottest.fixest (1), boottest.ivreg (1), boottest.lm (1), check_boot_algo3 (1), check_boottest_args_plus (1), check_mboottest_args_plus (1), check_params_in_model (1), check_r_lean (1), check_set_nthreads (1), confint.boottest (1), crosstab4 (1), get_seed (1), get_start_vals (1), getBoottest_boot_algo (1), getBoottest_nthreads (1), glance.boottest (1), invert_p_val (1), is_juliaconnector_prepared (1), mboottest (1), mboottest.felm (1), mboottest.fixest (1), mboottest.lm (1), model_matrix.felm (1), p_val_null2 (1), p_val_null2_x (1), p_val_null2_x_sign_level (1), preprocess2.ivreg (1), to_integer (1), wildboottestHC (1)

stats

weights (25), model.matrix (12), formula (8), coef (6), na.omit (6), model.frame (5), nobs (4), aggregate (3), model.response (3), na.exclude (3), reformulate (2), vcov (2), na.action (1), na.pass (1), rlnorm (1), update (1)

collapse

fsum (7), GRP (4), qF (3)

dreamerr

validate_dots (10)

utils

data (7), combn (1)

fabricatr

draw_binary (2), draw_normal_icc (2), draw_ordered (1), fabricate (1)

dqrng

dqsample (4), dqset.seed (1)

generics

tidy (4), glance (1)

MASS

ginv (4)

graphics

abline (3)

Matrix

t (2), Diagonal (1)

Matrix.utils

aggregate.Matrix (3)

compiler

cmpfun (1)

JuliaConnectoR

juliaImport (1)

sandwich

vcovCL (1)

summclust

vcov_CR3J (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

---

3. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in C++ (7% in 3 files) and R (93% in 32 files)
• 2 authors
• 3 vignettes
• 1 internal data file
• 12 imported packages
• 28 exported functions (median 9 lines of code)
• 140 non-exported functions in R (median 24 lines of code)
• 14 R functions (median 14 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	32	90.5
files_src	3	84.3
files_vignettes	3	92.4
files_tests	17	95.3
loc_R	4252	94.1
loc_src	341	37.9
loc_vignettes	496	77.9
loc_tests	5516	98.5	TRUE
num_vignettes	3	94.2
data_size_total	14024	72.7
data_size_median	14024	81.0
n_fns_r	168	87.0
n_fns_r_exported	28	76.4
n_fns_r_not_exported	140	89.2
n_fns_src	14	36.7
n_fns_per_file_r	3	53.1
n_fns_per_file_src	5	47.8
num_params_per_fn	2	11.9
loc_per_fn_r	23	66.0
loc_per_fn_r_exp	9	19.2
loc_per_fn_r_not_exp	24	70.4
loc_per_fn_src	14	46.6
rel_whitespace_R	19	94.1
rel_whitespace_src	33	52.2
rel_whitespace_vignettes	41	84.9
rel_whitespace_tests	12	96.6	TRUE
doclines_per_fn_exp	30	32.9
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	141	84.4

---

3a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

---

4. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
2899111163	pages build and deployment	success	de3182	176	2022-08-21
2921823435	pkgcheck	failure	00c38b	41	2022-08-24
2899087820	pkgdown	success	aba1d7	124	2022-08-21
2921823433	R-CMD-check	success	00c38b	484	2022-08-24
2899015892	test-coverage	success	aba1d7	457	2022-08-21

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following error:

1. checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
   1. ├─fwildclusterboot::boottest(...) at test-new-bootstrap-variants.R:243:2
   2. └─fwildclusterboot:::boottest.lm(...)
   3. └─fwildclusterboot:::boot_algo_julia(...)

   4. └─JuliaConnectoR::juliaEval("using WildBootTests")
      

   5.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
      

   6.     ├─base::tryCatch(...)
      

   7.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      

   8.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      

   9.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
      

   10.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
       

   11.       └─JuliaConnectoR:::handleCallbacksAndOutput()
       

[ FAIL 1 | WARN 6 | SKIP 14 | PASS 75 ] Error: Test failures Execution halted

R CMD check generated the following notes:

1. checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: libs 6.5Mb
2. checking R code for possible problems ... NOTE boot_algo3: no visible binding for '<<-' assignment to ‘beta_2g_tilde’

R CMD check generated the following test_fail:

1. library(testthat)

library(fwildclusterboot)

test_check("fwildclusterboot") Loading required namespace: fixest The variable 'X2' has been removed because of collinearity (see $collin.var). The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test_tidy.R, q = 1 skipped as 'JULIA_BINDIR' not found. The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test_tidy.R, q > 1 skipped as 'JULIA_BINDIR' not found. Loading required namespace: data.table The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-error_warning.R with q = 1 skipped as JULIA_BINDIR not found. Loading required namespace: ivreg Loading required namespace: clubSandwich The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-error_warning.R with q > 1 skipped as JULIA_BINDIR not found. Error in post1 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | 0 | 0 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | Utility_state : operations are possible only for numeric, logical or complex types Error in post1 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | 0 | 0 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | Utility_state : operations are possible only for numeric, logical or complex types Error in post1 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | 0 | 0 | SEclusters : operations are possible only for numeric, logical or complex types Error in post1 | Utility_state : operations are possible only for numeric, logical or complex types The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-global_vars.R skipped as JULIA_BINDR not found. The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-method_equivalence.R I skipped as JULIA_BINDR not found. The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-method_equivalence.R II skipped as JULIA_BINDR not found. Starting Julia ... test-r-vs-julia.R skipped as JULIA_BINDIR not found. The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-seed.R skipped as JULIA_BINDR not found. The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-tstat_equivalence.R I skipped as JULIA_BINDR not found. The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-tstat_equivalence.R II skipped as JULIA_BINDR not found. The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
test-stat_equivalence.R III skipped as JULIA_BINDR not found. Error in Q1_immigration + Q2_defense : non-numeric argument to binary operator Error in Q1_immigration + Q2_defense : non-numeric argument to binary operator [ FAIL 1 | WARN 6 | SKIP 14 | PASS 75 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (14)

══ Warnings ════════════════════════════════════════════════════════════════════ ── Warning (test_multicollinearity.R:17:3): test multicollinearity ───────────── the matrix is either rank-deficient or indefinite Backtrace:

1. lfe::felm(Y ~ X1 + X2, data = data) at test_multicollinearity.R:17:2
2. lfe:::felm.mm(...)
3. lfe:::newols(...)
4. lfe:::cholx(cp)
5. base::chol.default(mat, pivot = TRUE, tol = tol) ── Warning (test-new-bootstrap-variants.R:243:3): variants 31 R vs Julia ─────── There are only 1024 unique draws from the rademacher distribution for 10 bootstrap clusters. Therefore, B = 1024 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 1024 bootstrap draws, only 2^(#clusters - 1) = 512 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
6. fwildclusterboot::boottest(...) at test-new-bootstrap-variants.R:243:2
7. fwildclusterboot:::boottest.lm(...)
8. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:45:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
9. fwildclusterboot::boottest(...) at test-uncategorized.R:45:2
10. fwildclusterboot:::boottest.fixest(...)
11. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:53:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
12. fwildclusterboot::boottest(...) at test-uncategorized.R:53:2
13. fwildclusterboot:::boottest.fixest(...)
14. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:61:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
15. fwildclusterboot::boottest(...) at test-uncategorized.R:61:2
16. fwildclusterboot:::boottest.fixest(...)
17. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:69:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
18. fwildclusterboot::boottest(...) at test-uncategorized.R:69:2
19. fwildclusterboot:::boottest.fixest(...)
20. fwildclusterboot:::check_set_full_enumeration(...)

══ Failed tests ════════════════════════════════════════════════════════════════ ── Error (test-new-bootstrap-variants.R:243:3): variants 31 R vs Julia ───────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package WildBootTests not found in current path.

• Run import Pkg; Pkg.add("WildBootTests") to install the WildBootTests package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─fwildclusterboot::boottest(...) at test-new-bootstrap-variants.R:243:2
  2. └─fwildclusterboot:::boottest.lm(...)
  3. └─fwildclusterboot:::boot_algo_julia(...)

  4. └─JuliaConnectoR::juliaEval("using WildBootTests")
     

  5.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  6.     ├─base::tryCatch(...)
     

  7.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

  8.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     

  9.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     

10.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

11.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

[ FAIL 1 | WARN 6 | SKIP 14 | PASS 75 ] Error: Test failures Execution halted

R CMD check generated the following check_fails:

1. rcmdcheck_tests_pass
2. rcmdcheck_reasonable_installed_size

Test coverage with covr

ERROR: Test Coverage Failed

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
get_cluster	45
gtools_permutations	34
boot_algo3	23
boot_algo_julia	21
getBoottest_nthreads	16
check_boottest_args_plus	15

Static code analyses with lintr

lintr found the following 33 potential issues:

message	number of times
Avoid library() and require() calls in packages	13
Lines should not be more than 80 characters.	20

---

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages:

• • pval from CIPerm, dostats, dostats, GUIDE, learnstats, molic, mosaic, overlapptest, RPtests, timereg

---

Package Versions

package	version
pkgstats	0.1.1.20
pkgcheck	0.1.0.9
srr	0.0.1.178

---

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.

[s3alfisc]

I just ran the pkgcheck action in my own repo, and - even though the pkgcheck still complained about my compliance with standards - it finished! This of course means that from now on, I will be able to test in my own repo and can stop polluting this space 😄

[s3alfisc]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

:rocket:

Editor check started

:wave:

[ropensci-review-bot]

Checks for fwildclusterboot (v0.11.2)

git hash: 94019e7e

• :heavy_check_mark: Package is already on CRAN.
• :heavy_check_mark: has a 'codemeta.json' file.
• :heavy_check_mark: has a 'contributing' file.
• :heavy_multiplication_x: The following function has no documented return value: [sunab]
• :heavy_check_mark: uses 'roxygen2'.
• :heavy_check_mark: 'DESCRIPTION' has a URL field.
• :heavy_check_mark: 'DESCRIPTION' has a BugReports field.
• :heavy_check_mark: Package has at least one HTML vignette
• :heavy_multiplication_x: These functions do not have examples: [sunab].
• :heavy_check_mark: Package has continuous integration checks.
• :heavy_multiplication_x: Package coverage failed
• :heavy_multiplication_x: R CMD check found 1 error.
• :heavy_multiplication_x: R CMD check found 2 warnings.
• :eyes: Function names are duplicated in other packages

Important: All failing checks above must be addressed prior to proceeding

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL-3

---

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

• Regression and Supervised Learning

:heavy_check_mark: All applicable standards [v0.1.0] have been documented in this package (70 complied with; 46 N/A standards)

Click to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

---

2. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	516
internal	fwildclusterboot	128
internal	stats	84
internal	utils	9
internal	graphics	3
internal	compiler	1
imports	collapse	14
imports	dreamerr	10
imports	generics	5
imports	dqrng	5
imports	MASS	4
imports	Matrix	3
imports	Matrix.utils	3
imports	JuliaConnectoR	1
imports	summclust	1
imports	sandwich	1
imports	Formula	NA
imports	Rcpp	NA
suggests	fabricatr	6
suggests	fixest	NA
suggests	lfe	NA
suggests	ivreg	NA
suggests	clubSandwich	NA
suggests	lmtest	NA
suggests	data.table	NA
suggests	covr	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	broom	NA
suggests	modelsummary	NA
suggests	bench	NA
suggests	testthat	NA
suggests	tibble	NA
suggests	did2s	NA
linking_to	Rcpp	NA
linking_to	RcppArmadillo	NA
linking_to	RcppEigen	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

length (44), list (34), call (31), c (22), lapply (22), names (18), t (15), unique (15), drop (13), vapply (13), as.vector (12), paste0 (12), data.frame (10), rep (10), stop (10), ifelse (9), mode (9), Reduce (9), vector (9), which (9), for (8), nrow (8), sqrt (8), match.call (7), as.matrix (6), ncol (6), replace (6), sum (6), switch (6), is.null (5), matrix (5), seq_along (5), as.numeric (4), crossprod (4), gsub (4), mean (4), sample (4), solve (4), tcrossprod (4), abs (3), col (3), colnames (3), colSums (3), environment (3), getOption (3), if (3), min (3), paste (3), q (3), unlist (3), as.factor (2), as.integer (2), attr (2), cbind (2), grepl (2), loadedNamespaces (2), max (2), norm (2), Recall (2), return (2), sign (2), split (2), sprintf (2), substr (2), suppressWarnings (2), Sys.getenv (2), append (1), as.character (1), class (1), diag (1), dim (1), do.call (1), eval (1), exp (1), integer (1), is.na (1), is.numeric (1), isTRUE (1), logical (1), message (1), nchar (1), row (1), sample.int (1), sapply (1), seq (1), sort (1), tryCatch (1)

fwildclusterboot

format_message (8), get_ssc_julia (8), check_set_full_enumeration (7), set_seed (7), teststat (6), boot_algo_julia (5), crosstab (4), get_bootstrap_pvalue (4), get_cluster (4), boot_algo2 (3), cpp_get_nb_threads (3), eigenMapMatMult (3), get_ssc (3), get_weights (3), model_matrix (3), process_R (3), boottest (2), demean_fe (2), get_scores (2), gtools_permutations (2), matrix_split (2), preprocess2.felm (2), preprocess2.fixest (2), preprocess2.lm (2), transform_fe (2), boot_aggregate (1), boot_algo3 (1), boot_algo3_crv1 (1), boot_algo3_crv3 (1), boottest.felm (1), boottest.fixest (1), boottest.ivreg (1), boottest.lm (1), check_boot_algo3 (1), check_boottest_args_plus (1), check_engine_btype (1), check_mboottest_args_plus (1), check_params_in_model (1), check_r_lean (1), check_set_nthreads (1), confint.boottest (1), crosstab4 (1), format_alert (1), format_error (1), format_warning (1), get_c_all_boot_cpp (1), get_se_all_boot_cpp (1), get_seed (1), get_start_vals (1), getBoottest_engine (1), getBoottest_nthreads (1), glance.boottest (1), invert_p_val (1), is_juliaconnector_prepared (1), manipulate_object (1), p_val_null2 (1), p_val_null2_x (1), p_val_null2_x_sign_level (1), preprocess2.ivreg (1), to_integer (1), wildboottestHC (1)

stats

weights (24), model.matrix (13), formula (8), coef (7), na.omit (6), model.frame (5), nobs (4), aggregate (3), model.response (3), na.exclude (3), reformulate (2), vcov (2), na.action (1), na.pass (1), rlnorm (1), update (1)

collapse

fsum (7), GRP (4), qF (3)

dreamerr

validate_dots (10)

utils

data (7), combn (1), txtProgressBar (1)

fabricatr

draw_binary (2), draw_normal_icc (2), draw_ordered (1), fabricate (1)

dqrng

dqsample (4), dqset.seed (1)

generics

tidy (4), glance (1)

MASS

ginv (4)

graphics

abline (3)

Matrix

t (2), Diagonal (1)

Matrix.utils

aggregate.Matrix (3)

compiler

cmpfun (1)

JuliaConnectoR

juliaImport (1)

sandwich

vcovCL (1)

summclust

vcov_CR3J (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

---

3. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in C++ (10% in 4 files) and R (90% in 34 files)
• 2 authors
• 3 vignettes
• 1 internal data file
• 12 imported packages
• 34 exported functions (median 9 lines of code)
• 168 non-exported functions in R (median 20 lines of code)
• 21 R functions (median 17 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	34	91.4
files_src	4	87.0
files_vignettes	3	92.4
files_tests	18	95.7
loc_R	4677	94.8
loc_src	500	46.8
loc_vignettes	586	81.7
loc_tests	5821	98.6	TRUE
num_vignettes	3	94.2
data_size_total	14024	72.7
data_size_median	14024	81.0
n_fns_r	202	89.9
n_fns_r_exported	34	81.0
n_fns_r_not_exported	168	91.5
n_fns_src	21	47.2
n_fns_per_file_r	3	55.2
n_fns_per_file_src	5	53.2
num_params_per_fn	2	11.9
loc_per_fn_r	18	54.7
loc_per_fn_r_exp	9	19.2
loc_per_fn_r_not_exp	20	63.0
loc_per_fn_src	17	59.6
rel_whitespace_R	20	95.3	TRUE
rel_whitespace_src	30	58.7
rel_whitespace_vignettes	35	84.9
rel_whitespace_tests	13	97.2	TRUE
doclines_per_fn_exp	31	34.8
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	181	87.5

---

3a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

---

4. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
3118455761	pages build and deployment	success	e98a12	189	2022-09-24
3118431180	pkgcheck	NA	ee479f	93	2022-09-24
3118431181	pkgdown	success	ee479f	138	2022-09-24
3118431178	R-CMD-check	success	ee479f	542	2022-09-24
3118431179	test-coverage	success	ee479f	478	2022-09-24

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following error:

1. checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 4. ├─fwildclusterboot::boottest(...) 5. └─fwildclusterboot:::boottest.ivreg(...) 6. └─fwildclusterboot:::set_seed(...) 7. └─JuliaConnectoR::juliaEval("using StableRNGs") 8. └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr) 9. ├─base::tryCatch(...) 10. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 13. └─JuliaConnectoR:::doCallJulia(funName, jlargs) 14. └─JuliaConnectoR:::handleCallbacksAndOutput()

[ FAIL 16 | WARN 11 | SKIP 0 | PASS 414 ] Error: Test failures Execution halted

R CMD check generated the following warnings:

1. checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘rstudioapi’ 'loadNamespace' or 'requireNamespace' call not declared from: ‘rstudioapi’
2. checking S3 generic/method consistency ... WARNING tidy: function(x, ...) tidy.boottest: function(object, ...)

tidy: function(x, ...) tidy.mboottest: function(object, ...)

See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual.

R CMD check generated the following notes:

1. checking installed package size ... NOTE installed size is 8.8Mb sub-directories of 1Mb or more: libs 7.7Mb
2. checking R code for possible problems ... NOTE .wrap_message_line: no visible global function definition for ‘.bold’ .wrap_message_line: no visible global function definition for ‘.italic’ .wrap_message_line: no visible global function definition for ‘.blue’ Undefined global functions or variables: .blue .bold .italic

R CMD check generated the following test_fail:

1. library(testthat)

library(fwildclusterboot)

test_check("fwildclusterboot") Loading required namespace: fixest The variable 'X2' has been removed because of collinearity (see $collin.var). Starting Julia ... Loading required namespace: data.table R Variables 'log_income::17.2069212919256:Q1_immigration::3' and 'log_income::18.0802367820713:Q1_immigration::3' have been removed because of collinearity (see $collin.var). NOTE: 2 fixed-effect singletons were removed (2 observations). WildBootTests.jl Loading required namespace: ivreg Part 1: Full enumeration Tests (deterministic) start ols/wls type: rademacher p-val: two-tailed null imposed: TRUE rademacher two-tailed TRUE type: rademacher p-val: equal-tailed null imposed: TRUE rademacher equal-tailed TRUE type: rademacher p-val: > null imposed: TRUE rademacher

TRUE type: rademacher p-val: < null imposed: TRUE rademacher < TRUE julia connector prepared? TRUEPart 1: Full enumeration Tests (deterministic) start ols/wls type: rademacher p-val: two-tailed null imposed: TRUE rademacher two-tailed TRUE Variance contained negative values in the diagonal and was 'fixed' (a la Cameron, Gelbach & Miller 2011). Variance contained negative values in the diagonal and was 'fixed' (a la Cameron, Gelbach & Miller 2011). Variance contained negative values in the diagonal and was 'fixed' (a la Cameron, Gelbach & Miller 2011). Variance contained negative values in the diagonal and was 'fixed' (a la Cameron, Gelbach & Miller 2011). boottest() boottest() start ols/wls Part 1: Large B Tests start ols/wls type: rademacher p-val: two-tailed null imposed: TRUE rademacher two-tailed TRUE The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
julia connector prepared? TRUE The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
julia connector prepared? TRUE The Julia environment variable 'JULIA_BINDIR' could not be found.Therefore, all tests that involve 'WildBootTests.jl' will be skipped.
julia connector prepared? TRUE [ FAIL 16 | WARN 11 | SKIP 0 | PASS 414 ]

══ Warnings ════════════════════════════════════════════════════════════════════ ── Warning (test_tidy.R:22:5): test tidiers with q = 1 ───────────────────────── There are only 1024 unique draws from the rademacher distribution for 10 bootstrap clusters. Therefore, B = 1024 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 1024 bootstrap draws, only 2^(#clusters - 1) = 512 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:

1. fwildclusterboot::boottest(...) at test_tidy.R:22:4
2. fwildclusterboot:::boottest.lm(...)
3. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test_tidy.R:28:5): test tidiers with q = 1 ───────────────────────── There are only 1024 unique draws from the rademacher distribution for 10 bootstrap clusters. Therefore, B = 1024 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 1024 bootstrap draws, only 2^(#clusters - 1) = 512 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
4. fwildclusterboot::boottest(...) at test_tidy.R:28:4
5. fwildclusterboot:::boottest.lm(...)
6. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-error_warning.R:1208:9): errors and warnings q = 1 ──────────── Currently, boottest() calculates confidence intervals for one-sided hypotheses only for engine = 'WildBootTests.jl'. Backtrace:
7. testthat::expect_error(...) at test-error_warning.R:1208:8
8. fwildclusterboot:::boottest.fixest(...)
9. fwildclusterboot:::r_algo_checks(...) ── Warning (test-error_warning.R:1220:9): errors and warnings q = 1 ──────────── Currently, boottest() calculates confidence intervals for one-sided hypotheses only for engine = 'WildBootTests.jl'. Backtrace:
10. testthat::expect_error(...) at test-error_warning.R:1220:8
11. fwildclusterboot:::boottest.felm(...)
12. fwildclusterboot:::r_algo_checks(...) ── Warning (test-method_equivalence.R:135:5): Do different, but equivalent ways to specify linear models lead to equivalent results? ── Negative eigenvalues set to zero in multiway clustered variance matrix. See felm(...,psdef=FALSE) Backtrace:
13. lfe::felm(...) at test-method_equivalence.R:135:4
14. lfe:::felm.mm(...)
15. lfe:::newols(...) ── Warning (test-method_equivalence.R:160:5): Do different, but equivalent ways to specify linear models lead to equivalent results? ── Negative eigenvalues set to zero in multiway clustered variance matrix. See felm(...,psdef=FALSE) Backtrace:
16. lfe::felm(...) at test-method_equivalence.R:160:4
17. lfe:::felm.mm(...)
18. lfe:::newols(...) ── Warning (test-method_equivalence.R:167:5): Do different, but equivalent ways to specify linear models lead to equivalent results? ── Negative eigenvalues set to zero in multiway clustered variance matrix. See felm(...,psdef=FALSE) Backtrace:
19. lfe::felm(...) at test-method_equivalence.R:167:4
20. lfe:::felm.mm(...)
21. lfe:::newols(...) ── Warning (test-uncategorized.R:45:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
22. fwildclusterboot::boottest(...) at test-uncategorized.R:45:2
23. fwildclusterboot:::boottest.fixest(...)
24. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:53:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
25. fwildclusterboot::boottest(...) at test-uncategorized.R:53:2
26. fwildclusterboot:::boottest.fixest(...)
27. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:61:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
28. fwildclusterboot::boottest(...) at test-uncategorized.R:61:2
29. fwildclusterboot:::boottest.fixest(...)
30. fwildclusterboot:::check_set_full_enumeration(...) ── Warning (test-uncategorized.R:69:3): uncategorized tests ──────────────────── There are only 64 unique draws from the rademacher distribution for 6 bootstrap clusters. Therefore, B = 64 with full enumeration. Consider using webb weights instead. Further, note that under full enumeration and with B = 64 bootstrap draws, only 2^(#clusters - 1) = 32 distinct t-statistics and p-values can be computed. For a more thorough discussion, see Webb Reworking wild bootstrap based inference for clustered errors (2013). Backtrace:
31. fwildclusterboot::boottest(...) at test-uncategorized.R:69:2
32. fwildclusterboot:::boottest.fixest(...)
33. fwildclusterboot:::check_set_full_enumeration(...)

══ Failed tests ════════════════════════════════════════════════════════════════ ── Error (test_tidy.R:35:5): test tidiers with q = 1 ─────────────────────────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─fwildclusterboot::boottest(...) at test_tidy.R:35:4
  2. └─fwildclusterboot:::boottest.lm(...)
  3. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)

  4. └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  5.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  6.     ├─base::tryCatch(...)
     

  7.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

  8.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     

  9.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     

10.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

11.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test_tidy.R:82:3): test tidiers with q > 1 ─────────────────────────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─fwildclusterboot::mboottest(...) at test_tidy.R:82:2
  2. └─fwildclusterboot:::mboottest.lm(...)
  3. └─fwildclusterboot:::set_seed(...)

  4. └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  5.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  6.     ├─base::tryCatch(...)
     

  7.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

  8.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     

  9.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     

10.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

11.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Failure (test-error_warning.R:625:7): errors and warnings q = 1 ───────────── boottest(...) did not throw the expected message. ── Failure (test-error_warning.R:638:9): errors and warnings q = 1 ───────────── boottest(...) did not throw the expected message. ── Failure (test-error_warning.R:650:9): errors and warnings q = 1 ───────────── boottest(...) did not throw the expected message. ── Error (test-error_warning.R:246:9): errors and warnings q = 1 ─────────────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─base::suppressWarnings(...) at test-error_warning.R:246:8
  2. │ └─base::withCallingHandlers(...)
  3. ├─testthat::expect_warning(...)
  4. │ └─testthat:::expect_condition_matching(...)
  5. │ └─testthat:::quasi_capture(...)
  6. │ ├─testthat (local) .capture(...)
  7. │ │ └─base::withCallingHandlers(...)
  8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  9. ├─fwildclusterboot::boottest(...)

10. └─fwildclusterboot:::boottest.lm(...)
11. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)

12. └─JuliaConnectoR::juliaEval("using StableRNGs")
    

13.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
    

14.     ├─base::tryCatch(...)
    

15.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    

16.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

17.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

18.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

19.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-error_warning.R:1509:5): error warning IV/WRE and q > 1 ───────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─testthat::expect_warning(...) at test-error_warning.R:1509:4
  2. │ └─testthat:::expect_condition_matching(...)
  3. │ └─testthat:::quasi_capture(...)
  4. │ ├─testthat (local) .capture(...)
  5. │ │ └─base::withCallingHandlers(...)
  6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. ├─base::suppressMessages(...)
  8. │ └─base::withCallingHandlers(...)
  9. ├─fwildclusterboot::boottest(...)

10. └─fwildclusterboot:::boottest.ivreg(...)
11. └─fwildclusterboot:::set_seed(...)

12. └─JuliaConnectoR::juliaEval("using StableRNGs")
    

13.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
    

14.     ├─base::tryCatch(...)
    

15.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    

16.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

17.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

18.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

19.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-full-enumeration.R:295:13): test full enumeration cases: r and julia ── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─base::suppressWarnings(...) at test-full-enumeration.R:295:12
  2. │ └─base::withCallingHandlers(...)
  3. ├─fwildclusterboot::boottest(...)
  4. └─fwildclusterboot:::boottest.lm(...)
  5. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)

  6. └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  7.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  8.     ├─base::tryCatch(...)
     

  9.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

10.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

11.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

12.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

13.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-global_vars.R:18:5): global engine ────────────────────────────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─base::suppressWarnings(...) at test-global_vars.R:18:4
  2. │ └─base::withCallingHandlers(...)
  3. ├─fwildclusterboot::boottest(...)
  4. └─fwildclusterboot:::boottest.lm(...)
  5. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)

  6. └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  7.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  8.     ├─base::tryCatch(...)
     

  9.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

10.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

11.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

12.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

13.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-method_equivalence.R:1227:5): Do different, but equivalent ways to specify linear models lead to equivalent results? ── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. └─fwildclusterboot (local) create_models(clustid = "group_id1") at test-method_equivalence.R:1227:4
  2. ├─base::assign(...) at test-method_equivalence.R:187:8
  3. ├─base::suppressWarnings(...)
  4. │ └─base::withCallingHandlers(...)
  5. ├─fwildclusterboot::boottest(...)
  6. └─fwildclusterboot:::boottest.lm(...)

  7. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)
     

  8.   └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  9.     └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

10.       ├─base::tryCatch(...)
    

11.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    

12.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

13.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

14.       └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

15.         └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-new-bootstrap-variants.R:271:5): variants 31 R vs Julia ───────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─fwildclusterboot::boottest(...) at test-new-bootstrap-variants.R:271:4
  2. └─fwildclusterboot:::boottest.lm(...)
  3. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)

  4. └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  5.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  6.     ├─base::tryCatch(...)
     

  7.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

  8.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     

  9.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     

10.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

11.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-r-vs-julia.R:86:15): test r against Julia I: stochastic tests ─── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─base::suppressWarnings(...) at test-r-vs-julia.R:86:14
  2. │ └─base::withCallingHandlers(...)
  3. ├─fwildclusterboot::boottest(...)
  4. └─fwildclusterboot:::boottest.lm(...)
  5. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)

  6. └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  7.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  8.     ├─base::tryCatch(...)
     

  9.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

10.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

11.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

12.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

13.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-seed.R:31:7): seed works for OLS ──────────────────────────────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─base::suppressMessages(...) at test-seed.R:31:6
  2. │ └─base::withCallingHandlers(...)
  3. ├─fwildclusterboot::boottest(...)
  4. └─fwildclusterboot:::boottest.lm(...)
  5. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)

  6. └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  7.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  8.     ├─base::tryCatch(...)
     

  9.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

10.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

11.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

12.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

13.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-tstat_equivalence.R:428:19): t-stat equivalence OLS - WildBootTests ── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. ├─base::suppressWarnings(...) at test-tstat_equivalence.R:428:18
  2. │ └─base::withCallingHandlers(...)
  3. ├─fwildclusterboot::boottest(...)
  4. └─fwildclusterboot:::boottest.lm(...)
  5. └─fwildclusterboot:::set_seed(seed = seed, engine = engine, type = type)

  6. └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  7.   └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  8.     ├─base::tryCatch(...)
     

  9.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     

10.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

11.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

12.     └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

13.       └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-tstat_equivalence.R:882:5): t-stat equivalence OLS q > 1 ──────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. └─fwildclusterboot (local) wald_test(run_this_test = TRUE) at test-tstat_equivalence.R:882:4
  2. ├─base::suppressWarnings(...) at test-tstat_equivalence.R:671:8
  3. │ └─base::withCallingHandlers(...)
  4. ├─fwildclusterboot::mboottest(...)
  5. └─fwildclusterboot:::mboottest.lm(...)

  6. └─fwildclusterboot:::set_seed(...)
     

  7.   └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  8.     └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  9.       ├─base::tryCatch(...)
     

10.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    

11.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

12.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

13.       └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

14.         └─JuliaConnectoR:::handleCallbacksAndOutput()
    

── Error (test-tstat_equivalence.R:966:5): t-stat equivalence IV ─────────────── Error: Evaluation in Julia failed. Original Julia error message: LoadError: ArgumentError: Package StableRNGs not found in current path.

• Run import Pkg; Pkg.add("StableRNGs") to install the StableRNGs package. Stacktrace: [1] macro expansion @ ./loading.jl:1163 [inlined] [2] macro expansion @ ./lock.jl:223 [inlined] [3] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [4] eval @ ./boot.jl:368 [inlined] [5] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:1428 [6] include_string (repeats 2 times) @ ./loading.jl:1438 [inlined] [7] mainevalcmd(str::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:150 [8] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./essentials.jl:729 [9] invokelatest(::Any, ::Any, ::Vararg{Any}) @ Base ./essentials.jl:726 [10] evaluate!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:67 [11] evaluate_checked!(call::Main.RConnector.Call, communicator::Main.RConnector.CommunicatoR{Sockets.TCPSocket}) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/evaluating.jl:55 [12] serve_repl(sock::Sockets.TCPSocket) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:185 [13] serve(port_hint::Int64; multiclient::Bool, portfile::String) @ Main.RConnector /usr/local/lib/R/site-library/JuliaConnectoR/Julia/communicating.jl:152 [14] top-level scope @ /usr/local/lib/R/site-library/JuliaConnectoR/Julia/main.jl:23 [15] include(mod::Module, _path::String) @ Base ./Base.jl:419 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:303 [17] _start() @ Base ./client.jl:522 in expression starting at string:1 Backtrace: ▆
  1. └─fwildclusterboot (local) iv_test(run_this_test = TRUE) at test-tstat_equivalence.R:966:4
  2. ├─base::suppressWarnings(...) at test-tstat_equivalence.R:931:8
  3. │ └─base::withCallingHandlers(...)
  4. ├─fwildclusterboot::boottest(...)
  5. └─fwildclusterboot:::boottest.ivreg(...)

  6. └─fwildclusterboot:::set_seed(...)
     

  7.   └─JuliaConnectoR::juliaEval("using StableRNGs")
     

  8.     └─JuliaConnectoR::juliaCall("RConnector.mainevalcmd", expr)
     

  9.       ├─base::tryCatch(...)
     

10.       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    

11.       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    

12.       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    

13.       └─JuliaConnectoR:::doCallJulia(funName, jlargs)
    

14.         └─JuliaConnectoR:::handleCallbacksAndOutput()
    

[ FAIL 16 | WARN 11 | SKIP 0 | PASS 414 ] Error: Test failures Execution halted

R CMD check generated the following check_fails:

1. rcmdcheck_undeclared_imports
2. rcmdcheck_undeclared_loadnamespace_requirenamespace
3. rcmdcheck_undefined_globals
4. rcmdcheck_tests_pass
5. rcmdcheck_reasonable_installed_size

Test coverage with covr

ERROR: Test Coverage Failed

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
get_cluster	35
gtools_permutations	34
boot_algo3	24
boot_aggregate	22
boot_algo_julia	21
getBoottest_nthreads	16
boottest.fixest	15
boottest.lm	15
check_boottest_args_plus	15

Static code analyses with lintr

lintr found the following 70 potential issues:

message	number of times
Avoid library() and require() calls in packages	13
Avoid using sapply, consider vapply instead, that's type safe	1
Lines should not be more than 80 characters.	11
Use <-, not =, for assignment.	45

---

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 2 function names are duplicated in other packages:

• • format_message from insight
• • pval from CIPerm, dostats, dostats, GUIDE, learnstats, molic, mosaic, overlapptest, RPtests, timereg

---

Package Versions

package	version
pkgstats	0.1.1.44
pkgcheck	0.1.0.24
srr	0.0.1.180

---

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.

[maurolepore]

Dear @s3alfisc

Today starts my rotation as EiC and I'm reviewing the status of current open reviews.

Thanks a lot for your efforts in meeting our standards. Where are we standing now? Do you feel ready for me to resume the review process? The next step would be to re-run checks and then look for a handling editor.

[s3alfisc]

Hi @maurolepore - thanks for reaching out - I was actually about to do the same this weekend! Unfortunately, I never got the pkgcheck to run properly, neither on my local machine nor on github actions. But I have not really tried in a while (I had given up at some point) - so I'll try once again and if I cannot get it to run locally, is it ok if I trigger the workflow bot one more time? One complication is that I am running unit tests against WildBootTests.jl, and in order to run the pkgcheck workflows, I'd have to skip those tests, which would lead to a drop in test coverage to around 65%.

[s3alfisc]

Actually, pkgcheck is now running on my local machine - so I'll respond to it's feedback, update all standards based on a few new features, and will notify you once everything is done!

[s3alfisc]

I've run the pkgcheck action, with the following results:

• the pkgcheck coverage test fails, as pkgcheck does not run some tests that my local github actions CI runs (coverage is at 89% running all tests, codecov link)
• installation on ubuntu-lastest fails. No problems on older versions of ubuntu via github actions.
• The following functions are used in other packages: pval, error_message - which I think should be fine?

I'll start the bot to confirm all of this later today & then you can decide if you think everything is good enough to proceed, @maurolepore ?

[s3alfisc]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

:rocket:

Editor check started

:wave: