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pre-submission test #34

Open mpadge opened 2 years ago

mpadge commented 2 years ago

Submitting Author Name: Eunseop Kim Submitting Author Github Handle: !--author1-->@markean<!--end-author1-- Repository: https://github.com/markean/melt Submission type: Pre-submission Language: en

(Copied from software-review#549 to test bot pre-review commands)

Type: Package
Package: melt
Title: Multiple Empirical Likelihood Tests
Version: 1.6.0
Authors@R: c(
    person("Eunseop", "Kim", , "kim.7302@osu.edu", role = c("aut", "cre")),
    person("Steven", "MacEachern", role = c("ctb", "ths")),
    person("Mario", "Peruggia", role = c("ctb", "ths"))
  )
Description: Performs multiple empirical likelihood tests for linear and
    generalized linear models. The core computational routines are
    implemented using the 'Eigen' C++ library and 'RcppEigen' interface,
    with OpenMP for parallel computation. Details of multiple testing
    procedures are given in Kim, MacEachern, and Peruggia (2021)
    <arxiv:2112.09206>.
License: GPL (>= 2)
URL: https://github.com/markean/melt, https://markean.github.io/melt/
BugReports: https://github.com/markean/melt/issues
Depends: 
    R (>= 4.0.0)
Imports: 
    graphics,
    methods,
    Rcpp,
    stats
Suggests: 
    covr,
    ggplot2,
    knitr,
    microbenchmark,
    rmarkdown,
    spelling,
    testthat (>= 3.0.0),
    withr
LinkingTo: 
    BH,
    dqrng,
    Rcpp,
    RcppEigen
VignetteBuilder: 
    knitr
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: yes
Roxygen: list (markdown = TRUE, roclets = c ("namespace", "rd",
    "srr::srr_stats_roclet"))
RoxygenNote: 7.2.0

Scope

mpadge commented 2 years ago

@ropensci-review-bot help

ropensci-review-bot commented 2 years ago

Hello @mpadge, here are the things you can ask me to do:


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mpadge commented 2 years ago

@ropensci-review-bot check srr

mpadge commented 2 years ago

@ropensci-review-bot check package

ropensci-review-bot commented 2 years ago

Thanks, about to send the query.

ropensci-review-bot commented 2 years ago

:rocket:

Error: Issue template has no 'repourl'

:wave:

mpadge commented 2 years ago

@ropensci-review-bot check srr

mpadge commented 2 years ago

@ropensci-review-bot help

ropensci-review-bot commented 2 years ago

Hello @mpadge, here are the things you can ask me to do:


# Add a review's info to the ROpenSci logs
@ropensci-review-bot submit review <REVIEW_URL> time <REVIEW_HOURS(ex. 10.5)>

# List all available commands
@ropensci-review-bot help

# Show our Code of Conduct
@ropensci-review-bot code of conduct

# Switch to "seeking reviewers"
@ropensci-review-bot seeking reviewers

# Approves a package. This command will close the issue.
@ropensci-review-bot approve package-name

# Adds package's repo to the rOpenSci team. This command should be issued after approval and transfer of the package.
@ropensci-review-bot finalize transfer of package-name

# Mint package as [bronze/silver/gold]
@ropensci-review-bot mint silver

# Add a user to this issue's reviewers list
@ropensci-review-bot assign xxxxx as reviewer

# Remove a user from the reviewers list
@ropensci-review-bot remove xxxxx from reviewers

# Assign a user as the editor of this submission
@ropensci-review-bot assign @username as editor

# Put the submission on hold for the next 90 days
@ropensci-review-bot put on hold

# Remove the editor assigned to this submission
@ropensci-review-bot remove editor

# Change or add a review's due date for a reviewer
@ropensci-review-bot set due date for @reviewer to YYYY-MM-DD

# Close the issue
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# Various package checks
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# Checks srr documentation for stats packages
@ropensci-review-bot check srr
mpadge commented 2 years ago

@ropensci-review-bot check srr

ropensci-review-bot commented 2 years ago

'srr' standards compliance:

:heavy_check_mark: This package complies with > 50% of all standads and may be submitted.

ropensci-review-bot commented 2 years ago

Note: The following R packages were unable to be installed/upgraded on our system: [viridisLite, StanHeaders, rstan]; some checks may be unreliable.

ropensci-review-bot commented 2 years ago

'srr' standards compliance:

:heavy_check_mark: This package complies with > 50% of all standads and may be submitted.

ropensci-review-bot commented 2 years ago

Checks for dynamite (v0.0.1)

git hash: a8d932ca

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:

:heavy_check_mark: All applicable standards [v0.1.0] have been documented in this package (129 complied with; 42 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 | 1102| |internal |dynamite | 418| |internal |graphics | 21| |internal |methods | 3| |imports |utils | 81| |imports |stats | 59| |imports |dplyr | 29| |imports |rlang | 16| |imports |checkmate | 11| |imports |glue | 11| |imports |cli | 6| |imports |ggplot2 | 4| |imports |posterior | 4| |imports |tidyr | 4| |imports |rstan | 3| |imports |data.table | 2| |imports |bayesplot | 1| |imports |MASS | NA| |suggests |covr | NA| |suggests |knitr | NA| |suggests |plm | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |linking_to |NA | 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()', and examining the 'external_calls' table.

base

c (108), list (96), length (69), paste0 (66), args (53), for (47), attr (44), data.frame (39), as.list (32), match.call (32), rep (31), seq_len (25), unique (25), do.call (22), character (19), which (18), vapply (17), is.na (16), names (16), logical (15), seq_along (15), drop (13), by (12), deparse1 (11), is.null (10), mean (10), nzchar (10), all (9), apply (9), debug (9), lapply (9), parent.frame (9), as.integer (7), integer (7), rank (7), seq.int (7), sort (6), unlist (6), array (5), assign (5), colnames (5), dim (5), log (5), message (5), mode (5), nrow (5), try (5), vector (5), as.numeric (4), call (4), diff (4), eval (4), gsub (4), as.data.frame (3), cbind (3), I (3), identical (3), setdiff (3), sub (3), sum (3), any (2), aperm (2), expand.grid (2), levels (2), max (2), ncol (2), seq (2), structure (2), suppressWarnings (2), t (2), beta (1), class (1), det (1), diag (1), duplicated (1), get (1), gl (1), gregexec (1), ifelse (1), intersect (1), is.factor (1), is.finite (1), match (1), min (1), new.env (1), numeric (1), parse (1), paste (1), prod (1), range (1), regmatches (1), replace (1), replicate (1), row.names (1), sample (1), sample.int (1), signif (1), strsplit (1), substitute (1), typeof (1), union (1), warning (1), which.max (1), which.min (1), with (1)

dynamite

ifelse_ (84), paste_rows (41), get_responses (17), data_lines_default (10), get_predictors (10), onlyif (10), model_lines_default (9), warning_ (9), prepare_channel_default (8), formula_rhs (6), get_quoted (5), as.data.frame.dynamitefit (4), get_families (4), has_past (4), coef.dynamitefit (3), evaluate_specials (3), get_formulas (3), assign_deterministic (2), complete_lags (2), create_blocks (2), cs (2), default_priors (2), default_priors_categorical (2), deterministic_response (2), extract_lags (2), extract_nonlags (2), find_lags (2), formula_lhs (2), formula_past (2), formula_terms (2), full_model.matrix (2), full_model.matrix_predict (2), get_originals (2), get_terms (2), indenter_ (2), join_dynamiteformulas (2), lag_ (2), parse_global_lags (2), parse_lags (2), parse_new_lags (2), parse_singleton_lags (2), prepare_eval_envs (2), prepare_lagged_response (2), stop_ (2), which_deterministic (2), which_stochastic (2), abort_factor (1), abort_negative (1), abort_nonunit (1), add_dynamiteformula (1), as_data_frame_alpha (1), as_data_frame_beta (1), as_data_frame_corr_nu (1), as_data_frame_default (1), as_data_frame_delta (1), as_data_frame_lambda (1), as_data_frame_nu (1), as_data_frame_omega (1), as_data_frame_omega_alpha (1), as_data_frame_phi (1), as_data_frame_sigma (1), as_data_frame_sigma_nu (1), as_data_frame_tau (1), as_data_frame_tau_alpha (1), as_draws_df.dynamitefit (1), as_draws.dynamitefit (1), assign_initial_values (1), assign_lags (1), assign_lags_init (1), aux (1), check_ndraws (1), check_newdata (1), check_priors (1), clear_nonfixed (1), confint.dynamitefit (1), create_blocks.default (1), create_data (1), create_functions (1), create_generated_quantities (1), create_model (1), create_parameters (1), create_transformed_data (1), create_transformed_parameters (1), data_lines_bernoulli (1), data_lines_beta (1), data_lines_binomial (1), data_lines_categorical (1), data_lines_exponential (1), data_lines_gamma (1), data_lines_gaussian (1), data_lines_negbin (1), data_lines_poisson (1), drop_terms (1), drop_unused (1), dynamite (1), dynamitechannel (1), dynamitefamily (1), dynamiteformula (1), dynamiteformula_ (1), evaluate_deterministic (1), fill_time (1), fill_time_predict (1), fitted.dynamitefit (1), formula_specials (1), formula.dynamitefit (1), generate_random_intercept (1), generate_sim_call (1), get_code (1), get_code.dynamitefit (1), get_code.dynamiteformula (1), get_data (1), get_data.dynamitefit (1), get_data.dynamiteformula (1), get_priors (1), get_priors.dynamitefit (1), get_priors.dynamiteformula (1), get_special_term_indices (1), impute_newdata (1), increment_formula (1), initialize_deterministic (1), is_supported (1), is.dynamitefamily (1), is.dynamitefit (1), is.dynamiteformula (1), lags (1), lines_wrap (1), locf (1), mcmc_diagnostics (1), mcmc_diagnostics.dynamitefit (1), message_ (1), model_lines_bernoulli (1), model_lines_beta (1), model_lines_binomial (1), model_lines_categorical (1), model_lines_exponential (1), model_lines_gamma (1), model_lines_gaussian (1), model_lines_negbin (1), model_lines_poisson (1), ndraws.dynamitefit (1), nobs.dynamitefit (1), parameters_lines_bernoulli (1), parameters_lines_beta (1), parameters_lines_binomial (1), parameters_lines_categorical (1), parameters_lines_default (1), parameters_lines_exponential (1), parameters_lines_gamma (1), parameters_lines_gaussian (1), parameters_lines_negbin (1), parameters_lines_poisson (1), parse_data (1), parse_newdata (1), parse_past (1), parse_present_lags (1), plot_betas (1), plot_deltas (1), plot_nus (1), plot.dynamitefit (1), predict_dynamitefit (1), predict.dynamitefit (1), prepare_channel_bernoulli (1), prepare_channel_beta (1), prepare_channel_binomial (1), prepare_channel_categorical (1), prepare_channel_exponential (1), prepare_channel_gamma (1), prepare_channel_gaussian (1), prepare_channel_negbin (1), prepare_channel_poisson (1), prepare_common_priors (1), prepare_prior (1), prepare_splines (1), prepare_stan_input (1), values (1), verify_lag (1)

utils

data (79), capture.output (1), combn (1)

stats

formula (21), var (7), df (5), sd (4), D (3), model.matrix.lm (3), na.action (3), na.pass (3), offset (3), complete.cases (2), setNames (2), terms (2), sigma (1)

dplyr

bind_rows (12), filter (7), mutate (3), summarise (3), left_join (2), matches (1), n (1)

graphics

mtext (10), title (9), pairs (2)

rlang

caller_env (16)

checkmate

test_character (3), test_flag (3), test_string (3), test_int (2)

glue

glue (11)

cli

cli_abort (2), qty (2), cli_inform (1), cli_warn (1)

ggplot2

labs (3), position_dodge (1)

posterior

summarise_draws (2), as_draws (1), ndraws (1)

tidyr

expand_grid (2), full_seq (1), unnest (1)

methods

is (2), new (1)

rstan

extract (2), check_hmc_diagnostics (1)

data.table

setDT (1), setkeyv (1)

bayesplot

mcmc_combo (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 R (100% in 30 files) and - 2 authors - 1 vignette - 6 internal data files - 14 imported packages - 36 exported functions (median 7 lines of code) - 404 non-exported functions in R (median 9 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](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 30| 89.3| | |files_vignettes | 2| 85.7| | |files_tests | 11| 91.7| | |loc_R | 5956| 96.5|TRUE | |loc_vignettes | 877| 89.0| | |loc_tests | 2413| 95.3|TRUE | |num_vignettes | 1| 64.8| | |data_size_total | 2661885| 98.5|TRUE | |data_size_median | 349085| 96.0|TRUE | |n_fns_r | 440| 96.6|TRUE | |n_fns_r_exported | 36| 82.0| | |n_fns_r_not_exported | 404| 97.8|TRUE | |n_fns_per_file_r | 8| 83.4| | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 9| 24.3| | |loc_per_fn_r_exp | 7| 13.5| | |loc_per_fn_r_not_exp | 9| 27.1| | |rel_whitespace_R | 4| 76.1| | |rel_whitespace_vignettes | 13| 68.1| | |rel_whitespace_tests | 9| 86.4| | |doclines_per_fn_exp | 37| 45.3| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 696| 96.9|TRUE | ---

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 [![R-CMD-check](https://github.com/santikka/dynamite/workflows/R-CMD-check/badge.svg)](https://github.com/santikka/dynamite/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:-------------|:----------|:------|----------:|:----------| | 2903919221|R-CMD-check |success |a8d932 | 295|2022-08-22 | | 2903919220|test-coverage |success |a8d932 | 295|2022-08-22 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following note: 1. checking installed package size ... NOTE installed size is 11.1Mb sub-directories of 1Mb or more: data 7.2Mb doc 1.0Mb R 2.5Mb R CMD check generated the following check_fail: 1. rcmdcheck_reasonable_installed_size #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 97.82 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) No functions have cyclocomplexity >= 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 6 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 5 unexpected symbol | 1

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 10 function names are duplicated in other packages: - - `aux` from seewave - - `get_code` from norgeo, rmonad, xpose - - `get_data` from canvasXpress.data, cbsodataR, cimir, completejourney, CVXR, danstat, deckgl, ecb, finnishgrid, ggPMX, ggvis, hydroscoper, insight, jtools, mapbayr, metacoder, missCompare, optimall, qrmtools, r4googleads, radiant.data, radous, rbedrock, rchallenge, rsimsum, SWIM, swissparl, tidyLPA, tidySEM, trending, tsmp, ugatsdb, xpose - - `get_priors` from CausalQueries, insight - - `lags` from smooth, tis, TTR - - `mcmc_diagnostics` from bpr, rater, rnmamod - - `obs` from metacoder, observer - - `plot_deltas` from spruce - - `random` from CoOL, decisionSupport, distributions3, gam, gamlss, ggdmc, lidR, messydates, simr, sodium - - `splines` from rpatrec

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.