software-review baRulho

Submitting Author Name: Marcelo Araya-Salas Submitting Author Github Handle: @maRce10 Repository: https://github.com/maRce10/baRulho/ Version submitted: 2.1.0 Submission type: Standard Editor: @jhollist Reviewers: @mikemahoney218, @DenaJGibbon

Archive: TBD Version accepted: TBD Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: baRulho
Type: Package
Title: Quantifying (Animal) Sound Degradation  
Version: 2.1.0
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <[email protected]>
Description: Intended to facilitate acoustic analysis of (animal) sound transmission experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
License: GPL (>= 2)
Imports: utils, stats, seewave, tuneR, fftw, methods, viridis, Sim.DiffProc, png, checkmate, cli
Depends: R (>= 3.2.1), warbleR (>= 1.1.29), ohun (>= 1.0.0)
LazyData: TRUE
URL: https://github.com/maRce10/baRulho
BugReports: https://github.com/maRce10/baRulho/issues
Suggests:
    rmarkdown,
    ggplot2,
    knitr,
    kableExtra,
    testthat (>= 3.0.0),
    covr,
    formatR,
    Rraven
VignetteBuilder: knitr
RoxygenNote: 7.2.3
Repository: CRANs
Language: en-US
Authors@R: person("Marcelo", "Araya-Salas", role = c("aut", "cre"), email = "[email protected]")
Config/testthat/edition: 3

Scope

Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
- [ ] data retrieval
- [x] data extraction
- [x] data munging
- [ ] data deposition
- [ ] data validation and testing
- [ ] workflow automation
- [ ] version control
- [ ] citation management and bibliometrics
- [ ] scientific software wrappers
- [ ] field and lab reproducibility tools
- [ ] database software bindings
- [ ] geospatial data
- [ ] text analysis
Explain how and why the package falls under these categories (briefly, 1-2 sentences):

It estimates degradation measures from sounds that have been re-recorded in standard playback experiments. It also helps to prepare acoustic data for playback experiments.

Who is the target audience and what are scientific applications of this package?

Scientific community working with bioacoustic data. Useful to automate analysis of animal acoustic signals for a variety of research questions (e.g. behavior, ecology, evolution, conservation)

Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
To the best of my knowledge the only other similar tools is the warbleR package, which has similar functions for measuring features from annotation tables but not specifically related to sound degradation (I am also the maintainer) except for sig2noise.
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
Explain reasons for any pkgcheck items which your package is unable to pass.

Somehow continuous integration is not detected when running pkgcheck::pkgcheck(), but it is fully implemented https://app.codecov.io/gh/maRce10/baRulho?branch=master

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 to find a replacement.

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.
[x] includes documentation with examples for all functions, created with roxygen2.
[x] contains a vignette with examples of its essential functions and uses.
[x] has a test suite.
[x] has continuous integration, including reporting of test coverage.

Publication options

[x] Do you intend for this package to go on CRAN?
[ ] Do you intend for this package to go on Bioconductor?
[x] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

[x] The package is novel and will be of interest to the broad readership of the journal.
[x] The manuscript describing the package is no longer than 3000 words.
[x] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
(Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
(Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
(Please do not submit your package separately to Methods in Ecology and Evolution)

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.

Sep 29 '23 01:09 maRce10

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

Sep 29 '23 01:09 ropensci-review-bot

:rocket:

Editor check started

:wave:

Sep 29 '23 01:09 ropensci-review-bot

Checks for baRulho (v2.1.0)

git hash: 128b6ca3

: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_check_mark: All functions have examples.
:heavy_multiplication_x: Package has no continuous integration checks.
:heavy_check_mark: Package coverage is 75.2%.
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no 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 (>= 2)

1. 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	702
internal	baRulho	46
internal	graphics	45
internal	parallel	15
internal	grDevices	10
internal	ohun	1
internal	tools	1
depends	warbleR	76
imports	seewave	26
imports	stats	19
imports	methods	16
imports	tuneR	7
imports	checkmate	6
imports	cli	2
imports	utils	1
imports	fftw	NA
imports	viridis	NA
imports	Sim.DiffProc	NA
imports	png	NA
suggests	rmarkdown	NA
suggests	ggplot2	NA
suggests	knitr	NA
suggests	kableExtra	NA
suggests	testthat	NA
suggests	covr	NA
suggests	formatR	NA
suggests	Rraven	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(<path/to/repo>)', and examining the 'external_calls' table.

base

c (80), names (36), nrow (30), for (26), if (25), unique (25), vapply (25), seq_len (24), length (22), args (21), match.call (21), as.list (20), which (19), lapply (18), getOption (15), is.na (14), list (13), options (13), plot (13), paste (12), rep (12), seq (12), as.character (10), ncol (9), numeric (9), sum (9), do.call (8), rbind (8), data.frame (7), on.exit (7), paste0 (7), seq_along (7), abs (6), min (6), nchar (6), pretty (6), return (5), t (5), as.data.frame (4), cbind (4), character (4), drop (4), labels (4), log10 (4), matrix (4), sort (4), unlist (4), any (3), diff (3), exp (3), file.path (3), max (3), sub (3), units (3), which.min (3), expand.grid (2), rev (2), sqrt (2), suppressWarnings (2), tempdir (2), all (1), call (1), factor (1), file (1), grepl (1), levels (1), list.files (1), match.arg (1), mean (1), range (1), rank (1), setdiff (1), split (1), sprintf (1), strwrap (1), Sys.info (1), tapply (1), tempfile (1), try (1), vector (1), which.max (1)

warbleR

pblapply_wrblr_int (27), read_sound_file (26), envelope (5), cross_correlation (3), freq_range_detec (3), read_wave (3), image_to_wave (2), lessdB (2), check_sels (1), info_sound_files (1), rename_est_waves (1), selection_table (1), simulate_songs (1)

baRulho

check_arguments (21), FUN (12), check_unique_sels (3), check_unique_sound.id (3), check_deprecated (2), check_several_distances (2), attenuation (1), find_peaks_bRlh_int (1), rbind2 (1)

graphics

par (23), grconvertX (9), lines (5), grid (3), grconvertY (2), split.screen (2), close.screen (1)

seewave

env (7), rms (7), pastew (5), duration (3), fpeaks (2), cutw (1), spec (1)

stats

frequency (8), dist (5), approx (1), ave (1), end (1), spectrum (1), start (1), time (1)

methods

new (16)

parallel

makePSOCKcluster (15)

grDevices

palette (4), colors (3), dev.off (1), recordPlot (1), X11 (1)

tuneR

silence (5), normalize (1), writeWave (1)

checkmate

makeAssertionFunction (5), makeAssertCollection (1)

cli

make_ansi_style (1), num_ansi_colors (1)

ohun

template_correlator (1)

tools

find_gs_cmd (1)

utils

str (1)

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

2. 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 25 files) and
1 authors
2 vignettes
2 internal data files
11 imported packages
24 exported functions (median 73 lines of code)
92 non-exported functions in R (median 22 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	25	86.3
files_vignettes	2	85.7
files_tests	20	96.3
loc_R	5188	95.6	TRUE
loc_vignettes	791	87.2
loc_tests	582	77.8
num_vignettes	2	89.2
data_size_total	1092464	95.5	TRUE
data_size_median	546232	97.2	TRUE
n_fns_r	116	79.9
n_fns_r_exported	24	72.5
n_fns_r_not_exported	92	82.2
n_fns_per_file_r	3	45.6
num_params_per_fn	12	96.6	TRUE
loc_per_fn_r	34	81.2
loc_per_fn_r_exp	73	87.7
loc_per_fn_r_not_exp	22	66.9
rel_whitespace_R	20	95.9	TRUE
rel_whitespace_vignettes	60	96.8	TRUE
rel_whitespace_tests	60	92.1
doclines_per_fn_exp	110	92.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	94	78.3

2a. Network visualisation

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

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following note:

checking installed package size ... NOTE installed size is 10.8Mb sub-directories of 1Mb or more: data 1.6Mb doc 8.7Mb

R CMD check generated the following check_fails:

cyclocomp
no_description_depends
no_import_package_as_a_whole
rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 75.21

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
check_arguments	74
manual_realign	64
plot_degradation	48
plot_blur_FUN	26
signal_to_noise_ratio	26
synth_sounds	23
noise_profile	22
master_sound_file	18
set_reference_sounds	17
detection_distance	15

Static code analyses with lintr

lintr found the following 664 potential issues:

message	number of times
Avoid 1:nrow(...) expressions, use seq_len.	2
Avoid library() and require() calls in packages	12
Avoid using sapply, consider vapply instead, that's type safe	1
Lines should not be more than 80 characters.	649

4. Other Checks

Details of other checks (click to open)

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

- attenuation from seewave
- find_markers from dtangle

Package Versions

package	version
pkgstats	0.1.3.9
pkgcheck	0.1.2.3

Editor-in-Chief Instructions:

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

Sep 29 '23 01:09 ropensci-review-bot

Thank you for this submission @maRce10! Two quick notes before I start the process:

Some things in our checks are being triggered by some extraneous files committed in your repository: .Rproj.user, .Rhistory, etc. Some of these are in .gitignore, but probably were committed before that was created. You can get git of these with the git rm --cached <file>.
@mpadge, it appears our package checks are not picking up the continuous integration tests in this package, which are set up using {tic}. Is this a bug of ours or due to something in the package setup?

Sep 29 '23 11:09 noamross

@ropensci-review-bot assign @jhollist as editor

Sep 29 '23 14:09 noamross

Assigned! @jhollist is now the editor

Sep 29 '23 14:09 ropensci-review-bot

Thank you for this submission @maRce10! Two quick notes before I start the process:

* Some things in our checks are being triggered by some extraneous files committed in your repository: `.Rproj.user`, `.Rhistory`, etc. Some of these are in .gitignore, but probably were committed before that was created.  You can get git of these with the [`git rm --cached <file>`](https://stackoverflow.com/a/1274447/1757441).

* @mpadge, it appears our package checks are not picking up the continuous integration tests in this package, which are set up using {tic}. Is this a bug of ours or due to something in the package setup?

Hi @noamross!

I just removed those weird files maRce10/baRulho@e6f1b4dd5592b290fe1875fe6aee88b683d1f14a

Sep 29 '23 15:09 maRce10

Hey @maRce10. Long time no see (ha!)

I will get started on this early next week.

Just wanted to let you know that the impending US Gov shutdown may impact my ability to work on this. I am good to work all next week, but if we do shutdown and it is not resolved, I will have to stop all work activities (my serving as an editor counts as one) after the 7th and I can't resume until the shutdown has been lifted. Hopefully this all for naught and I am able to keep on working on this. But I will do what I can to make progress next week.

Sep 29 '23 15:09 jhollist

@noamross @maRce10 The failing "no continuous integration" check is because it actually just checks for an R CMD check badge in the readme, which this package does not have. It has a lot of badges, but not that critical one. Obviously not a big issue here, and we can clearly accept regardless, but @maRce10 if you want that test to pass, just put a badge linking to your r cmd check status on the README.

Sep 29 '23 15:09 mpadge

@noamross @maRce10 The failing "no continuous integration" check is because it actually just checks for an R CMD check badge in the readme, which this package does not have. It has a lot of badges, but not that critical one. Obviously not a big issue here, and we can clearly accept regardless, but @maRce10 if you want that test to pass, just put a badge linking to your r cmd check status on the README.

Thanks! I added the R CMD check badge.

Hey @maRce10. Long time no see (ha!)

I will get started on this early next week.

Just wanted to let you know that the impending US Gov shutdown may impact my ability to work on this. I am good to work all next week, but if we do shutdown and it is not resolved, I will have to stop all work activities (my serving as an editor counts as one) after the 7th and I can't resume until the shutdown has been lifted. Hopefully this all for naught and I am able to keep on working on this. But I will do what I can to make progress next week.

Thanks for letting me know!

Sep 29 '23 23:09 maRce10

@ropensci-review-bot check baRulho

Oct 03 '23 20:10 jhollist

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@ropensci-review-bot help

Oct 03 '23 20:10 ropensci-review-bot

@ropensci-review-bot check package

Oct 03 '23 20:10 jhollist

Thanks, about to send the query.

Oct 03 '23 20:10 ropensci-review-bot

:rocket:

Editor check started

:wave:

Oct 03 '23 20:10 ropensci-review-bot

Checks for baRulho (v2.1.0)

git hash: 46763a23

: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_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_multiplication_x: Package coverage failed
:heavy_multiplication_x: R CMD check process failed with message: 'Build process failed'.
: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 (>= 2)

1. 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	731
internal	baRulho	48
internal	graphics	45
internal	parallel	16
internal	grDevices	10
internal	ohun	1
internal	tools	1
depends	warbleR	83
imports	seewave	23
imports	stats	20
imports	methods	17
imports	tuneR	7
imports	checkmate	7
imports	cli	2
imports	utils	1
imports	fftw	NA
imports	viridis	NA
imports	Sim.DiffProc	NA
imports	png	NA
suggests	rmarkdown	NA
suggests	ggplot2	NA
suggests	knitr	NA
suggests	kableExtra	NA
suggests	testthat	NA
suggests	covr	NA
suggests	formatR	NA
suggests	Rraven	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(<path/to/repo>)', and examining the 'external_calls' table.

base

c (83), names (36), nrow (33), seq_len (28), for (27), if (27), unique (25), vapply (25), length (23), match.call (22), args (21), as.list (21), lapply (19), which (19), getOption (18), is.na (14), list (13), options (13), paste (12), rep (12), seq (12), plot (11), as.character (10), ncol (9), numeric (9), sum (9), do.call (8), rbind (8), attributes (7), data.frame (7), on.exit (7), paste0 (7), seq_along (7), abs (6), min (6), nchar (6), pretty (6), return (5), t (5), as.data.frame (4), cbind (4), character (4), drop (4), labels (4), log10 (4), matrix (4), sort (4), unlist (4), any (3), diff (3), exp (3), file.path (3), max (3), sub (3), units (3), which.min (3), expand.grid (2), is.null (2), mean (2), rev (2), sqrt (2), suppressWarnings (2), tempdir (2), all (1), call (1), factor (1), file (1), grepl (1), levels (1), list.files (1), match.arg (1), q (1), range (1), rank (1), setdiff (1), split (1), sprintf (1), strwrap (1), Sys.info (1), tapply (1), tempfile (1), try (1), vector (1), which.max (1)

warbleR

pblapply_wrblr_int (30), read_sound_file (27), envelope (8), cross_correlation (3), freq_range_detec (3), read_wave (3), image_to_wave (2), lessdB (2), check_sels (1), info_sound_files (1), rename_est_waves (1), selection_table (1), simulate_songs (1)

baRulho

check_arguments (21), FUN (12), check_unique_sels (3), by_element_est (2), check_deprecated (2), check_extended_selection_table (2), check_several_distances (2), attenuation (1), check_unique_sound.id (1), find_peaks_bRlh_int (1), rbind2 (1)

graphics

par (23), grconvertX (9), lines (5), grid (3), grconvertY (2), split.screen (2), close.screen (1)

seewave

rms (6), env (5), pastew (5), duration (3), fpeaks (2), cutw (1), spec (1)

stats

frequency (8), dist (5), approx (2), ave (1), end (1), spectrum (1), start (1), time (1)

methods

new (16), formalArgs (1)

parallel

makePSOCKcluster (16)

grDevices

palette (4), colors (3), dev.off (1), recordPlot (1), X11 (1)

checkmate

makeAssertionFunction (6), makeAssertCollection (1)

tuneR

silence (5), normalize (1), writeWave (1)

cli

make_ansi_style (1), num_ansi_colors (1)

ohun

template_correlator (1)

tools

find_gs_cmd (1)

utils

str (1)

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

2. 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 25 files) and
1 authors
2 vignettes
2 internal data files
11 imported packages
24 exported functions (median 74 lines of code)
98 non-exported functions in R (median 21 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	25	86.3
files_vignettes	2	85.7
files_tests	21	96.6
loc_R	5307	95.8	TRUE
loc_vignettes	791	87.2
loc_tests	685	80.8
num_vignettes	2	89.2
data_size_total	1092464	95.5	TRUE
data_size_median	546232	97.2	TRUE
n_fns_r	122	81.1
n_fns_r_exported	24	72.5
n_fns_r_not_exported	98	83.4
n_fns_per_file_r	3	47.2
num_params_per_fn	12	96.6	TRUE
loc_per_fn_r	38	83.7
loc_per_fn_r_exp	74	87.9
loc_per_fn_r_not_exp	22	66.5
rel_whitespace_R	20	96.2	TRUE
rel_whitespace_vignettes	60	96.8	TRUE
rel_whitespace_tests	54	92.7
doclines_per_fn_exp	110	92.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	98	78.9

2a. Network visualisation

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

3. `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
6384082445	.github/workflows/deploy_ghpages.yaml	failure	d5364f	4	2023-10-02
6385163073	Continuous Deployment	failure	1b0f43	6	2023-10-02
6385275826	pages build and deployment	success	995476	75	2023-10-02
6396499245	R-CMD-check	failure	c488df	16	2023-10-03
6393038656	Render README	success	833ca7	17	2023-10-03
6397662241	tic	failure	46763a	100	2023-10-03
6396505549	Update CITATION.cff	success	0925c7	1	2023-10-03

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following error:

Error in proc$get_built_file() : Build process failed

R CMD check generated the following check_fails:

no_description_depends
no_import_package_as_a_whole

Test coverage with covr

ERROR: Test Coverage Failed

Cyclocomplexity with cyclocomp

Error : Build failed, unknown error, standard output:

checking for file ‘baRulho/DESCRIPTION’ ... OK
preparing ‘baRulho’:
checking DESCRIPTION meta-information ... OK
installing the package to build vignettes -----------------------------------
installing source package ‘baRulho’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘baRulho’ in namespaceExport(ns, exports): undefined exports: add_noise Error: loading failed Execution halted ERROR: loading failed
removing ‘/tmp/RtmpaoozZw/Rinst16cd73656348/baRulho’ ----------------------------------- ERROR: package installation failed

Static code analyses with lintr

lintr found the following 680 potential issues:

message	number of times
Avoid 1:nrow(...) expressions, use seq_len.	2
Avoid library() and require() calls in packages	12
Avoid using sapply, consider vapply instead, that's type safe	1
Lines should not be more than 80 characters.	665

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 3 function names are duplicated in other packages:

- add_noise from errorlocate, pauwels2014, spant, tdaunif, TestFunctions, vpc
- attenuation from seewave
- find_markers from dtangle

Package Versions

package	version
pkgstats	0.1.3.9
pkgcheck	0.1.2.9

Editor-in-Chief Instructions:

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

Oct 03 '23 20:10 ropensci-review-bot

Editor checks:

[x] Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package. In particular,
- [x] Is the case for the package well made?
- [x] Is the reference index page clear (grouped by topic if necessary)?
- [x] Are vignettes readable, sufficiently detailed and not just perfunctory?
[x] Fit: The package meets criteria for fit and overlap.
[x] Installation instructions: Are installation instructions clear enough for human users?
[x] Tests: If the package has some interactivity / HTTP / plot production etc. are the tests using state-of-the-art tooling?
[x] Contributing information: Is the documentation for contribution clear enough e.g. tokens for tests, playgrounds?
[x] License: The package has a CRAN or OSI accepted license.
[ ] Project management: Are the issue and PR trackers in a good shape, e.g. are there outstanding bugs, is it clear when feature requests are meant to be tackled?

Editor comments

@maRce10 See checks in previous comment. R CMD Check is now failing. I did see that you recently merged some new work and that is triggering this failure. I assume you are still doing a bit of work on this. Let me know when you have that completed and your checks pass. I will check again and then move forward with finding reviewers.

I also noted a few others things. Data is a bit large, not sure if you can reduce that.

❯ checking installed package size ... NOTE
    installed size is 10.8Mb
    sub-directories of 1Mb or more:
      data   1.6Mb
      doc    7.5Mb
      help   1.5Mb

I see 6 Open Issues - what are the status on those? If closed or no longer relevant, clean those up. If still relevant provide updates in issues so that reviewers can asses the status.

Oct 03 '23 20:10 jhollist

OK I solved and closed the issues and now R CMD check is working again. The size of data is probably due to having sounds as examples. I shrank it as much as I could.

Oct 04 '23 23:10 maRce10

@ropensci-review-bot check package

Oct 05 '23 13:10 jhollist

Thanks, about to send the query.

Oct 05 '23 13:10 ropensci-review-bot

:rocket:

Editor check started

:wave:

Oct 05 '23 13:10 ropensci-review-bot

Checks for baRulho (v2.1.0)

git hash: 36f90248

: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_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_check_mark: Package coverage is 79.9%.
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Function names are duplicated in other packages

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

Package License: GPL (>= 2)

1. 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	750
internal	baRulho	54
internal	graphics	45
internal	parallel	16
internal	grDevices	10
internal	ohun	1
internal	tools	1
depends	warbleR	81
imports	seewave	23
imports	stats	19
imports	methods	17
imports	checkmate	8
imports	tuneR	7
imports	cli	2
imports	utils	1
imports	fftw	NA
imports	viridis	NA
imports	Sim.DiffProc	NA
imports	png	NA
suggests	rmarkdown	NA
suggests	ggplot2	NA
suggests	knitr	NA
suggests	kableExtra	NA
suggests	testthat	NA
suggests	covr	NA
suggests	formatR	NA
suggests	Rraven	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(<path/to/repo>)', and examining the 'external_calls' table.

base

c (83), names (38), nrow (34), seq_len (29), for (28), if (26), unique (26), vapply (25), match.call (24), args (23), as.list (23), length (23), which (20), lapply (19), getOption (18), is.na (14), list (14), options (13), paste (12), plot (12), rep (12), seq (12), as.character (10), sum (10), ncol (9), numeric (9), attributes (8), do.call (8), rbind (8), on.exit (7), paste0 (7), seq_along (7), abs (6), data.frame (6), min (6), nchar (6), pretty (6), return (6), t (5), as.data.frame (4), cbind (4), character (4), drop (4), file.path (4), labels (4), log10 (4), matrix (4), sort (4), unlist (4), any (3), diff (3), exp (3), max (3), sub (3), units (3), vector (3), which.min (3), expand.grid (2), is.null (2), mean (2), rev (2), sqrt (2), suppressWarnings (2), tempdir (2), all (1), call (1), factor (1), file (1), grepl (1), levels (1), list.files (1), match.arg (1), q (1), range (1), sapply (1), setdiff (1), split (1), sprintf (1), strwrap (1), Sys.info (1), tapply (1), tempfile (1), try (1), which.max (1)

warbleR

pblapply_wrblr_int (31), read_sound_file (27), envelope (6), cross_correlation (3), freq_range_detec (3), read_wave (3), image_to_wave (2), lessdB (2), check_sels (1), info_sound_files (1), rename_est_waves (1), simulate_songs (1)

baRulho

check_arguments (23), FUN (13), by_element_est (2), check_deprecated (2), check_extended_selection_table (2), check_several_distances (2), check_sound_files_found (2), check_unique_sels (2), attenuation (1), check_unique_sound.id (1), colortext (1), find_peaks_bRlh_int (1), rbind2 (1), signal_to_noise_ratio (1)

graphics

par (23), grconvertX (9), lines (5), grid (3), grconvertY (2), split.screen (2), close.screen (1)

seewave

rms (6), env (5), pastew (5), duration (3), fpeaks (2), cutw (1), spec (1)

stats

frequency (8), dist (5), approx (2), end (1), runif (1), start (1), time (1)

methods

new (16), formalArgs (1)

parallel

makePSOCKcluster (16)

grDevices

palette (4), colors (3), dev.off (1), recordPlot (1), X11 (1)

checkmate

makeAssertionFunction (7), makeAssertCollection (1)

tuneR

silence (5), normalize (1), writeWave (1)

cli

make_ansi_style (1), num_ansi_colors (1)

ohun

template_correlator (1)

tools

find_gs_cmd (1)

utils

str (1)

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

2. 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 26 files) and
1 authors
2 vignettes
2 internal data files
11 imported packages
25 exported functions (median 74 lines of code)
103 non-exported functions in R (median 23 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	26	87.0
files_vignettes	2	85.7
files_tests	21	96.6
loc_R	5626	96.1	TRUE
loc_vignettes	795	87.3
loc_tests	687	80.9
num_vignettes	2	89.2
data_size_total	1092464	95.5	TRUE
data_size_median	546232	97.2	TRUE
n_fns_r	128	82.1
n_fns_r_exported	25	73.6
n_fns_r_not_exported	103	84.4
n_fns_per_file_r	3	47.3
num_params_per_fn	12	96.6	TRUE
loc_per_fn_r	38	83.4
loc_per_fn_r_exp	74	87.9
loc_per_fn_r_not_exp	23	68.7
rel_whitespace_R	20	96.4	TRUE
rel_whitespace_vignettes	60	96.8	TRUE
rel_whitespace_tests	54	92.7
doclines_per_fn_exp	110	92.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	105	80.1

2a. Network visualisation

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

3. `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
6414603275	pages build and deployment	success	09b477	80	2023-10-05
6411731627	R-CMD-check	success	36f902	20	2023-10-04
6419119914	Render README	success	36f902	20	2023-10-05
6414533822	tic	success	36f902	111	2023-10-05
6396505549	Update CITATION.cff	success	0925c7	1	2023-10-03

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following note:

checking installed package size ... NOTE installed size is 12.2Mb sub-directories of 1Mb or more: data 1.6Mb doc 8.8Mb help 1.5Mb

R CMD check generated the following check_fails:

cyclocomp
no_description_depends
no_import_package_as_a_whole
rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 79.91

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
check_arguments	84
manual_realign	64
plot_degradation	48
signal_to_noise_ratio	29
plot_blur_FUN	26
synth_sounds	25
noise_profile	22
master_sound_file	18
set_reference_sounds	17
detection_distance	15

Static code analyses with lintr

lintr found the following 703 potential issues:

message	number of times
Avoid 1:nrow(...) expressions, use seq_len.	2
Avoid library() and require() calls in packages	12
Avoid using sapply, consider vapply instead, that's type safe	3
Lines should not be more than 80 characters.	686

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 3 function names are duplicated in other packages:

- add_noise from errorlocate, pauwels2014, spant, tdaunif, TestFunctions, vpc
- attenuation from seewave
- find_markers from dtangle

Package Versions

package	version
pkgstats	0.1.3.9
pkgcheck	0.1.2.9

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

Oct 05 '23 13:10 ropensci-review-bot

@maRce10 I think we are good to move on to review.

Couple of things to think about in the lintr results, in particular the 1:nrow and sapply ones. The library calls you can ignore since those are in Rmd and tests.

Look through those results for other ideas as well. For instance, your lines of code are on the high side, but so is cyclomatic complexity. If you can simplify some of these functions you could probably reduce both and make future maintenance a little easier.

That being said, we are good to go for reviewers. I'll start pinging on a few folks today.

Oct 05 '23 14:10 jhollist

@ropensci-review-bot seeking reviewers

Oct 05 '23 14:10 jhollist

Please add this badge to the README of your package repository:

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/609_status.svg)](https://github.com/ropensci/software-review/issues/609)

Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news

Oct 05 '23 14:10 ropensci-review-bot

@ropensci-review-bot assign @mikemahoney218 as reviewer

Oct 05 '23 20:10 jhollist

@mikemahoney218 added to the reviewers list. Review due date is 2023-10-26. Thanks @mikemahoney218 for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

Oct 05 '23 20:10 ropensci-review-bot

@mikemahoney218: If you haven't done so, please fill this form for us to update our reviewers records.

Oct 05 '23 20:10 ropensci-review-bot

@ropensci-review-bot set due date for @mikemahoney218 to 2023-11-03

Oct 05 '23 20:10 jhollist

Review due date for @mikemahoney218 is now 03-November-2023

Oct 05 '23 20:10 ropensci-review-bot

software-review software-review copied to clipboard

baRulho

Scope

Technical checks

Publication options

Code of conduct

Checks for baRulho (v2.1.0)

1. Package Dependencies

2. Statistical Properties

2a. Network visualisation

3. goodpractice and other checks

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

4. Other Checks

Editor-in-Chief Instructions:

Checks for baRulho (v2.1.0)

1. Package Dependencies

2. Statistical Properties

2a. Network visualisation

3. goodpractice and other checks

3a. Continuous Integration Badges

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

4. Other Checks

Editor-in-Chief Instructions:

Editor checks:

Editor comments

Checks for baRulho (v2.1.0)

1. Package Dependencies

2. Statistical Properties

2a. Network visualisation

3. goodpractice and other checks

3a. Continuous Integration Badges

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

4. Other Checks

Editor-in-Chief Instructions:

software-review
software-review copied to clipboard

3. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

3. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

3. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck