pkgcheck results - master

[github-actions]

Checks for mobsim (v0.2.0.9015)

git hash: 3948453b

• ✔️ Package name is available
• ✔️ has a 'CITATION' file.
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✖️ These functions do not have examples: [abund_rect, mobsim, plot.divar, rThomas_rcpp, sampling_grids, sampling_one_quadrat, sampling_random_bruteforce, sampling_random_overlap, sampling_random_spatstat, sampling_transects, summary.community, summary.sad].
• ✔️ Package has continuous integration checks.
• ✖️ Package coverage is 68.9% (should be at least 75%).
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

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

Package License: GPL (>= 3)

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1. 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++ (15% in 3 files) and R (85% in 7 files)
• 2 authors
• 5 vignettes
• no internal data file
• 7 imported packages
• 31 exported functions (median 16 lines of code)
• 33 non-exported functions in R (median 21 lines of code)
• 8 R functions (median 7 lines of code)

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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

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	7	45.7
files_src	3	84.3
files_vignettes	5	96.9
files_tests	12	92.5
loc_R	773	60.8
loc_src	136	20.8
loc_vignettes	768	86.7
loc_tests	743	82.3
num_vignettes	5	97.9	TRUE
n_fns_r	64	64.2
n_fns_r_exported	31	79.2
n_fns_r_not_exported	33	55.8
n_fns_src	8	24.6
n_fns_per_file_r	6	76.4
n_fns_per_file_src	3	27.4
num_params_per_fn	5	69.6
loc_per_fn_r	17	52.0
loc_per_fn_r_exp	16	38.0
loc_per_fn_r_not_exp	21	64.9
loc_per_fn_src	8	12.7
rel_whitespace_R	33	76.4
rel_whitespace_src	28	29.9
rel_whitespace_vignettes	32	88.5
rel_whitespace_tests	16	76.4
doclines_per_fn_exp	28	29.1
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	25	51.3

---

1a. Network visualisation

An interactive visualisation of calls between objects in the package has been uploaded as a workflow artefact. To view it, click on results from the latest 'pkgcheck' action, scroll to the bottom, and click on the 'visual-network' artefact.

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2. goodpractice and other checks

Details of goodpractice and other checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

name	conclusion	sha	date
pkgcheck		394845	2022-03-15
R-CMD-check		394845	2022-03-15

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following note:

1. checking dependencies in R code ... NOTE
   Namespace in Imports field not imported from: ‘sads’
   All declared Imports should be used.

R CMD check generated the following check_fails:

1. cyclocomp
2. no_description_date
3. rcmdcheck_imports_not_imported_from

Test coverage with covr

Package coverage: 68.92

The following files are not completely covered by tests:

file	coverage
R/Diversity_Area_Relationships.R	54.96%
R/SAC_spatial.R	30.23%
src/SAC_spatial.cpp	0%

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
sim_thomas_coords	60
sim_sad	42

Static code analyses with lintr

lintr found the following 336 potential issues:

message	number of times
Avoid 1:length(...) expressions, use seq_len.	3
Avoid 1:nrow(...) expressions, use seq_len.	1
Avoid 1L:length(...) expressions, use seq_len.	2
Avoid 1L:nrow(...) expressions, use seq_len.	1
Avoid using sapply, consider vapply instead, that's type safe	9
Lines should not be more than 80 characters.	286
Use <-, not =, for assignment.	34

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Package Versions

package	version
pkgstats	0.0.3.89
pkgcheck	0.0.2.259