rpigpior

[mnr]

Submitting Author Name: Mark Niemann-Ross
Submitting Author Github Handle: @mnr
Other Package Authors Github handles: (comma separated, delete if none)
Repository: https://github.com/mnr/rpigpior
Version submitted:0.0.0.1
Submission type: Standard
Editor: TBD
Reviewers: TBD

Archive: TBD
Version accepted: TBD
Language: en

---

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

This provides R with access to the Raspberry Pi General Purpose Input Output (GPIO) via 'libgpiod'. This includes detecting a gpio chip as well as turning pins on and off via [gpioset()] and reading the state of pins via [gpioget()]. No additional libraries need to be installed; Raspbian includes 'libgpiod' as part of the standard installation.

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
  • data extraction
  • 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):
  Raspberry Pi is part of the Internet of Things and is used as laboratory equipment. Other applications include automation, field sampling and analysis, and prototyping.

• Who is the target audience and what are scientific applications of this package?
  Field analysts and prototype creators.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
  https://r4pi.org provides a version of R for the Raspberry Pi, but does not provide packaged access to the general purpose input/output (GPIO) pins. At some point, it is possible rpigpior could be included with their distribution.

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

• 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.

Technical checks

Confirm each of the following by checking the box.

• I have read the rOpenSci packaging guide.
• 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:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions, created with roxygen2.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage.

Publication options

• Do you intend for this package to go on CRAN?

• Do you intend for this package to go on Bioconductor?

• Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

• The package is novel and will be of interest to the broad readership of the journal.
• The manuscript describing the package is no longer than 3000 words.
• 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

• 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]

🚀

Editor check started

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[ropensci-review-bot]

Checks for rpigpior (v0.1.0)

git hash: 30e4ba66

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✖️ does not have a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✖️ Package coverage failed
• ✖️ R CMD check found 1 error.
• ✖️ R CMD check found 1 warning.

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

Package License: MIT + file LICENSE

---

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	21
internal	rpigpior	10
internal	utils	1
imports	NA	NA
suggests	knitr	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(<path/to/repo>)', and examining the 'external_calls' table.

base

paste (6), system (3), c (2), for (2), as.integer (1), if (1), length (1), names (1), paste0 (1), regexec (1), regmatches (1), tryCatch (1)

rpigpior

rpi_pinToBCM (4), is.rpi (1), pwm_func (1), rpi_get (1), rpi_i2c_get (1), rpi_i2c_set (1), rpi_pin_desc (1)

utils

read.table (1)

NOTE: No imported packages appear to have 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 10 files) and
• 1 authors
• 6 vignettes
• 1 internal data file
• 1 imported package
• 8 exported functions (median 19 lines of code)
• 10 non-exported functions in R (median 29 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	10	59.0
files_vignettes	6	97.9
files_tests	10	90.7
loc_R	266	29.4
loc_vignettes	293	62.8
loc_tests	137	46.6
num_vignettes	6	98.7	TRUE
data_size_total	483	58.5
data_size_median	483	60.2
n_fns_r	18	25.1
n_fns_r_exported	8	38.3
n_fns_r_not_exported	10	22.3
n_fns_per_file_r	1	16.1
num_params_per_fn	2	30.8
loc_per_fn_r	22	63.6
loc_per_fn_r_exp	20	46.3
loc_per_fn_r_not_exp	30	78.0
rel_whitespace_R	17	32.6
rel_whitespace_vignettes	60	81.6
rel_whitespace_tests	6	18.6
doclines_per_fn_exp	22	17.3
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	9	30.9

---

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
8832736528	pages build and deployment	success	b265f5	121	2024-04-25
8832871972	pkgdown	failure	30e4ba	151	2024-04-25
8832871969	R-CMD-check	failure	30e4ba	146	2024-04-25

---

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:
   'test-rpi_i2c_get.R:11:3', 'test-rpi_i2c_get.R:20:3',
   'test-rpi_i2c_get.R:29:3', 'test-rpi_monitor.R:2:3', 'test-rpi_pwm.R:2:3',
   'test-rpi_pwm.R:7:3', 'test-rpi_pwm.R:12:3', 'test-rpi_pwm.R:17:3',
   'test-rpi_set.R:3:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-is.R:2:3'): is.rpi confirms/denies RPi ───────────────────────
if (...) NULL is not TRUE

actual is NULL
expected is a logical vector (TRUE)

[ FAIL 1 | WARN 0 | SKIP 10 | PASS 43 ]
Error: Test failures
Execution halted

R CMD check generated the following warning:

1. checking package subdirectories ... WARNING
   Invalid citation information in ‘inst/CITATION’:
   Error in bibentry(bibtype = entry, textVersion = textVersion, header = header, footer = footer, ...): argument is missing, with no default

R CMD check generated the following test_fail:

1. This file is part of the standard setup for testthat.

It is recommended that you do not modify it.

Where should you do additional test configuration?

Learn more about the roles of various files in:

* https://r-pkgs.org/tests.html

* https://testthat.r-lib.org/reference/test_package.html#special-files

library(testthat)
library(rpigpior)

test_check("rpigpior")
Real world test of setting board pin 11
[ FAIL 1 | WARN 0 | SKIP 10 | PASS 43 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• is.rpi() is not TRUE (10): 'test-rpi_i2c_get.R:2:3',
'test-rpi_i2c_get.R:11:3', 'test-rpi_i2c_get.R:20:3',
'test-rpi_i2c_get.R:29:3', 'test-rpi_monitor.R:2:3', 'test-rpi_pwm.R:2:3',
'test-rpi_pwm.R:7:3', 'test-rpi_pwm.R:12:3', 'test-rpi_pwm.R:17:3',
'test-rpi_set.R:3:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-is.R:2:3'): is.rpi confirms/denies RPi ───────────────────────
if (...) NULL is not TRUE

actual is NULL
expected is a logical vector (TRUE)

[ FAIL 1 | WARN 0 | SKIP 10 | PASS 43 ]
Error: Test failures
Execution halted

R CMD check generated the following check_fail:

1. rcmdcheck_tests_pass

Test coverage with covr

ERROR: Test Coverage Failed

Cyclocomplexity with cyclocomp

The following function have cyclocomplexity >= 15:

function	cyclocomplexity
rpi_pwm	29

Static code analyses with lintr

lintr found the following 50 potential issues:

message	number of times
Avoid library() and require() calls in packages	6
Lines should not be more than 80 characters.	43
unexpected symbol	1

---

Package Versions

package	version
pkgstats	0.1.3.13
pkgcheck	0.1.2.21

---

Editor-in-Chief Instructions:

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

[ldecicco-USGS]

Hi @mnr ! Please click the 3 dots in the upper right corner of your original comment to edit, then fill in the response to the fields. A quick glance at your package makes me think it could fit in the "field and laboratory reproducibility tools" category. Playing with a Raspberry Pi is high on my list of things to do, so I'm excited to see this submission.

Once the grey "X"'s are fixed and the original submission fields are updated, I'll take a closer look. Thanks for your submission.

[mnr]

Thanks for the advice. I missed the questions below the scroll and have filled those out.

I was also able to clean up the R CMD checks.

So...I think we are good to go?

MNR

[ldecicco-USGS]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

🚀

Editor check started

👋

[ropensci-review-bot]

Checks for rpigpior (v0.1.0)

git hash: 6885db4d

• ✔️ Package name is available
• ✔️ 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
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✖️ Package coverage is 14.4% (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: MIT + file LICENSE

---

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	21
internal	rpigpior	10
internal	utils	1
imports	NA	NA
suggests	knitr	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(<path/to/repo>)', and examining the 'external_calls' table.

base

paste (6), system (3), c (2), for (2), as.integer (1), if (1), length (1), names (1), paste0 (1), regexec (1), regmatches (1), tryCatch (1)

rpigpior

rpi_pinToBCM (4), is.rpi (1), pwm_func (1), rpi_get (1), rpi_i2c_get (1), rpi_i2c_set (1), rpi_pin_desc (1)

utils

read.table (1)

NOTE: No imported packages appear to have 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 10 files) and
• 1 authors
• 6 vignettes
• 1 internal data file
• 1 imported package
• 8 exported functions (median 19 lines of code)
• 10 non-exported functions in R (median 29 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	10	59.0
files_vignettes	6	97.9
files_tests	10	90.7
loc_R	266	29.4
loc_vignettes	293	62.8
loc_tests	138	46.7
num_vignettes	6	98.7	TRUE
data_size_total	483	58.5
data_size_median	483	60.2
n_fns_r	18	25.1
n_fns_r_exported	8	38.3
n_fns_r_not_exported	10	22.3
n_fns_per_file_r	1	16.1
num_params_per_fn	2	30.8
loc_per_fn_r	22	63.6
loc_per_fn_r_exp	20	46.3
loc_per_fn_r_not_exp	30	78.0
rel_whitespace_R	18	33.1
rel_whitespace_vignettes	60	81.6
rel_whitespace_tests	6	18.6
doclines_per_fn_exp	22	17.3
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	9	30.9

---

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
8871392503	pages build and deployment	success	d9ee99	134	2024-04-29
8871375569	pkgdown	success	6885db	164	2024-04-29
8871375565	R-CMD-check	success	6885db	159	2024-04-29

---

3b. goodpractice results

R CMD check with rcmdcheck

rcmdcheck found no errors, warnings, or notes

Test coverage with covr

Package coverage: 14.36

The following files are not completely covered by tests:

file	coverage
R/rpi_get.R	0%
R/rpi_i2c_get.R	0%
R/rpi_i2c_set.R	0%
R/rpi_monitor.R	0%
R/rpi_pwm.R	0%
R/rpi_set.R	0%

Cyclocomplexity with cyclocomp

The following function have cyclocomplexity >= 15:

function	cyclocomplexity
rpi_pwm	29

Static code analyses with lintr

lintr found the following 50 potential issues:

message	number of times
Avoid library() and require() calls in packages	6
Lines should not be more than 80 characters.	43
unexpected symbol	1

---

Package Versions

package	version
pkgstats	0.1.3.13
pkgcheck	0.1.2.21

---

Editor-in-Chief Instructions:

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

[mnr]

So - I need some guidance on this. It appears that covr doesn't like my unit tests.

Here's the problem:

• most of these tests will fail if there isn't a Raspberry Pi GPIO present to test.
• To avoid those failures, I always check for presence of Raspberry Pi. skip_if_not(is.rpi(), message = "Not a Raspberry Pi")
• many of these tests will fail if there isn't a switch, or LED, or i2c device connected to the RPi GPIO

Because I'm avoiding obvious failures, covr states "The following files are not completely covered by tests:"

In some cases, there is a robust set of tests - but requires significant set-up to test. For example, rpi_i2c_get includes this test...

` test_that("rpi_i2c_get err chip address", {

skip_if_not(is.rpi(), message = "Not a Raspberry Pi")

expect_error(rpi_i2c_get(

    chip_address = 0x07,

    data_address = 0xf0,

    data_size = "b"

  ))

 }) `

...which means a successful test requires an i2c device is connected to the RPi and is configured to appear at chip address 0x77 and produces expected data at 0xf0

Your help is appreciated.
MNR

[mpadge]

@mnr The inability to test coverage is in your case not a problem. Special hardware requirements are not something we even thought about in developing this system. I might have a play on my own pi, but other than that we can just wait for Editor-in-Chief @jooolia to make a judgement on scope here and proceed regardless of reported coverage.

[jooolia]

Thank you for your submission to rOpenSci.

After careful consideration, we have determined that your submission is out of scope for our "field and lab reproducibility tools" category. While we recognise the utility of your package for many users, it is not specifically aligned to rOpenSci's focus on reproducibility in lab and field through the standardization and automation of real-world workflows.

Thank you again for considering rOpenSci, and please feel free to submit other packages for consideration in the future.

Sincerely, Julia Gustavsen

[jooolia]

@ropensci-review-bot out of scope