Submission: {cffr} Generate Citation File Format ('cff') Metadata for R Packages

[dieghernan]

Submitting Author Name: Diego Hernangómez
Submitting Author Github Handle: @dieghernan
Repository: https://github.com/dieghernan/cffr
Version submitted: 0.0.1.9001
Submission type: Standard
Editor: @emilyriederer
Reviewers: @sckott, @zambujo

Due date for @sckott: 2021-10-19

Due date for @zambujo: 2021-10-20
Archive: TBD
Version accepted: TBD

---

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

Package: cffr
Title: Generate Citation File Format ('cff') Metadata for R Packages
Version: 0.0.1.9001
Authors@R: 
    person(given = "Diego",
           family = "Hernangómez",
           role = c("aut", "cre"),
           email = "diego.hernangomezherrero@gmail.com",
           comment = c(ORCID = "0000-0001-8457-4658"))
Description: The Citation File Format version 1.2.0 (Druskat, S. et al.
    (2021) <doi:10.5281/zenodo.5171937>) is a human and machine readable
    file format which provides citation metadata for software. This
    package provides core utilities to generate and validate this
    metadata.
License: GPL (>= 3)
URL: https://dieghernan.github.io/cffr/,
    https://github.com/dieghernan/cffr
BugReports: https://github.com/dieghernan/cffr/issues
Depends: 
    R (>= 3.6.0)
Imports: 
    crayon (>= 1.4.1),
    desc (>= 1.3.0),
    jsonlite (>= 1.7.2),
    jsonvalidate (>= 1.1.0),
    yaml (>= 2.2.1)
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: 
    knitr
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
X-schema.org-keywords: attribution, citation, credit, citation-files, cff,
    metadata

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
  • 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):

The package extract metadata from DESCRIPTION and CITATION and generates a CITATION.cff file.

CITATION.cff files are plain text files with human- and machine-readable citation information for software (and datasets).

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

Any R package developer. A CITATION.cff file provides clarity when citating R packages. GitHub, Zenodo and Zotero supports this format.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

{citation}: The development version (at the time of this writing) includes a new function r2cff that creates a minimal CITATION.cff file (v1.1.0) using the information of your DESCRIPTION file. It also provide minimal validity checks.

{handlr}: Tool for converting among citation formats, including *.cff files. At the time of
this writing only CFF v1.1.0 was supported (see #24).

{cffr} performs an extensive extraction of DESCRIPTION and CITATION, as well as validation via {jsonvalidate} against the
official schema.json. None of the packages mentioned before supports CFF v1.2.0, that is the latest released version.

It also provides parsers for person and citation/bibentry classes.

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

N/A

• 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.

#462 @noamross

Technical checks

Confirm each of the following by checking the box.

• I have read the guide for authors and rOpenSci packaging guide.

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 using services such as Travis CI, Coveralls and/or CodeCov.

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]

Error (500). The editorcheck service is currently unavailable

[ropensci-review-bot]

Checks for cffr (v0.0.1.9001)

git hash: cc7c87d1

• ✔️ Package uses 'roxygen2'
• ✔️ Package has a 'contributing.md' file
• ✔️ Package has a 'CITATION' file
• ✔️ Package has a 'codemeta.json' file
• ✔️ All functions have examples
• ✔️ Package 'DESCRIPTION' has a URL field
• ✔️ Package 'DESCRIPTION' has a BugReports field
• ✔️ Package name is available
• ✔️ Package has continuous integration checks
• ✔️ Package coverage is 99%
• ✔️ R CMD check found no errors
• ✔️ R CMD check found no warnings

Package License: GPL (>= 3)

---

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 R (100% in 13 files) and
• 1 authors
• 1 vignette
• no internal data file
• 5 imported packages
• 12 exported functions (median 21 lines of code)
• 74 non-exported functions in R (median 13 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

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	13	65.6
files_vignettes	2	83.0
files_tests	13	91.6
loc_R	896	63.0
loc_vignettes	174	66.6
loc_tests	802	80.8
num_vignettes	1	60.7
n_fns_r	86	66.2
n_fns_r_exported	12	48.2
n_fns_r_not_exported	74	70.6
n_fns_per_file_r	4	50.4
num_params_per_fn	1	1.1	TRUE
loc_per_fn_r	14	56.3
loc_per_fn_r_exp	22	51.8
loc_per_fn_r_not_exp	13	59.8
rel_whitespace_R	28	74.5
rel_whitespace_vignettes	52	85.5
rel_whitespace_tests	30	94.7
doclines_per_fn_exp	44	55.3
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	96	76.3

---

1a. Network visualisation

Interactive network visualisation of calls between objects in package can be viewed by clicking here

---

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
lint	success	cc7c87	2021-09-16
pkgdown-gh-pages	success	cc7c87	2021-09-16
R-CMD-check	success	cc7c87	2021-09-16
Test on GHA	success	cc7c87	2021-09-16
test-coverage	success	cc7c87	2021-09-16

---

3b. goodpractice results

R CMD check with rcmdcheck

rcmdcheck found no errors, warnings, or notes

Test coverage with covr

Package coverage: 99.04

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
cff_create	15
clean_str	15

Static code analyses with lintr

lintr found the following 13 potential issues:

message	number of times
Lines should not be more than 80 characters.	13

---

Package Versions

package	version
pkgstats	0.0.0.309
pkgcheck	0.0.1.428

---

Editor-in-Chief Instructions:

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

[noamross]

Thanks, @dieghernan! @emilyriederer will be your editor. FYI, our check-bot failed because the <!--repourl--><!--end-repourl--> tags were absent from your submission template. I've added them back in. We're looking into ways to make that more robust!

[dieghernan]

My bad, thank you!

[emilyriederer]

Hi @dieghernan - so nice to meet you and thank you for submitting this great package!

I did not notice any causes for concern on my first review, and the only enhancement found by the testing suite is perhaps splitting up a few of the long lines of code found by lintr. You can run lintr::lint_package(".") within your R package to reproduce these locally.

I think we are ready to move to the next stage, so I will begin to look for reviewers. We will be in touch soon!

In the meantime on your end, could you please add the rOpenSci badge to your repo? You can use the helper function rodev::use_review_badge(463) to accomplish this

(P.S. Love the hex sticker design 😍 )

---

Editor checks:

• Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package.
• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via a CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly

---

Editor comments

lintr identifies a small number of particularly long lines of code. You can run lintr::lint_package(".") within your R package to reproduce these locally and might want to consider if there are opportunities to shorten or to break across lines for readability.

---

Reviewers:
Due date:

[dieghernan]

Thanks @emilyriederer , nice to meet you as well.

I did my best trying to remove long lines of code, most of them were links to long urls, but I managed to get no lint warning on that, see:

https://github.com/dieghernan/cffr/actions/runs/1244840358

I also added the badge to the README, thanks for the rodev::use_review_badge(463)

(PS: I was looking for images of neural networks and I found that fantastic .png 😄 )

[dieghernan]

@ropensci-review-bot check package

[ropensci-review-bot]

I'm sorry @dieghernan, I'm afraid I can't do that. That's something only editors are allowed to do.

[noamross]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.