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mregions2: Access Data from Marineregions.org: The Marine Regions Gazetteer and the Marine Regions Data Products
Submitting Author Name: Salvador Fernández Bejarano Submitting Author Github Handle: @salvafern Other Package Authors Github handles: (comma separated, delete if none) @lottepohl Repository: https://github.com/lifewatch/mregions2 Version submitted: Submission type: Standard Editor: @jooolia Reviewers: @Kattuvan, @sheilasaia
Due date for @Kattuvan: 2023-06-20Due date for @sheilasaia: 2023-06-21 Archive: TBD Version accepted: TBD Language: en
- Paste the full DESCRIPTION file inside a code block below:
Package: mregions2
Type: Package
Title: Access Data from Marineregions.org: The Marine Regions Gazetteer and the Marine Regions Data Products
Version: 1.0.0
Authors@R: c(
person(given = "Salvador", family = "Fernandez-Bejarano", role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-0535-7677", github = "salvafern")),
person(given = "Lotte",family = "Pohl", role = "aut",
email = "[email protected]",
comment = c(ORCID = "0000-0002-7607-7018", github = "whaleshark99")),
person("LifeWatch Belgium", role = "fnd", comment = "https://lifewatch.be")
)
Maintainer: Salvador Fernandez-Bejarano <[email protected]>
Description: Explore and retrieve marine geo-spatial data from the Marine Regions Gazetteer and the Marine Regions Data Products, including the Maritime Boundaries.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Config/testthat/edition: 3
Imports:
checkmate,
glue,
httr2,
magrittr,
sf,
utils,
rdflib,
ISOcodes,
memoise,
cli,
dplyr,
xml2,
wrapr,
methods,
curl,
digest
RoxygenNote: 7.2.0
URL: https://github.com/lifewatch/mregions2,
https://lifewatch.github.io/mregions2/
BugReports: https://github.com/lifewatch/mregions2/issues
Suggests:
ows4R (>= 0.3),
httptest2,
jsonlite,
knitr,
leaflet,
leaflet.extras2,
mapview,
mregions,
rmarkdown,
testthat,
wk,
purrr,
withr
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Depends:
R (>= 2.10)
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.):
- [x] 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
- [x] geospatial data
- [ ] text analysis
- Explain how and why the package falls under these categories (briefly, 1-2 sentences):
This package reads the Marine Regions Gazetteer and the Marine Regions Data Products via a REST API and OGC web services respectively. The data is mostly geospatial as it contains locations of marine places in the world.
- Who is the target audience and what are scientific applications of this package?
The main purpose of Marine Regions is to serve as the geographical backbone of biodiversity databases such as WoRMS or EurOBIS, hence the main user will be scientists that want to geo-reference their research. But it can also be useful for industry, policy and law makers.
- Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
There is already a package to read Marine Regions. The need for this second package is explained in one of the package's articles: Why mregions2? . It was also discussed beforehand that a new package was the best approach: https://github.com/ropensci/mregions/pull/62 (Mostly to not break compatibility)
- (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
In general I think this does not apply. The only data being collected from users is the user-agent in all HTTP requests. This gets the environment variable HTTPUserAgent via getOption() in mr_user_agent
On the other hand, Marine Regions has sensitive data products such as the maritime boundaries. It is stated clearly on our disclaimer that the data has no legal value whatsoever.
- 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
pkgcheckitems which your package is unable to pass.
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?
-
[ ] 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
- [x] I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.
Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.
Checks for mregions2 (v1.0.0)
git hash: 9ed0de6d
- :heavy_check_mark: Package name is available
- :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 91.5%.
- :heavy_check_mark: R CMD check found no errors.
- :heavy_check_mark: R CMD check found no warnings.
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 | 176 |
| internal | mregions2 | 121 |
| internal | stats | 24 |
| imports | magrittr | 200 |
| imports | httr2 | 51 |
| imports | checkmate | 45 |
| imports | methods | 19 |
| imports | glue | 18 |
| imports | sf | 14 |
| imports | cli | 7 |
| imports | memoise | 5 |
| imports | utils | 3 |
| imports | dplyr | 3 |
| imports | ISOcodes | 2 |
| imports | digest | 2 |
| imports | rdflib | 1 |
| imports | xml2 | 1 |
| imports | wrapr | NA |
| imports | curl | NA |
| suggests | leaflet | 10 |
| suggests | ows4R | NA |
| suggests | httptest2 | NA |
| suggests | jsonlite | NA |
| suggests | knitr | NA |
| suggests | leaflet.extras2 | NA |
| suggests | mapview | NA |
| suggests | mregions | NA |
| suggests | rmarkdown | NA |
| suggests | testthat | NA |
| suggests | wk | NA |
| suggests | purrr | NA |
| suggests | withr | 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.
magrittr
%>% (200)
base
c (28), url (11), source (9), tolower (9), for (8), list (8), names (8), subset (8), all (7), as.character (7), unique (7), file.path (5), options (5), paste0 (5), data.frame (4), format (4), length (4), seq_along (4), gsub (3), if (3), version (3), class (2), dim (2), is.null (2), lapply (2), nrow (2), tempdir (2), as.integer (1), by (1), difftime (1), file.info (1), getOption (1), ifelse (1), is.na (1), readLines (1), rm (1), sort (1), substitute (1), Sys.getenv (1), unlist (1), with (1)
mregions2
mrp_view (14), is_error (11), marineregions.org (9), base_map (3), gaz_records_by_name_at (3), gaz_rest_sources (3), get_records_by_lat_long_at (3), get_records_by_type_at (3), get_source_at (3), gaz_rest_geometries (2), gaz_rest_record_by_mrgid (2), gaz_rest_records_by_lat_long (2), gaz_rest_records_by_names (2), gaz_rest_source_by_sourceid (2), gaz_rest_types (2), gaz_search.sfg (2), add_labels (1), assert_deps (1), assert_internet (1), assert_mrgid_exists (1), assert_only_one_filter (1), assert_placetype (1), assert_service (1), assert_typeid (1), c_rdf (1), cache_max_time (1), check_if_missing (1), check_server_warning (1), gaz_add_geometry (1), gaz_geometry (1), gaz_geometry.mr_df (1), gaz_geometry.numeric (1), gaz_relations (1), gaz_relations.mr_df (1), gaz_relations.numeric (1), gaz_rest_geometry (1), gaz_rest_names_by_mrgid (1), gaz_rest_records_by_name (1), gaz_rest_records_by_source (1), gaz_rest_records_by_type (1), gaz_rest_relations_by_mrgid (1), gaz_rest_wmses (1), gaz_search (1), gaz_search_by_source (1), gaz_search_by_source.character (1), gaz_search_by_source.numeric (1), gaz_search_by_type (1), gaz_search_by_type.character (1), gaz_search_by_type.numeric (1), gaz_search.character (1), gaz_search.numeric (1), gaz_search.sf (1), gaz_search.sfc (1), geom_perform (1), is_internet_down (1), is_test (1), mr_memoise (1), mrp_get (1), mrp_get_sanity_check (1), mrp_view_cds (1), mrp_view_eca_reg13_nox (1), mrp_view_eca_reg14_sox_pm (1), mrp_view_ecoregions (1), mrp_view_ecs (1), mrp_view_ecs_boundaries (1), mrp_view_eez (1), mrp_view_eez_12nm (1), mrp_view_eez_24nm (1), mrp_view_eez_archipelagic_waters (1), mrp_view_eez_boundaries (1), mrp_view_eez_iho (1)
httr2
req_headers (12), req_error (11), resp_check_status (8), resp_status (5), req_url_query (4), request (3), url_parse (3), url_build (2), resp_body_string (1), resp_is_error (1), resp_status_desc (1)
checkmate
assert_character (15), assert_integerish (15), assert_int (4), assert_logical (4), assert_numeric (3), assert_data_frame (2), assert_double (2)
stats
offset (18), filter (5), df (1)
methods
coerce (18), is (1)
glue
glue (18)
sf
st_read (3), st_as_sfc (2), st_bbox (2), st_crs (2), st_point (2), st_sfc (2), st_coordinates (1)
leaflet
tileOptions (3), leafletCRS (2), leafletOptions (2), addTiles (1), leaflet (1), WMSTileOptions (1)
cli
cli_abort (7)
memoise
memoise (5)
dplyr
right_join (2), bind_rows (1)
utils
unzip (3)
digest
digest (2)
ISOcodes
ISO_639_2$Alpha_2 (1), ISO_639_2$Name (1)
rdflib
rdf_serialize (1)
xml2
xml_attr (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 12 files) and
- 2 authors
- 3 vignettes
- 1 internal data file
- 16 imported packages
- 59 exported functions (median 3 lines of code)
- 123 non-exported functions in R (median 6 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 | 12 | 65.5 | |
| files_vignettes | 3 | 92.4 | |
| files_tests | 43 | 99.0 | |
| loc_R | 1104 | 70.7 | |
| loc_vignettes | 391 | 71.7 | |
| loc_tests | 1807 | 93.2 | |
| num_vignettes | 3 | 94.2 | |
| data_size_total | 7328 | 69.2 | |
| data_size_median | 7328 | 77.0 | |
| n_fns_r | 182 | 88.4 | |
| n_fns_r_exported | 59 | 90.2 | |
| n_fns_r_not_exported | 123 | 87.4 | |
| n_fns_per_file_r | 10 | 87.7 | |
| num_params_per_fn | 2 | 11.9 | |
| loc_per_fn_r | 5 | 8.1 | |
| loc_per_fn_r_exp | 3 | 1.5 | TRUE |
| loc_per_fn_r_not_exp | 6 | 13.8 | |
| rel_whitespace_R | 35 | 85.0 | |
| rel_whitespace_vignettes | 55 | 86.2 | |
| rel_whitespace_tests | 12 | 86.1 | |
| doclines_per_fn_exp | 55 | 68.4 | |
| doclines_per_fn_not_exp | 0 | 0.0 | TRUE |
| fn_call_network_size | 100 | 79.2 |
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 |
|---|---|---|---|---|---|
| 4809625294 | pages build and deployment | success | c80782 | 33 | 2023-04-26 |
| 4807668829 | pkgcheck | success | 9ed0de | 82 | 2023-04-26 |
| 4809552258 | pkgdown | success | 9ed0de | 49 | 2023-04-26 |
| 4807666863 | R-CMD-check | success | 9ed0de | 31 | 2023-04-26 |
| 4807668826 | R-CMD-check-schedule | success | 9ed0de | 122 | 2023-04-26 |
| 4807666847 | test-coverage | success | 9ed0de | 30 | 2023-04-26 |
3b. goodpractice results
R CMD check with rcmdcheck
R CMD check generated the following note:
- checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string
R CMD check generated the following check_fail:
- rcmdcheck_non_ascii_characters_in_data
Test coverage with covr
Package coverage: 91.54
Cyclocomplexity with cyclocomp
The following functions have cyclocomplexity >= 15:
| function | cyclocomplexity |
|---|---|
| gaz_rest_records_by_name | 19 |
| gaz_add_geometry | 15 |
Static code analyses with lintr
lintr found the following 403 potential issues:
| message | number of times |
|---|---|
| Avoid library() and require() calls in packages | 11 |
| Lines should not be more than 80 characters. | 392 |
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3.4 |
| pkgcheck | 0.1.1.23 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
Thanks @salvafern for this submission and for pointing to https://github.com/ropensci/mregions/pull/62.
How can we leave a record that the maintainer of mregions is OK with the decision of submitting mregions2? Maybe you can point me to an GH-issue comment?
Hi @maurolepore, thanks for checking out! 🚀
I am actually the current maintainer of mregions (https://github.com/ropensci/mregions/commit/e5fb45be93a957e4ccc51158bb900f72dbcd08a1). Before me were @LennertSchepers and @sckott (https://github.com/ropensci/mregions/commit/dd7b6e44aef74808f3f0f75a09d0568356ce632d).
Since we had this public conversation on https://github.com/ropensci/mregions/pull/62, and also got the idea of a new package from @maelle (see https://github.com/ropensci/mregions/pull/62#issuecomment-1061969979), I think we are all on the same page about submitting mregions2. But if there is any objection from Lennert or Scott I'm happy to discuss of course 😃
No objection from me, @salvafern is in our team so we discussed the whole process in detail.
Worth noting if you need written approval: we are also the Marine Regions data system developers/maintainers/owners (see e.g. https://marineregions.org/editors.php)
Thanks @salvafern and everyone else for your support. I'll stat searching for a handling editor.
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] 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?
- Yes httptest2
-
[ ] Contributing information: Is the documentation for contribution clear enough e.g. tokens for tests, playgrounds?
- .github/CONTRIBUTING.md exists, but only gives detail to email one of the authors and to abide by the Code of Conduct rules. I think this could be improved with resources contained here: https://devguide.ropensci.org/collaboration.html?q=contribu#contributing-guide
-
[X] License: The package has a CRAN or OSI accepted license.
-
[X] 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? Github action checks are kept open as issues, one for each branch.
Editor comments
Dear @salvafern and @whaleshark99,
Thanks for your submission. Overall the package is in great shape. The only thing that I would note would that it would be even better with more information on how to contribute to the package. Feel free to let me know if there is a reason that additional info should not be added. I will start looking for reviewers.
Cheers, Julia
Please add this badge to the README of your package repository:
[](https://github.com/ropensci/software-review/issues/590)
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
@jooolia I accept your invitation to review it. This is my first attempt to review a package. Do you have a Test Case to look for bugs. Do I have to get a data frame to test all those 30 functions/methods
@jooolia I found the guidelines https://devguide.ropensci.org/reviewerguide.html I am sorry for my earlier mail
@Kattuvan added to the reviewers list. Review due date is 2023-06-20. Thanks @Kattuvan 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.
@sheilasaia added to the reviewers list. Review due date is 2023-06-21. Thanks @sheilasaia 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.
Thanks @sheilasaia for agreeing to review. Please feel free to reach out if you have any questions. Thanks, Julia
Hi Julia, Please find below the results I obtained using the 'pkgcheck' on 'mregions2'. Are you expecting me to use the package against the data for further check. This is my first review of any package. I appreciate your guidance. Thanks Murali.
summary(x)
── mregions2 1.0.0 ──────────────────────────────────────────────────────────────
✔ 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 no continuous integration checks. ✔ Package coverage is 91.5%. ✖ R CMD check found 1 error. ✖ R CMD check found 1 warning.
ℹ Current status: ✖ This package is not ready to be submitted.
print(x)
── mregions2 1.0.0 ──────────────────────────────────────────────────────────────
✔ 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 no continuous integration checks. ✔ Package coverage is 91.5%. ✖ R CMD check found 1 error. ✖ R CMD check found 1 warning.
ℹ Current status: ✖ This package is not ready to be submitted.
── git ──
• HEAD: 9ed0de6d • Default branch: main • Number of commits: 134 • First commit: 27-04-2022 • Number of authors: 3
── Package Structure ──
ℹ Package uses the following languages: • : %
ℹ Package has • 2 authors. • 3 vignettes. • 1 internal data file. • 16 imported packages. • 59 exported functions (median 3 lines of code). • 123 non-exported functions (median 6 lines of code). • 2 parameters per function (median).
── Package statistics ──
measure value percentile noteworthy
1 files_R 0.0 0.0 TRUE
4 files_vignettes 0.0 0.0 TRUE
5 files_tests 0.0 0.0 TRUE
6 num_vignettes 3.0 94.2
7 data_size_total 7328.0 69.2
8 data_size_median 7328.0 77.0
9 n_fns_r 182.0 88.4
10 n_fns_r_exported 59.0 90.2
11 n_fns_r_not_exported 123.0 87.4
12 n_fns_per_file_r 10.2 87.7
13 num_params_per_fn 2.0 11.9
14 loc_per_fn_r 5.0 8.1
15 loc_per_fn_r_exp 3.0 1.5 TRUE
16 loc_per_fn_r_not_exp 6.0 13.8
17 doclines_per_fn_exp 55.0 68.4
18 doclines_per_fn_not_exp 0.0 0.0 TRUE
19 fn_call_network_size 100.0 79.2
ℹ Package network diagram is at [C:/Users/Murali/AppData/Local/Cache/R/pkgcheck/static/mregions2_pkgstats9ed0de6d.html].
── goodpractice ──
── GP mregions2 ─────────────────────────────────────────────────────────────────
It is good practice to
✖ write unit tests for all functions, and all package code in general. 91% of code lines are covered by test cases.
R/00_gaz_geom.R:54:NA
R/00_gaz_geom.R:338:NA
R/00_gaz_geom.R:339:NA
R/00_gaz_geom.R:340:NA
R/00_gaz_geom.R:341:NA
... and 71 more lines
✖ avoid long code lines, it is bad for readability. Also, many people prefer editor windows that are about 80 characters wide. Try make your lines shorter than 80 characters
data-raw\mrp_list.R:20:81
R\00_gaz_geom.R:6:81
R\00_gaz_geom.R:9:81
R\00_gaz_geom.R:10:81
R\00_gaz_geom.R:13:81
... and 387 more lines
✖ fix this R CMD check NOTE: Note: found 1 marked UTF-8 string ✖ fix this R CMD check WARNING: LaTeX errors when creating PDF version. This typically indicates Rd problems. ───────────────────────────────────────────────────────────────────────────────── ── Package Versions ──
pkgstats: 0.1.3.4 pkgcheck: 0.1.1.24
results_of_x <- print(x)
── mregions2 1.0.0 ──────────────────────────────────────────────────────────────
✔ 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 no continuous integration checks. ✔ Package coverage is 91.5%. ✖ R CMD check found 1 error. ✖ R CMD check found 1 warning.
ℹ Current status: ✖ This package is not ready to be submitted.
── git ──
• HEAD: 9ed0de6d • Default branch: main • Number of commits: 134 • First commit: 27-04-2022 • Number of authors: 3
── Package Structure ──
ℹ Package uses the following languages: • : %
ℹ Package has • 2 authors. • 3 vignettes. • 1 internal data file. • 16 imported packages. • 59 exported functions (median 3 lines of code). • 123 non-exported functions (median 6 lines of code). • 2 parameters per function (median).
── Package statistics ──
measure value percentile noteworthy
1 files_R 0.0 0.0 TRUE
4 files_vignettes 0.0 0.0 TRUE
5 files_tests 0.0 0.0 TRUE
6 num_vignettes 3.0 94.2
7 data_size_total 7328.0 69.2
8 data_size_median 7328.0 77.0
9 n_fns_r 182.0 88.4
10 n_fns_r_exported 59.0 90.2
11 n_fns_r_not_exported 123.0 87.4
12 n_fns_per_file_r 10.2 87.7
13 num_params_per_fn 2.0 11.9
14 loc_per_fn_r 5.0 8.1
15 loc_per_fn_r_exp 3.0 1.5 TRUE
16 loc_per_fn_r_not_exp 6.0 13.8
17 doclines_per_fn_exp 55.0 68.4
18 doclines_per_fn_not_exp 0.0 0.0 TRUE
19 fn_call_network_size 100.0 79.2
ℹ Package network diagram is at [C:/Users/Murali/AppData/Local/Cache/R/pkgcheck/static/mregions2_pkgstats9ed0de6d.html].
── goodpractice ──
── GP mregions2 ─────────────────────────────────────────────────────────────────
It is good practice to
✖ write unit tests for all functions, and all package code in general. 91% of code lines are covered by test cases.
R/00_gaz_geom.R:54:NA
R/00_gaz_geom.R:338:NA
R/00_gaz_geom.R:339:NA
R/00_gaz_geom.R:340:NA
R/00_gaz_geom.R:341:NA
... and 71 more lines
✖ avoid long code lines, it is bad for readability. Also, many people prefer editor windows that are about 80 characters wide. Try make your lines shorter than 80 characters
data-raw\mrp_list.R:20:81
R\00_gaz_geom.R:6:81
R\00_gaz_geom.R:9:81
R\00_gaz_geom.R:10:81
R\00_gaz_geom.R:13:81
... and 387 more lines
✖ fix this R CMD check NOTE: Note: found 1 marked UTF-8 string ✖ fix this R CMD check WARNING: LaTeX errors when creating PDF version. This typically indicates Rd problems. ───────────────────────────────────────────────────────────────────────────────── ── Package Versions ──
pkgstats: 0.1.3.4 pkgcheck: 0.1.1.24 On Tuesday, May 30, 2023 at 11:37:37 p.m. EDT, Julia Gustavsen @.***> wrote:
Thanks @sheilasaia for agreeing to review. Please feel free to reach out if you have any questions. Thanks, Julia
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
Dear @Kattuvan , Great that you ran {pkgcheck}, will you follow up with the review template ? Here there are specific things to check and an opportunity to provide your comments on the package to the authors (related to the code, the usability and functionality). Thanks, Julia
Hi Julia, Please find attached duly filled review template herewith. Thank you. Murali On Monday, June 5, 2023 at 02:16:43 a.m. EDT, Julia Gustavsen @.***> wrote:
Dear @Kattuvan , Great that you ran {pkgcheck}, will you follow up with the review template ? Here there are specific things to check and an opportunity to provide your comments on the package to the authors (related to the code, the usability and functionality). Thanks, Julia
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
Hi @Kattuvan, thanks for the doing the review. I think you may have attached something via email, but this did not appear on Github. Could you paste your review directly in the issue by logging into Github? Thanks, Julia
Package Review
Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide
- Briefly describe any working relationship you have (had) with the package authors.
- ☒ As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).
Documentation
The package includes all the following forms of documentation:
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☒ A statement of need: clearly stating problems the software is designed to solve and its target audience in README
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☒ Installation instructions: for the development version of package and any non-standard dependencies in README
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dependencies ‘sf’; ‘dplyr’; ‘magritter’ are referenced elsewhere. https://lifewatch.github.io/mregions2/articles/mregions2.html/
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☒ Vignette(s): demonstrating major functionality that runs successfully locally
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Package has at least one HTML vignette
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But Vignette is available only through 'READ.md'
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☐ Function Documentation: for all exported functions
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☒ Examples: (that run successfully locally) for all exported functions
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Examples don’t run in place.
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All functions have examples
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☒ Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with
URL,BugReportsandMaintainer(which may be autogenerated viaAuthors@R). -
availble
Functionality
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☒ Installation: Installation succeeds as documented.
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Removed ‘sf’; ‘dplyr’; ‘magritter’ from local system to test installation of ‘mregion2’
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I get error message “Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘magrittr’”
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So, I installed ‘magrittr’ before attempting again ‘mregion2’
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‘mregions2’ installs dependencies ‘sf’ and ‘dplyr’
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☐ Functionality: Any functional claims of the software been confirmed.
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☐ Performance: Any performance claims of the software been confirmed.
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☒ Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
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It is good practice to write unit tests for all functions, and all package code in general. 91% of code lines are covered by test cases.
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avoid long code lines, it is bad for readability. Also, many people prefer editor windows that are about 80 characters wide. Try make your lines shorter than 80 characters
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☒ Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.
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This package is not ready to be submitted.
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Package has no continuous integration checks.
Estimated hours spent reviewing: 16 Hours
- ☒ Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer (“rev” role) in the package DESCRIPTION file.