Closed wfrierson closed 1 year ago
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git hash: 0fe1132f
Important: All failing checks above must be addressed prior to proceeding
Package License: MIT + file LICENSE
This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.
The package has: - code in R (100% in 6 files) and - 1 authors - no vignette - no internal data file - 1 imported package - 14 exported functions (median 15 lines of code) - 15 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](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 6| 40.3| | |files_vignettes | 0| 0.0|TRUE | |files_tests | 4| 79.0| | |loc_R | 345| 36.3| | |loc_tests | 186| 53.2| | |num_vignettes | 0| 0.0|TRUE | |n_fns_r | 29| 39.2| | |n_fns_r_exported | 14| 56.3| | |n_fns_r_not_exported | 15| 32.7| | |n_fns_per_file_r | 2| 43.8| | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 17| 52.0| | |loc_per_fn_r_exp | 15| 35.6| | |loc_per_fn_r_not_exp | 22| 66.9| | |rel_whitespace_R | 21| 43.1| | |rel_whitespace_tests | 9| 31.9| | |doclines_per_fn_exp | 15| 6.0| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 11| 34.5| | ---
Click to see the interactive network visualisation of calls between objects in package
goodpractice
and other checks--- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) rcmdcheck found no errors, warnings, or notes #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 90.68 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) No functions have cyclocomplexity >= 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 39 potential issues: message | number of times --- | --- Lines should not be more than 80 characters. | 38 Use <-, not =, for assignment. | 1
|package |version | |:--------|:---------| |pkgstats |0.0.3.94 | |pkgcheck |0.0.2.275 |
Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.
Dear @wfrierson, thank you for your submission following your pre-submission.
Could you address the issues regarding the codemeta.json file, the contributing file, the vignette(s), and the examples. I see that you have continuous integration checks on Travis-CI so this X can be ignored. Please see the packaging guide and feel free to ask any questions if you need help. Thanks, Julia
Dear @wfrierson, Do you have any updates here? If I do not hear back from you in a week I will close this issue (but feel free to reopen). Thanks, Julia
Thanks, Julia. Sorry for the delay! I'm working on these now.
Re: the examples, all the listed functions with a '.' prefix are not exported (and therefore not intended for end users). I added roxygen frameworks for these functions for curious users. The last 'wmm' reference is for the package-level wmm.R file, i.e., it's not a function.
Do I still need examples for these?
Hi @wfrierson, Thanks for the update. Regarding the functions without examples, if you add the Roxygen "@keywords internal" to these functions then this check should be ok for your "." fucntions.
Thanks, Julia
One minor update on @jooolia's comment: the rOpenSci DevGuide recommends using @noRd
instead of @Keywords internal
.
Hello @wfrierson, Do you have any updates on your submission? Do you need any support from our side? Thanks, Julia
Apologies for the delay. I'm updating my package on CRAN to be consistent with the ropensci changes and am waiting for their approval. I'll check on its status since it's been awhile.
On Fri, Jun 3, 2022, 7:28 AM Julia Gustavsen @.***> wrote:
Hello @wfrierson https://github.com/wfrierson, Do you have any updates on your submission? Do you need any support from our side? Thanks, Julia
— Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/522#issuecomment-1146021195, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKYZJLM44WIISXSSJT5XK5DVNII6ZANCNFSM5RZPSZPQ . You are receiving this because you were mentioned.Message ID: @.***>
thanks @wfrierson! let us know when you get some updates.
@jooolia, is it possible for my latest changes to be reviewed before I submit to CRAN? If I submit to CRAN and then realize I missed something for ropensci, the CRAN volunteers will be less than excited to review a 2nd submission within the same month.
My changes to be compliant with ropensci are in the ropensci_updates branch (link).
Hi @wfrierson, I had a quick look and most of the issues appear to be fixed (I don't know why our CI checks are not being picked up, I will ask the other editors). Let me know when your changes will be merged into main and then I will find a handling editor who can then start looking for reviewers. Cheers, Julia
Ok, will do. Thanks!
On Tue, Jun 14, 2022, 11:38 AM Julia Gustavsen @.***> wrote:
Hi @wfrierson https://github.com/wfrierson, I had a quick look and most of the issues appear to be fixed (I don't know why our CI checks are not being picked up, I will ask the other editors). Let me know when your changes will be merged into main and then I will find a handling editor who can then start looking for reviewers. Cheers, Julia
— Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/522#issuecomment-1155588103, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKYZJLIQKPESC4SRZGOFDA3VPDGQ5ANCNFSM5RZPSZPQ . You are receiving this because you were mentioned.Message ID: @.***>
@jooolia, I've merged the feature branch into main. Let me know if there are any questions.
Thanks again!
@ropensci-review-bot check package
Thanks, about to send the query.
:rocket:
Editor check started
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Oops, something went wrong with our automatic package checks. Our developers have been notified and package checks will appear here as soon as we've resolved the issue. Sorry for any inconvenience.
Hi, I am going to ask about what is going on with the bot.
@ropensci-review-bot check package
Thanks, about to send the query.
:rocket:
Editor check started
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Oops, something went wrong with our automatic package checks. Our developers have been notified and package checks will appear here as soon as we've resolved the issue. Sorry for any inconvenience.
Hello, @mpadge will be looking into this later. Cheers, Julia
git hash: d9d4a37a
Important: All failing checks above must be addressed prior to proceeding
Package License: MIT + file LICENSE
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 | 43|
|internal |stats | 1|
|imports |NA | NA|
|suggests |testthat | NA|
|suggests |data.table | NA|
|suggests |knitr | NA|
|suggests |rmarkdown | 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(
list (12), sqrt (4), t (4), sin (3), atan2 (2), cos (2), do.call (2), length (2), outer (2), asin (1), if (1), mode (1), rbind (1), rowSums (1), seq (1), seq_along (1), union (1), vector (1), with (1)
time (1)
base
stats
This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.
The package has: - code in R (100% in 6 files) and - 1 authors - 1 vignette - no internal data file - 1 imported package - 14 exported functions (median 15 lines of code) - 15 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](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 6| 40.3| | |files_vignettes | 2| 85.7| | |files_tests | 4| 79.0| | |loc_R | 345| 36.3| | |loc_vignettes | 62| 12.8| | |loc_tests | 186| 53.2| | |num_vignettes | 1| 64.8| | |n_fns_r | 29| 39.2| | |n_fns_r_exported | 14| 56.3| | |n_fns_r_not_exported | 15| 32.7| | |n_fns_per_file_r | 2| 43.8| | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 17| 52.0| | |loc_per_fn_r_exp | 15| 35.6| | |loc_per_fn_r_not_exp | 22| 66.9| | |rel_whitespace_R | 21| 43.1| | |rel_whitespace_vignettes | 85| 40.8| | |rel_whitespace_tests | 9| 31.9| | |doclines_per_fn_exp | 15| 6.0| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 11| 34.5| | ---
Click to see the interactive network visualisation of calls between objects in package
goodpractice
and other checks--- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) rcmdcheck found no errors, warnings, or notes #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 90.68 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) No functions have cyclocomplexity >= 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 39 potential issues: message | number of times --- | --- Lines should not be more than 80 characters. | 38 Use <-, not =, for assignment. | 1
|package |version | |:--------|:--------| |pkgstats |0.0.4.89 | |pkgcheck |0.0.3.62 |
Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.
@jooolia Our automated system only checks for continuous integration on GitHub. This package uses travis for CI, so that failing check may be ignored. (We officially advise using alternatives to travis, but that advice itself may need updating?)
Edit: rOpenSci's updated statement on travis is here.
@jooolia, I just realized that I didn't update the NAMESPACE to reflect the @noRd changes. This is resolved in the latest commit. My apologies for that!
I see that ropensci-review-bot has noted the renv
library. wmm
is pure R, but I use renv
for the packages used for unit tests. When installed from CRAN, no other packages are installed (noted in the DESCRIPTION file). Do I really need to remove renv
?
@wfrierson No, you don't need to remove renv
, just deactivate it. That only changes the local .Rprofile
file by commenting out the source
line. Alternatively, just remove that file from the repo and keep a local version only.
Thanks, @mpadge!
@jooolia, I've deactivated renv
, which should be the last requested change. Are there any other changes needed?
Hi @wfrierson, To me it is looking good. I will look for a handling editor who can then look for reviewers. Thanks!
@mpadge do you know why the internal functions are coming up as not having examples? This is why I suggested using "@keyword internal" because then for me the check was ok with pkgcheck(https://github.com/ropensci/software-review/issues/522#issuecomment-1114566751). Do you see the issue why it is not working with “@noRd“?
@jooolia I've no idea, but nor is it repeatable: The bot checks on current system work fine and do not generate those failing "no examples" checks. Sorry for temporary inconvenience there.
@ropensci-review-bot assign @maelle as editor
Assigned! @maelle is now the editor
@ropensci-review-bot check package
Thanks, about to send the query.
:rocket:
Editor check started
:wave:
git hash: 6f5ecb53
Important: All failing checks above must be addressed prior to proceeding
Package License: MIT + file LICENSE
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 | 43|
|internal |stats | 1|
|imports |NA | NA|
|suggests |testthat | NA|
|suggests |data.table | NA|
|suggests |knitr | NA|
|suggests |rmarkdown | 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(
list (12), sqrt (4), t (4), sin (3), atan2 (2), cos (2), do.call (2), length (2), outer (2), asin (1), if (1), mode (1), rbind (1), rowSums (1), seq (1), seq_along (1), union (1), vector (1), with (1)
time (1)
base
stats
This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.
The package has: - code in R (100% in 6 files) and - 1 authors - 1 vignette - no internal data file - 1 imported package - 1 exported function (median 23 lines of code) - 28 non-exported functions in R (median 16 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](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 6| 40.3| | |files_vignettes | 2| 85.7| | |files_tests | 4| 79.0| | |loc_R | 345| 36.3| | |loc_vignettes | 62| 12.8| | |loc_tests | 186| 53.2| | |num_vignettes | 1| 64.8| | |n_fns_r | 29| 39.2| | |n_fns_r_exported | 1| 0.0|TRUE | |n_fns_r_not_exported | 28| 50.8| | |n_fns_per_file_r | 2| 43.8| | |num_params_per_fn | 5| 69.6| | |loc_per_fn_r | 17| 52.0| | |loc_per_fn_r_exp | 23| 52.6| | |loc_per_fn_r_not_exp | 16| 52.7| | |rel_whitespace_R | 21| 43.1| | |rel_whitespace_vignettes | 85| 40.8| | |rel_whitespace_tests | 9| 31.9| | |doclines_per_fn_exp | 95| 89.6| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 11| 34.5| | ---
Click to see the interactive network visualisation of calls between objects in package
goodpractice
and other checks--- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) rcmdcheck found no errors, warnings, or notes #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 90.68 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) No functions have cyclocomplexity >= 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 39 potential issues: message | number of times --- | --- Lines should not be more than 80 characters. | 38 Use <-, not =, for assignment. | 1
|package |version | |:--------|:--------| |pkgstats |0.1.1.1 | |pkgcheck |0.0.3.74 |
Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.
:wave: @wfrierson!
Happy to help with technical problems!
Thanks for the feedback, @maelle. I'm working on these changes and will get back to you.
:wave: @wfrierson, any update? :smile_cat:
Hello! I'm troubleshooting GitHub Actions for CI. I expect to make more progress on this over the next few days. Sorry for the delay.
On Tue, Jul 19, 2022, 1:26 AM Maëlle Salmon @.***> wrote:
👋 @wfrierson https://github.com/wfrierson, any update? 😸
— Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/522#issuecomment-1188753693, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKYZJLPOULOWEWMON6OQXF3VUZRCXANCNFSM5RZPSZPQ . You are receiving this because you were mentioned.Message ID: @.***>
Ok, feel free to ask any question if needed!
@maelle, I'm stumped on getting GH actions working. I've read tutorials and tried the usethis
shortcuts. However, I continue to run into issue after issue. The script check_and_testthat.yml
fails due to something about making the vignette into a pdf. The script test-coverage.yaml
says it passes, but says "Request failed... Could not find a repository, try using repo upload token". I have researched these topics but with no progress.
I just need GH actions to do a few simple things:
check()
testthat
scriptsIf you have any recommendations, I'd appreciate any help (link). Thanks!
:wave: @wfrierson!
How did you create the check_and_testthat.yml
file? I'd suggest deleting it, then updating usethis to its latest version, and then running usethis::use_github_action_check_standard()
(that will create the R CMD check workflow). Then commit and push.
Regarding the test coverage error, do you have a codecov account linked to your GitHub account?
@ropensci-review-bot assign @adamhsparks as editor
Assigned! @adamhsparks is now the editor
@wfrierson change of editor for the next three weeks (thanks a ton @adamhsparks!) :smile_cat:
Thanks for your help, @maelle! Sorry for being slow here. Thanks for your recommendation re: GH actions. I got the R CMD check workflow to work via usethis
. I'm not troubleshooting running testthat
unit tests.
@adamhsparks, do you happen to know of any example GH action workflows that demonstrate how to run a testthat
sequence of unit tests?
Hi @wfrierson, is this what you're after?
https://github.com/adamhsparks/wmm/runs/7644467088?check_suite_focus=true
I set this up using usethis as below.
# set up regular package checks and tests
usethis::use_github_action_check_standard()
# set up code coverage
usethis::use_coverage("codecov")
# automate the code coverage
usethis::use_github_action("test-coverage")
@ropensci-review-bot assign @maelle as editor
Date accepted: 2023-10-30
Submitting Author Name: Will Frierson Submitting Author Github Handle: !--author1-->@wfrierson<!--end-author1-- Repository: https://github.com/wfrierson/wmm Version submitted: 1.1.1 Submission type: Standard Editor: !--editor-->@maelle<!--end-editor-- Reviewers: @drmowinckels, @HaoZeke
Due date for @drmowinckels: 2022-11-03Archive: TBD Version accepted: TBD Language: en
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.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences): The
wmm
package retrieves magnetic field components given a location and time. I'm including "data munging" as recommended by @noamross (link).Who is the target audience and what are scientific applications of this package? Physicists, geophysicists, & navigators could find the magnetic field components useful. Geo/physics students could find the construction of the magnetic field components helpful to their understanding.
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 my knowledge, the most similar package is
oce
which has the functionmagnetic.declination
that uses NOAA's WMM coefficients. However, theoce
package does not provide magnetic field components, which are included inwmm
.(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. Pre-submission inquiry: https://github.com/ropensci/software-review/issues/461
Explain reasons for any
pkgcheck
items which your package is unable to pass. As noted in the pre-submission inquiry, I could not getpkgcheck
to work. However, I read the guidelines associated withpkgcheck
and I thinkwmm
complies.Technical checks
Confirm each of the following by checking the box.
This package:
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