cancerprof: API Client for extracting data from State Cancer Profiles #637
Comments
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Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type |
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🚀 Editor check started 👋 |
Checks for cancerprof (v0.1.0)git hash: 36706151
Package License: MIT + file LICENSE 1. Package DependenciesDetails 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.
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. baselist (76), c (56), structure (28), body (20), class (12), url (9), options (8), paste0 (8), new.env (5), as.raw (4), date (4), which (2) magrittr%>% (122) cancerprofcreate_request (20), demo_crowding (1), demo_education (1), demo_food (1), demo_income (1), demo_insurance (1), demo_language (1), demo_mobility (1), demo_population (1), demo_poverty (1), demo_svi (1), demo_workforce (1), dput_resp_demo (1), dput_resp_incd (1), dput_resp_mortality (1), dput_resp_risk (1), fips_scp (1), get_area (1), handle_age (1), handle_alcohol (1), handle_cancer (1), handle_crowding (1), handle_datatype (1), handle_diet_exercise (1), handle_education (1), handle_food (1), handle_income (1), handle_insurance (1), handle_mobility (1), handle_non_english (1), handle_population (1), handle_poverty (1), handle_race (1), handle_screening (1), handle_sex (1), handle_smoking (1), handle_stage (1), handle_svi (1), handle_vaccine (1), handle_women_health (1), handle_workforce (1), handle_year (1), incidence_cancer (1), mortality_cancer (1), process_resp (1), risk_alcohol (1), risk_colorectal_screening (1) dplyracross (26), mutate (26), mutate_all (4), all_of (3), na_if (3), filter (2) clicli_abort (55) statssetNames (28) rlangis_na (23), sym (2) graphicsframe (8) httr2request (8) utilsdata (1), read.csv (1) cdlToolsfips (1) stringrstr_pad (1) 2. Statistical PropertiesThis 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:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
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| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 8546148980 | pages build and deployment | success | 13c6cf | 6 | 2024-04-03 |
| 8546127063 | pkgdown | success | 367061 | 17 | 2024-04-03 |
| 8546127064 | R-CMD-check | success | 367061 | 181 | 2024-04-03 |
| 8546127060 | test-coverage | success | 367061 | 19 | 2024-04-03 |
3b. goodpractice results
R CMD check with rcmdcheck
R CMD check generated the following check_fail:
- cyclocomp
Test coverage with covr
Package coverage: 97.93
Cyclocomplexity with cyclocomp
The following functions have cyclocomplexity >= 15:
| function | cyclocomplexity |
|---|---|
| risk_smoking | 106 |
| demo_population | 70 |
| incidence_cancer | 34 |
| mortality_cancer | 29 |
| demo_insurance | 27 |
| demo_poverty | 27 |
| risk_colorectal_screening | 21 |
| risk_women_health | 19 |
| demo_education | 18 |
Static code analyses with lintr
lintr found the following 102 potential issues:
| message | number of times |
|---|---|
| Avoid using sapply, consider vapply instead, that's type safe | 24 |
| Lines should not be more than 80 characters. | 78 |
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3.11 |
| pkgcheck | 0.1.2.21 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
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@ropensci-review-bot assign @ldecicco-USGS as editor |
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Assigned! @ldecicco-USGS is now the editor |
Editor checks:
Editor commentsThere could be more information added to the README, although the bare minimum to meet our criteria is there. In the examples I tried, my first thought was it might be nice to convert some of the text. For instance: x <- demo_income(
area = "usa",
areatype = "state",
income = "median family income",
race = "all races (includes hispanic)"
)
head(x$Rank)
[1] "52 of 52" "51 of 52" "50 of 52" "49 of 52" "48 of 52" "47 of 52"Seems like c(52, 51, 50, etc) would be a more useful output to an R user. You'd probably want/need another column or something to give the user the " of 52". Not mandatory, could be handy though (maybe a simple function to offer users outside of the function? or a simple example within the examples for how to extract the rank number). |
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@ropensci-review-bot seeking reviewers |
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Please add this badge to the README of your package repository: [](https://github.com/ropensci/software-review/issues/637)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 |
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Thank you for the feedback! I will make those changes in the upcoming version of cancerprof. I have added the ropensci badge and created a NEWS.md file. What are the next steps in the review process? |
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I'm asking around to find 2 reviewers. Hopefully that shouldn't take too long! |
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Great, thank you for a speedy response! |
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@ropensci-review-bot assign @jromanowska as reviewer |
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@jromanowska added to the reviewers list. Review due date is 2024-05-20. Thanks @jromanowska 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. |
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@jromanowska: If you haven't done so, please fill this form for us to update our reviewers records. |
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Hi! Just for your information: I'll start with the review soon. There are many free days in May here, in Norway, but I hope I will not need any extension of the review deadline. 🤞 |
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@ldecicco-USGS , I just wanted to notify that {goodpractice} package that is dependency for {pkgcheck} has been archived by CRAN (https://cran.r-project.org/web//packages/goodpractice/index.html) so I couldn't install {pkgcheck} and had to install the GitHub version of {goodpractice} by hand. |
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Hi, I'm having problems installing the package: pak::pak("getwilds/cancerprof")
#> Error: ! error in pak subprocess
#> Caused by error:
#> ! Could not solve package dependencies:
#> * getwilds/cancerprof: ! pkgdepends resolution error for getwilds/cancerprof.
#> Caused by error:
#> ! Bad GitHub credentials, make sure that your GitHub token is valid.
#> Caused by error in `stop(http_error(resp))`:
#> ! Unauthorized (HTTP 401).
devtools::install_github("getwilds/cancerprof")
#> Downloading GitHub repo getwilds/cancerprof@HEAD
#> Installing 3 packages: terra, raster, cdlTools
#> Installing packages into ‘/home/jro049/R/x86_64-pc-linux-gnu-library/4.3’
#> (as ‘lib’ is unspecified)
#> trying URL 'https://cloud.r-project.org/src/contrib/terra_1.7-71.tar.gz'
#> Content type 'application/x-gzip' length 836573 bytes (816 KB)
#> ==================================================
#> downloaded 816 KB
#>
#> trying URL 'https://cloud.r-project.org/src/contrib/raster_3.6-26.tar.gz'
#> Content type 'application/x-gzip' length 576421 bytes (562 KB)
#> ==================================================
#> downloaded 562 KB
#>
#> trying URL 'https://cloud.r-project.org/src/contrib/cdlTools_1.13.tar.gz'
#> Content type 'application/x-gzip' length 43089 bytes (42 KB)
#> ==================================================
#> downloaded 42 KB
#>
#> * installing *source* package ‘terra’ ...
#> ** package ‘terra’ successfully unpacked and MD5 sums checked
#> ** using staged installation
#> configure: CC: gcc
#> configure: CXX: g++ -std=gnu++17
#> checking for gdal-config... no
#> no
#> configure: error: gdal-config not found or not executable.
#> ERROR: configuration failed for package ‘terra’
#> * removing ‘/home/jro049/R/x86_64-pc-linux-gnu-library/4.3/terra’
#> ERROR: dependency ‘terra’ is not available for package ‘raster’
#> * removing ‘/home/jro049/R/x86_64-pc-linux-gnu-library/4.3/raster’
#> ERROR: dependencies ‘raster’, ‘terra’ are not available for package ‘cdlTools’
#> * removing ‘/home/jro049/R/x86_64-pc-linux-gnu-library/4.3/cdlTools’
#>
#> The downloaded source packages are in
#> ‘/tmp/RtmpyrNDzF/downloaded_packages’
#> ── R CMD build ─────────────────────────────────────────────────────────#> ──────────────────────────────────────────────────
#> ✔ checking for file ‘/tmp/RtmpyrNDzF/remotes24d8468ec6bf/getwilds-cancerprof-23dbd98/DESCRIPTION’ ...
#> ─ preparing ‘cancerprof’:
#> ✔ checking DESCRIPTION meta-information
#> ─ checking for LF line-endings in source and make files and shell scripts
#> ─ checking for empty or unneeded directories
#> ─ looking to see if a ‘data/datalist’ file should be added
#> ─ building ‘cancerprof_0.1.0.tar.gz’
#> Warning: invalid uid value replaced by that for user 'nobody'
#>
#> Installing package into ‘/home/jro049/R/x86_64-pc-linux-gnu-library/4.3’
#> (as ‘lib’ is unspecified)
#> ERROR: dependency ‘cdlTools’ is not available for package ‘cancerprof’
#> * removing ‘/home/jro049/R/x86_64-pc-linux-gnu-library/4.3/cancerprof’
#> Warning messages:
#> 1: In i.p(...) : installation of package ‘terra’ had non-zero exit status
#> 2: In i.p(...) : installation of package ‘raster’ had non-zero exit status
#> 3: In i.p(...) :
#> installation of package ‘cdlTools’ had non-zero exit status
#> 4: In i.p(...) :
#> installation of package ‘/tmp/RtmpyrNDzF/file24d821d2b458/cancerprof_0.1.0.tar.gz’ had non-zero exit status
#>
#> Created on 2024-04-30 with reprex v2.1.0 |
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Do you get the same error if you install terra and raster independently? install.packages(c("terra", "raster")) |
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Today I've tried on another computer (also Linux) and the |
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📆 @jromanowska you have 2 days left before the due date for your review (2024-05-20). |
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Hi @realbp! I'm sorry I haven't found a 2nd reviewer yet. I sent a few inquires out and didn't get responses back. I should have sent a 2nd batch out but that task got buried in my to-do list. Apologies for the delay! I've sent a few more requests out and hopefully we can get this review process (re)kicked off! |
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Hi, I'm sorry - I need another week to complete the review. May is horrible with lots of free days here in Norway, and a fantastic summer weather this year, leaving too little time for work! 😅 |
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@ropensci-review-bot assign @ginberg as reviewer |
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@ginberg added to the reviewers list. Review due date is 2024-06-12. Thanks @ginberg 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. |
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Thanks for the patience! Great work with {cancerprof}! 🙌 I'm done with reviewing, please check my comments below. Package Review
DocumentationThe package includes all the following forms of documentation:
Functionality
Estimated hours spent reviewing: 16
Review CommentsOverall, the package is really useful for batch retrieval of data. Are there improvements that could be made to the code style?
Is there code duplication in the package that should be reduced?
Are there user interface improvements that could be made?
Are there performance improvements that could be made?No issues here. Is the documentation clear and sufficient?Installation
(I got this resolved afterwards) Vignettes and function documentation
Does the documentation use the principle of multiple points of entry i.e. takes into account the fact that any piece of documentation may be the first encounter the user has with the package and/or the tool/data it wraps?
Were functions and arguments named to work together to form a common, logical programming API that is easy to read, and autocomplete?Yes - good choice of naming. Although the |
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@jromanowska Thank you so much for your hard work at reviewing cancerprof! I will get to work on implementing improvements based on your feedback. |
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📆 @ginberg you have 2 days left before the due date for your review (2024-06-12). |
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@ropensci-review-bot submit review #637 (comment) time 16 |
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Logged review for jromanowska (hours: 16) |
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Thank you @jromanowska for the thorough review! |
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Just a heads up that I'll be on leave from June 17-July 8 and may or may not be able to get to this issue during that time. |
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I will be on holidays entire July. I can probably read and comment here, but I won't be able to test anything. |
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Well done with creating this package! Package Review
DocumentationThe package includes all the following forms of documentation:
Functionality
Estimated hours spent reviewing: 6
Review Comments
It would be good to fail gracefully with an informative message if a resource is not available (and not give a error). See here for some ideas. You probably need to fix this anyway when you want the package to be on CRAN. |
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@ropensci-review-bot submit review #637 (comment) time 6 |
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Logged review for ginberg (hours: 6) |
ropensci-review-bot
added
4/review(s)-in-awaiting-changes
and removed
3/reviewer(s)-assigned
labels
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@realbp: please post your response with Here's the author guide for response. https://devguide.ropensci.org/authors-guide.html |
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Hi @realbp , checking in to see if you've got any updates to respond to the reviewers. |
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Hi @ldecicco-USGS, I supervised @realbp's work on this package as part of his internship at the Fred Hutch Data Science Lab, which has sadly ended. We loved working with Brian! Would it be possible for me to take reigns of this review? I plan to be the maintainer of this package once we eventually submit it to CRAN. |
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No problem! |
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@seankross checking in to see how things are going. From our end, we're waiting on a response to the reviews. |
Submitting Author Name: Brian Park
Submitting Author Github Handle: @realbp
Repository: https://github.com/getwilds/cancerprof
Version submitted: 0.1.0
Submission type: Standard
Editor: @ldecicco-USGS
Reviewers: @jromanowska, @ginberg
Archive: 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):
cancerprof allows users to retrieve data from State Cancer Profiles for programmable analysis. cancerprof makes accessing the undocumented API from State Cancer Profiles intuitive and easy.
The target audience for cancerprof is anyone who wants to access data from state cancer profiles to conduct programmable analysis without having to navigate the complex nature of its GUI. Specifically, cancer researchers could use cancerprof to conduct reproducable analysis of cancer crossed references with a variety of topics found within the data from state cancer profiles.
Currently there are no other softwares or packages that extracts the publicly available data from State Cancer Profiles.
Cancerprof does not breach any data privacy laws and complies with the ethics policies of ropensci.
#635
pkgcheckitems which your package is unable to pass.Cancerprof passes all pkgcheck items
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Confirm each of the following by checking the box.
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Code of conduct
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