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Adding a basic formatter CI and the empty renv (#4)
* Adding a basic formatter CI and the empty renv * adding lintr CI * Installing cyclocomp * Fixing lint errors * linting fixes
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‎.Rbuildignore‎

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^renv$
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^renv\.lock$
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^\.github$

‎.Rprofile‎

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source("renv/activate.R")

‎.github/.gitignore‎

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*.html

‎.github/workflows/format-suggest.yml‎

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# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
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on:
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# Using `pull_request_target` over `pull_request` for elevated `GITHUB_TOKEN`
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# privileges, otherwise we can't set `pull-requests: write` when the pull
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# request comes from a fork, which is our main use case (external contributors).
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#
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# `pull_request_target` runs in the context of the target branch (`main`, usually),
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# rather than in the context of the pull request like `pull_request` does. Due
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# to this, we must explicitly checkout `ref: ${{ github.event.pull_request.head.sha }}`.
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# This is typically frowned upon by GitHub, as it exposes you to potentially running
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# untrusted code in a context where you have elevated privileges, but they explicitly
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# call out the use case of reformatting and committing back / commenting on the PR
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# as a situation that should be safe (because we aren't actually running the untrusted
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# code, we are just treating it as passive data).
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# https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/
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pull_request_target:
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name: format-suggest.yml
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jobs:
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format-suggest:
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name: format-suggest
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runs-on: ubuntu-latest
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permissions:
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# Required to push suggestion comments to the PR
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pull-requests: write
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steps:
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- uses: actions/checkout@v4
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with:
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ref: ${{ github.event.pull_request.head.sha }}
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- name: Install
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uses: posit-dev/setup-air@v1
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- name: Format
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run: air format .
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- name: Suggest
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uses: reviewdog/action-suggester@v1
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with:
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level: error
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fail_level: error
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tool_name: air

‎.github/workflows/lint-project.yml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: lint-project.yml
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permissions: read-all
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jobs:
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lint-project:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install lintr
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run: install.packages("lintr")
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shell: Rscript {0}
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- name: Install cyclocomp
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run: install.packages("cyclocomp")
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shell: Rscript {0}
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- name: Lint root directory
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run: lintr::lint_dir()
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shell: Rscript {0}
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env:
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LINTR_ERROR_ON_LINT: true

‎.lintr‎

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################################################################################
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## File: .lintr ##
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## Project: msm-nida-ctn ##
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## Created Date: 2025-08-28 ##
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## Author: Matthew Carroll ##
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## ----- ##
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## Last Modified: 2025-11-05 ##
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## Modified By: Dimitri Baptiste ##
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## ----- ##
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## Copyright (c) 2025 Syndemics Lab at Boston Medical Center ##
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################################################################################
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linters: all_linters(
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assignment_linter = assignment_linter(operator = c("<-"), allow_trailing = FALSE),
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backport_linter = backport_linter("4.0.0"),
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object_name_linter = object_name_linter(styles = c("snake_case", "lowercase")),
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return_linter = return_linter(return_style = "explicit", allow_implicit_else = FALSE),
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cyclocomp_linter = cyclocomp_linter(complexity_limit = 10L),
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object_usage_linter = object_usage_linter(interpret_glue = TRUE),
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unused_import_linter = unused_import_linter(interpret_glue = TRUE),
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undesirable_function_linter = undesirable_function_linter(
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fun = modify_defaults(
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defaults = default_undesirable_functions,
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source = NULL,
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library = NULL,
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require = NULL)),
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object_usage_linter = NULL, # This doesn't work well with dplyr
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condition_call_linter = NULL,
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condition_message_linter = NULL,
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consecutive_mutate_linter = NULL,

‎R/utils.R‎

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#' @examples
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#' ensure_packages(c("dplyr", "here"))
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ensure_packages <- function(packages) {
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sapply(packages, function(package) {
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if (!(package %in% rownames(installed.packages()))) {
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install.packages(package, repos = "http://cran.us.r-project.org")
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}
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library(package, character.only = TRUE, warn.conflicts = FALSE)
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return(require(package, character.only = TRUE))
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})
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return(vapply(
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packages,
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function(package) {
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if (!(package %in% rownames(installed.packages()))) {
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install.packages(
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package,
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repos = "http://cran.us.r-project.org"
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)
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}
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library(package, character.only = TRUE, warn.conflicts = FALSE)
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return(require(package, character.only = TRUE))
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},
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logical(length(packages))
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))
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}

‎renv.lock‎

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{
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"R": {
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"Version": "4.5.2",
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"Repositories": [
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{
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"Name": "CRAN",
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"URL": "https://cloud.r-project.org"
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}
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]
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},
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"Packages": {
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"renv": {
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"Package": "renv",
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"Version": "1.1.5",
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"Source": "Repository",
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"Type": "Package",
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"Title": "Project Environments",
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"Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@rstudio.com\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
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"Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.",
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"License": "MIT + file LICENSE",
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"URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv",
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"BugReports": "https://github.com/rstudio/renv/issues",
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"Imports": [
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"utils"
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],
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"Suggests": [
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"BiocManager",
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"cli",
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"compiler",
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"covr",
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"cpp11",
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"devtools",
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"generics",
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"gitcreds",
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"jsonlite",
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"jsonvalidate",
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"knitr",
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"miniUI",
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"modules",
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"packrat",
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"pak",
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"R6",
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"remotes",
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"reticulate",
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"rmarkdown",
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"rstudioapi",
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"shiny",
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"testthat",
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"uuid",
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"waldo",
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"yaml",
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"webfakes"
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],
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"Encoding": "UTF-8",
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"RoxygenNote": "7.3.2",
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"VignetteBuilder": "knitr",
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"Config/Needs/website": "tidyverse/tidytemplate",
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"Config/testthat/edition": "3",
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"Config/testthat/parallel": "true",
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"Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes",
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"NeedsCompilation": "no",
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"Author": "Kevin Ushey [aut, cre] (ORCID: <https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (ORCID: <https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
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"Maintainer": "Kevin Ushey <kevin@rstudio.com>",
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"Repository": "CRAN"
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}
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}
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}

‎renv/.gitignore‎

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library/
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local/
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cellar/
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lock/
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python/
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sandbox/
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staging/

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