diff --git a/.Rprofile b/.Rprofile deleted file mode 100644 index 81b960f5..00000000 --- a/.Rprofile +++ /dev/null @@ -1 +0,0 @@ -source("renv/activate.R") diff --git a/R/checks.R b/R/checks.R index bf48ffbe..46e96d48 100644 --- a/R/checks.R +++ b/R/checks.R @@ -745,7 +745,7 @@ check_fields_are_checkboxes <- function(metadata_tbl, call = caller_env()) { #' @title Check equal distinct values between two columns #' #' @description -#' Takes a dataframe and two columns and checks if [n_distinct()] of the second +#' Takes a dataframe and two columns and checks if `n_distinct` of the second #' column is all unique based on grouping of the first column. #' #' @param data a dataframe @@ -757,8 +757,8 @@ check_fields_are_checkboxes <- function(metadata_tbl, call = caller_env()) { check_equal_col_summaries <- function(data, col1, col2, call = caller_env()) { summary <- data %>% summarise( - .by = {{ col1 }}, - n = n_distinct({{ col2 }}) + .by = col1, + n = n_distinct(col2) ) total_n <- summary %>% diff --git a/R/combine_checkboxes.R b/R/combine_checkboxes.R index 9a147ece..3de2ab34 100644 --- a/R/combine_checkboxes.R +++ b/R/combine_checkboxes.R @@ -19,8 +19,7 @@ #' #' @param supertbl A supertibble generated by [read_redcap()]. Required. #' @param tbl The `redcap_form_name` of the data tibble to extract. Required. -#' @param cols <[`tidy-select`][tidyr_tidy_select]> Checkbox columns to combine to -#' single column. Required. +#' @param cols Checkbox columns to combine to single column. Required. #' @param names_prefix String added to the start of every variable name. #' @param names_sep String to separate new column names from `names_prefix`. #' @param names_glue Instead of `names_sep` and `names_prefix`, you can supply @@ -192,15 +191,18 @@ get_metadata_spec <- function(metadata_tbl, if (!is.null(names_glue)) { # Similar to pivot_*, use of `names_glue` overrides use of names_prefix/sep glue_env <- out %>% - select(.data$.value) %>% - mutate(.new_value = as.character(glue::glue_data(., names_glue))) %>% # nolint: object_usage_linter + select(.data$.value) + + glue_env$.new_value <- as.character(glue::glue_data(glue_env, names_glue)) + + glue_env <- glue_env %>% select(.data$.new_value) out <- cbind(out, glue_env) } else { out <- out %>% mutate( - .new_value = case_when(names_prefix != "" ~ paste(names_prefix, .value, sep = names_sep), + .new_value = case_when(names_prefix != "" ~ paste(names_prefix, .data$.value, sep = names_sep), .default = paste(names_prefix, .data$.value, sep = "") ) ) @@ -208,7 +210,7 @@ get_metadata_spec <- function(metadata_tbl, # Check that for each unique value of .value there is one unique value of .new_value # May be removed in the future - check_equal_col_summaries(out, .value, .new_value) # nolint: object_usage_linter + check_equal_col_summaries(out, ".value", ".new_value") # nolint: object_usage_linter # Make sure selection is checkbox metadata field type check_fields_are_checkboxes(out) @@ -257,11 +259,11 @@ replace_true <- function(col, col_name, metadata, raw_or_label) { #' based on the overall data tibble cross referenced with a nested section of the #' metadata tibble. #' -#' [case_when()] logic helps determine whether the value is a coalesced singular +#' `case_when` logic helps determine whether the value is a coalesced singular #' value or a user-specified one via `multi_value_label` or `values_fill`. #' #' @details -#' This function is used in conjunction with [pmap()]. +#' This function is used in conjunction with `pmap()`. #' #' @keywords internal #' diff --git a/R/read_redcap.R b/R/read_redcap.R index af098fc7..6bcaf067 100644 --- a/R/read_redcap.R +++ b/R/read_redcap.R @@ -260,17 +260,24 @@ read_redcap <- function(redcap_uri, db_data <- multi_choice_to_labels(db_data, db_metadata, raw_or_label) } - # Longitudinal Arms Check and Cleaning Application ---- - # Check if database supplied is longitudinal to determine appropriate function - # to use - is_longitudinal <- if ("redcap_event_name" %in% names(db_data)) { - TRUE + # Database structure checks and definitions ---- + is_longitudinal <- "redcap_event_name" %in% names(db_data) + has_repeating_structure <- "redcap_repeat_instance" %in% names(db_data) + has_repeating_events <- if (is_longitudinal && has_repeating_structure) { + any( + is.na(db_data$redcap_repeat_instrument) & + !is.na(db_data$redcap_repeat_instance) + ) } else { FALSE } if (is_longitudinal) { - repeat_event_types <- get_repeat_event_types(db_data) + repeat_event_types <- if (has_repeating_events) { + get_repeat_event_types(db_data) + } else { + NULL + } linked_arms <- link_arms( redcap_uri = redcap_uri, @@ -453,11 +460,17 @@ add_metadata <- function(supertbl, db_metadata, redcap_uri, token, suppress_redc #' @keywords internal add_event_mapping <- function(supertbl, linked_arms, repeat_event_types) { - event_info <- linked_arms %>% - left_join(repeat_event_types, by = c("unique_event_name" = "redcap_event_name")) %>% + event_info <- linked_arms + + if (!is.null(repeat_event_types)) { + event_info <- event_info %>% + left_join(repeat_event_types, by = c("unique_event_name" = "redcap_event_name")) + } + + event_info <- event_info %>% add_partial_keys(.data$unique_event_name) %>% select( - redcap_form_name = "form", "redcap_event", "event_name", "redcap_arm", "arm_name", "repeat_type" + redcap_form_name = "form", "redcap_event", "event_name", "redcap_arm", "arm_name", any_of("repeat_type") ) %>% nest(redcap_events = !"redcap_form_name") diff --git a/README.Rmd b/README.Rmd index 78616343..97e91419 100644 --- a/README.Rmd +++ b/README.Rmd @@ -25,7 +25,7 @@ knitr::opts_chunk$set( [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/6845/badge)](https://bestpractices.coreinfrastructure.org/projects/6845) -The REDCapTidieR package provides an elegant way to [import](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#import) data from a [REDCap](https://www.project-redcap.org/) [project](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#project) into an R environment. It builds upon the [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package to query the [REDCap API](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#redcap-api) and then transforms the returned data into a set of [tidy](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tidy) [tibbles](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tibble). +The REDCapTidieR package provides an elegant way to [import](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#import) data from a [REDCap](https://projectredcap.org/) [project](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#project) into an R environment. It builds upon the [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package to query the [REDCap API](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#redcap-api) and then transforms the returned data into a set of [tidy](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tidy) [tibbles](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tibble). REDCapTidieR is especially useful for dealing with complex REDCap projects that are [longitudinal](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#longitudinal-project) or include [repeating](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#repeating) [instruments](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#instrument) or both. diff --git a/README.md b/README.md index c7d53d6b..d6df4826 100644 --- a/README.md +++ b/README.md @@ -16,12 +16,11 @@ status](https://www.r-pkg.org/badges/version/REDCapTidieR)](https://CRAN.R-proje coverage](https://codecov.io/gh/CHOP-CGTInformatics/REDCapTidieR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/CHOP-CGTInformatics/REDCapTidieR?branch=main) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/6845/badge)](https://bestpractices.coreinfrastructure.org/projects/6845) -[![DOI](https://joss.theoj.org/papers/10.21105/joss.06277/status.svg)](https://doi.org/10.21105/joss.06277) The REDCapTidieR package provides an elegant way to [import](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#import) -data from a [REDCap](https://www.project-redcap.org/) +data from a [REDCap](https://projectredcap.org/) [project](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#project) into an R environment. It builds upon the [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package to query the diff --git a/cran-comments.md b/cran-comments.md index b4191553..9afe9898 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,41 +2,27 @@ Thank you for taking the time to review this submission and please reach out to either Stephan Kadauke, Richard Hanna, or Ezra Porter for any questions, comments, or concerns. -This submission patches version 1.1.0 to fix a test failure introduced by an upcoming release of `labelled` 2.13.0. We have worked with the developer of `labelled` to ensure this patch resolves their reverse dependency check failures. +This submission for v1.2.0 adds new functionality, new documentation, and patches several minor bugs. ## New Features -There are no significant user-facing changes in this release. - -`read_redcap(raw_or_label = "haven")` now correctly casts categorical data values to character when their type is not character or numeric. This is a constraint of labels from the `haven` package which `labelled` will be checking for explicitly in their new release. +The only new feature in this release is an analytics function that exists in a silo away from the rest of the core package. ## Test environments -1. Local macOS Ventura 13.6.5, R 4.2.4 -2. R-hub - 1. [Ubuntu 22.04.4 LTS, R-next, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/8650642187/job/23719620675) - 2. [Ubuntu 22.04.4 LTS, R-release, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/8650642187/job/23719621223) - 3. [Ubuntu 22.04.4 LTS, R-devel, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/8650642187/job/23719620358) - 4. [Windows Server](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/8650642187/job/23719620965) -3. [win-builder](https://win-builder.r-project.org/V4B5Ar22pIf5/), development version. -4. [GiHub Actions](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions), Ubuntu 20.04.02 LTS +1. Local macOS Sonoma 14.6.1, R 4.4.0 +2. R-hub + 1. [Ubuntu 22.04.5 LTS, R-next, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486785018/job/31969845126) + 2. [Ubuntu 22.04.5 LTS, R-release, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486785018/job/31969845814) + 3. [Ubuntu 22.04.4 LTS, R-devel, GCC](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486785018/job/31969845504) + 4. [Microsoft Windows Server 2022, 10.0.20348](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486785018/job/31969846106) +3. [win-builder](https://win-builder.r-project.org/OQCea7cbW815/), development version. +4. [GiHub Actions](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions), Ubuntu 20.04.05 LTS ## R CMD check results: -- 0 ERRORs or WARNINGs on any builds - -- A NOTE is generated in win-builder resulting from the package maintainer email address changing relative to the last CRAN release. This is an artifact of a different email address than the package maintainer's being used for the submission to win-builder. - -``` -* checking CRAN incoming feasibility ... [14s] NOTE -Maintainer: 'Richard Hanna ' - -New maintainer: - Richard Hanna -Old maintainer(s): - Richard Hanna -``` +- 0 ERRORs or WARNINGs on any builds ## Downstream Dependencies: -No downstream packages are affected. No packages depend/import/suggest REDCapTidieR. Results: +All packages that depend/import/suggest REDCapTidieR pass the [Reverse dependency checks](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/runs/11486797194). diff --git a/inst/WORDLIST b/inst/WORDLIST index 5e73a514..7021a09c 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -17,8 +17,10 @@ REDCapTidieR's RStudio Recode Recoding +Stata Supertibble Supertibbles +TRUEs Tibble Tibble's Tibbles @@ -30,6 +32,7 @@ analytics api appendings cli +de dplyr dropdown edu @@ -38,6 +41,7 @@ ggplot gtsummary https httptest +interpretable labelled multiselection nonrepeat @@ -48,12 +52,15 @@ preprocess recode recoded recodes +recoding skimr summarise supertbl supertibble supertibble's +supertibbles tableStyleLight +tbl tibble tibble's tibbles @@ -62,7 +69,6 @@ tidyverse truefalse undirected unlabelled -wb xlsx yesno ︎ diff --git a/man/check_equal_col_summaries.Rd b/man/check_equal_col_summaries.Rd index 68af2920..0d74cf97 100644 --- a/man/check_equal_col_summaries.Rd +++ b/man/check_equal_col_summaries.Rd @@ -14,7 +14,7 @@ check_equal_col_summaries(data, col1, col2, call = caller_env()) \item{col2}{a column to check for uniqueness} } \description{ -Takes a dataframe and two columns and checks if \code{\link[=n_distinct]{n_distinct()}} of the second +Takes a dataframe and two columns and checks if \code{n_distinct} of the second column is all unique based on grouping of the first column. } \keyword{internal} diff --git a/man/combine_checkboxes.Rd b/man/combine_checkboxes.Rd index 4ba6def4..0497ba2d 100644 --- a/man/combine_checkboxes.Rd +++ b/man/combine_checkboxes.Rd @@ -23,8 +23,7 @@ combine_checkboxes( \item{tbl}{The \code{redcap_form_name} of the data tibble to extract. Required.} -\item{cols}{<\code{\link[=tidyr_tidy_select]{tidy-select}}> Checkbox columns to combine to -single column. Required.} +\item{cols}{Checkbox columns to combine to single column. Required.} \item{names_prefix}{String added to the start of every variable name.} diff --git a/man/convert_checkbox_vals.Rd b/man/convert_checkbox_vals.Rd index 9aa48cf4..b1398fbc 100644 --- a/man/convert_checkbox_vals.Rd +++ b/man/convert_checkbox_vals.Rd @@ -33,10 +33,10 @@ This function takes a single column of data and converts the values based on the overall data tibble cross referenced with a nested section of the metadata tibble. -\code{\link[=case_when]{case_when()}} logic helps determine whether the value is a coalesced singular +\code{case_when} logic helps determine whether the value is a coalesced singular value or a user-specified one via \code{multi_value_label} or \code{values_fill}. } \details{ -This function is used in conjunction with \code{\link[=pmap]{pmap()}}. +This function is used in conjunction with \code{pmap()}. } \keyword{internal} diff --git a/paper/paper.bib b/paper/paper.bib index aaf1765e..1fdd826f 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -54,7 +54,7 @@ @Manual{redcapr_cit author = {Will Beasley}, year = {2023}, url = {https://ouhscbbmc.github.io/REDCapR/}, - note = {https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://project-redcap.org}, + note = {https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://projectredcap.org}, } @Manual{redcapapi_cit, diff --git a/paper/paper.html b/paper/paper.html index ced32ac5..b561bac6 100644 --- a/paper/paper.html +++ b/paper/paper.html @@ -381,7 +381,7 @@

XX November 2023

Summary

Capturing and storing electronic data is integral in the research -world. REDCap (Harris et al. 2009, 2019) offers a secure web +world. REDCap (Harris et al. 2009, 2019) offers a secure web application that lets users build databases and surveys with a robust front-end interface that can support data of any type, including data requiring compliance with standards for protected information.

diff --git a/paper/paper.md b/paper/paper.md index 7f6430ec..a574b731 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -48,7 +48,7 @@ bibliography: paper.bib # Summary -Capturing and storing electronic data is integral in the research world. [REDCap](https://www.project-redcap.org/) [@Harris2009; @Harris2019] offers a secure web application that lets users build databases and surveys with a robust front-end interface that can support data of any type, including data requiring compliance with standards for protected information. +Capturing and storing electronic data is integral in the research world. [REDCap](https://projectredcap.org/) [@Harris2009; @Harris2019] offers a secure web application that lets users build databases and surveys with a robust front-end interface that can support data of any type, including data requiring compliance with standards for protected information. Many REDCap users use the R programming language [@r_cit] to extract and analyze their data. The [`REDCapR`](https://cran.r-project.org/web/packages/REDCapR/index.html) [@redcapr_cit] and [`redcapAPI`](https://cran.r-project.org/web/packages/redcapAPI/index.html) [@redcapapi_cit] packages allow R users to extract data directly into their programming environment. While this works well for simple REDCap databases, it becomes cumbersome for complex databases, because the REDCap API outputs a "block matrix"--a single table with varied granularity levels, which conflicts with the "tidy data" framework [@Wickham2014] that advocates for standardized data organization. diff --git a/renv.lock b/renv.lock deleted file mode 100644 index 82cdc659..00000000 --- a/renv.lock +++ /dev/null @@ -1,2011 +0,0 @@ -{ - "R": { - "Version": "4.4.0", - "Repositories": [ - { - "Name": "CRAN", - "URL": "https://cran.rstudio.com" - } - ] - }, - "Packages": { - "R.cache": { - "Package": "R.cache", - "Version": "0.16.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R.methodsS3", - "R.oo", - "R.utils", - "digest", - "utils" - ], - "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8" - }, - "R.methodsS3": { - "Package": "R.methodsS3", - "Version": "1.8.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "278c286fd6e9e75d0c2e8f731ea445c8" - }, - "R.oo": { - "Package": "R.oo", - "Version": "1.26.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R.methodsS3", - "methods", - "utils" - ], - "Hash": "4fed809e53ddb5407b3da3d0f572e591" - }, - "R.utils": { - "Package": "R.utils", - "Version": "2.12.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R.methodsS3", - "R.oo", - "methods", - "tools", - "utils" - ], - "Hash": "3dc2829b790254bfba21e60965787651" - }, - "R6": { - "Package": "R6", - "Version": "2.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "470851b6d5d0ac559e9d01bb352b4021" - }, - "REDCapR": { - "Package": "REDCapR", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "checkmate", - "dplyr", - "httr", - "jsonlite", - "magrittr", - "methods", - "readr", - "rlang", - "tibble", - "tidyr" - ], - "Hash": "eb44433e1017914d3fba431375aa6bab" - }, - "Rcpp": { - "Package": "Rcpp", - "Version": "1.0.12", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods", - "utils" - ], - "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" - }, - "askpass": { - "Package": "askpass", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "sys" - ], - "Hash": "cad6cf7f1d5f6e906700b9d3e718c796" - }, - "backports": { - "Package": "backports", - "Version": "1.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "c39fbec8a30d23e721980b8afb31984c" - }, - "base64enc": { - "Package": "base64enc", - "Version": "0.1-3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "543776ae6848fde2f48ff3816d0628bc" - }, - "bit": { - "Package": "bit", - "Version": "4.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "d242abec29412ce988848d0294b208fd" - }, - "bit64": { - "Package": "bit64", - "Version": "4.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bit", - "methods", - "stats", - "utils" - ], - "Hash": "9fe98599ca456d6552421db0d6772d8f" - }, - "brew": { - "Package": "brew", - "Version": "1.0-10", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8f4a384e19dccd8c65356dc096847b76" - }, - "brio": { - "Package": "brio", - "Version": "1.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "68bd2b066e1fe780bbf62fc8bcc36de3" - }, - "bslib": { - "Package": "bslib", - "Version": "0.6.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "base64enc", - "cachem", - "grDevices", - "htmltools", - "jquerylib", - "jsonlite", - "lifecycle", - "memoise", - "mime", - "rlang", - "sass" - ], - "Hash": "c0d8599494bc7fb408cd206bbdd9cab0" - }, - "cachem": { - "Package": "cachem", - "Version": "1.0.8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "fastmap", - "rlang" - ], - "Hash": "c35768291560ce302c0a6589f92e837d" - }, - "callr": { - "Package": "callr", - "Version": "3.7.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "processx", - "utils" - ], - "Hash": "9f0e4fae4963ba775a5e5c520838c87b" - }, - "checkmate": { - "Package": "checkmate", - "Version": "2.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "backports", - "utils" - ], - "Hash": "0e14e01ce07e7c88fd25de6d4260d26b" - }, - "cli": { - "Package": "cli", - "Version": "3.6.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "b21916dd77a27642b447374a5d30ecf3" - }, - "clipr": { - "Package": "clipr", - "Version": "0.8.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "utils" - ], - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" - }, - "clisymbols": { - "Package": "clisymbols", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "96c01552bfd5661b9bbdefbc762f4bcd" - }, - "codetools": { - "Package": "codetools", - "Version": "0.2-19", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "c089a619a7fae175d149d89164f8c7d8" - }, - "commonmark": { - "Package": "commonmark", - "Version": "1.9.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "5d8225445acb167abf7797de48b2ee3c" - }, - "covr": { - "Package": "covr", - "Version": "3.6.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "crayon", - "digest", - "httr", - "jsonlite", - "methods", - "rex", - "stats", - "utils", - "withr", - "yaml" - ], - "Hash": "0cbf0435830e767ba9b292b313592362" - }, - "cpp11": { - "Package": "cpp11", - "Version": "0.4.7", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "5a295d7d963cc5035284dcdbaf334f4e" - }, - "crayon": { - "Package": "crayon", - "Version": "1.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "methods", - "utils" - ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" - }, - "credentials": { - "Package": "credentials", - "Version": "2.0.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "askpass", - "curl", - "jsonlite", - "openssl", - "sys" - ], - "Hash": "c7844b32098dcbd1c59cbd8dddb4ecc6" - }, - "curl": { - "Package": "curl", - "Version": "5.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "411ca2c03b1ce5f548345d2fc2685f7a" - }, - "cyclocomp": { - "Package": "cyclocomp", - "Version": "1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "callr", - "crayon", - "desc", - "remotes", - "withr" - ], - "Hash": "cdc4a473222b0112d4df0bcfbed12d44" - }, - "desc": { - "Package": "desc", - "Version": "1.4.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "cli", - "utils" - ], - "Hash": "99b79fcbd6c4d1ce087f5c5c758b384f" - }, - "devtools": { - "Package": "devtools", - "Version": "2.4.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "desc", - "ellipsis", - "fs", - "lifecycle", - "memoise", - "miniUI", - "pkgbuild", - "pkgdown", - "pkgload", - "profvis", - "rcmdcheck", - "remotes", - "rlang", - "roxygen2", - "rversions", - "sessioninfo", - "stats", - "testthat", - "tools", - "urlchecker", - "usethis", - "utils", - "withr" - ], - "Hash": "ea5bc8b4a6a01e4f12d98b58329930bb" - }, - "diffobj": { - "Package": "diffobj", - "Version": "0.3.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "crayon", - "methods", - "stats", - "tools", - "utils" - ], - "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8" - }, - "digest": { - "Package": "digest", - "Version": "0.6.35", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31" - }, - "downlit": { - "Package": "downlit", - "Version": "0.4.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "brio", - "desc", - "digest", - "evaluate", - "fansi", - "memoise", - "rlang", - "vctrs", - "withr", - "yaml" - ], - "Hash": "14fa1f248b60ed67e1f5418391a17b14" - }, - "dplyr": { - "Package": "dplyr", - "Version": "1.1.4", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", - "cli", - "generics", - "glue", - "lifecycle", - "magrittr", - "methods", - "pillar", - "rlang", - "tibble", - "tidyselect", - "utils", - "vctrs" - ], - "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" - }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" - }, - "evaluate": { - "Package": "evaluate", - "Version": "0.23", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" - }, - "fansi": { - "Package": "fansi", - "Version": "1.0.6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "utils" - ], - "Hash": "962174cf2aeb5b9eea581522286a911f" - }, - "fastmap": { - "Package": "fastmap", - "Version": "1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" - }, - "fontawesome": { - "Package": "fontawesome", - "Version": "0.5.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "htmltools", - "rlang" - ], - "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" - }, - "forcats": { - "Package": "forcats", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "magrittr", - "rlang", - "tibble" - ], - "Hash": "1a0a9a3d5083d0d573c4214576f1e690" - }, - "formattable": { - "Package": "formattable", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "htmltools", - "htmlwidgets", - "knitr", - "methods", - "rmarkdown" - ], - "Hash": "870d6d5d39b23923d0c816f904075b4c" - }, - "fs": { - "Package": "fs", - "Version": "1.6.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "47b5f30c720c23999b913a1a635cf0bb" - }, - "generics": { - "Package": "generics", - "Version": "0.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "15e9634c0fcd294799e9b2e929ed1b86" - }, - "gert": { - "Package": "gert", - "Version": "2.0.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "askpass", - "credentials", - "openssl", - "rstudioapi", - "sys", - "zip" - ], - "Hash": "f70d3fe2d9e7654213a946963d1591eb" - }, - "gh": { - "Package": "gh", - "Version": "1.4.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "gitcreds", - "httr2", - "ini", - "jsonlite", - "rlang" - ], - "Hash": "03533b1c875028233598f848fda44c4c" - }, - "gitcreds": { - "Package": "gitcreds", - "Version": "0.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe" - }, - "glue": { - "Package": "glue", - "Version": "1.7.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "e0b3a53876554bd45879e596cdb10a52" - }, - "goodpractice": { - "Package": "goodpractice", - "Version": "1.0.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "clisymbols", - "covr", - "crayon", - "cyclocomp", - "desc", - "jsonlite", - "lintr", - "praise", - "rcmdcheck", - "rstudioapi", - "tools", - "utils", - "whoami", - "withr", - "xml2", - "xmlparsedata" - ], - "Hash": "0f6da9489ee2bc6197a4a4e845b5a217" - }, - "haven": { - "Package": "haven", - "Version": "2.5.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "cpp11", - "forcats", - "hms", - "lifecycle", - "methods", - "readr", - "rlang", - "tibble", - "tidyselect", - "vctrs" - ], - "Hash": "9171f898db9d9c4c1b2c745adc2c1ef1" - }, - "highr": { - "Package": "highr", - "Version": "0.11", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "xfun" - ], - "Hash": "d65ba49117ca223614f71b60d85b8ab7" - }, - "hms": { - "Package": "hms", - "Version": "1.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "lifecycle", - "methods", - "pkgconfig", - "rlang", - "vctrs" - ], - "Hash": "b59377caa7ed00fa41808342002138f9" - }, - "htmltools": { - "Package": "htmltools", - "Version": "0.5.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "base64enc", - "digest", - "ellipsis", - "fastmap", - "grDevices", - "rlang", - "utils" - ], - "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" - }, - "htmlwidgets": { - "Package": "htmlwidgets", - "Version": "1.6.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "htmltools", - "jsonlite", - "knitr", - "rmarkdown", - "yaml" - ], - "Hash": "04291cc45198225444a397606810ac37" - }, - "httpuv": { - "Package": "httpuv", - "Version": "1.6.14", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "Rcpp", - "later", - "promises", - "utils" - ], - "Hash": "16abeb167dbf511f8cc0552efaf05bab" - }, - "httr": { - "Package": "httr", - "Version": "1.4.7", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", - "curl", - "jsonlite", - "mime", - "openssl" - ], - "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" - }, - "httr2": { - "Package": "httr2", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "cli", - "curl", - "glue", - "lifecycle", - "magrittr", - "openssl", - "rappdirs", - "rlang", - "vctrs", - "withr" - ], - "Hash": "e2b30f1fc039a0bab047dd52bb20ef71" - }, - "hunspell": { - "Package": "hunspell", - "Version": "3.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "digest" - ], - "Hash": "e957e989ea17f937964f0d46b0f0bca0" - }, - "ini": { - "Package": "ini", - "Version": "0.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6154ec2223172bce8162d4153cda21f7" - }, - "jquerylib": { - "Package": "jquerylib", - "Version": "0.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "htmltools" - ], - "Hash": "5aab57a3bd297eee1c1d862735972182" - }, - "jsonlite": { - "Package": "jsonlite", - "Version": "1.8.8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods" - ], - "Hash": "e1b9c55281c5adc4dd113652d9e26768" - }, - "knitr": { - "Package": "knitr", - "Version": "1.48", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "evaluate", - "highr", - "methods", - "tools", - "xfun", - "yaml" - ], - "Hash": "acf380f300c721da9fde7df115a5f86f" - }, - "labelled": { - "Package": "labelled", - "Version": "2.12.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "dplyr", - "haven", - "lifecycle", - "rlang", - "stringr", - "tidyr", - "vctrs" - ], - "Hash": "1ec27c624ece6c20431e9249bd232797" - }, - "later": { - "Package": "later", - "Version": "1.3.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "Rcpp", - "rlang" - ], - "Hash": "a3e051d405326b8b0012377434c62b37" - }, - "lazyeval": { - "Package": "lazyeval", - "Version": "0.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "d908914ae53b04d4c0c0fd72ecc35370" - }, - "lifecycle": { - "Package": "lifecycle", - "Version": "1.0.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "rlang" - ], - "Hash": "b8552d117e1b808b09a832f589b79035" - }, - "lintr": { - "Package": "lintr", - "Version": "3.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "backports", - "codetools", - "cyclocomp", - "digest", - "glue", - "knitr", - "rex", - "stats", - "utils", - "xml2", - "xmlparsedata" - ], - "Hash": "93e9379f4be8c0bf1862dfc7f720193e" - }, - "lobstr": { - "Package": "lobstr", - "Version": "1.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11", - "crayon", - "methods", - "prettyunits", - "rlang" - ], - "Hash": "f2a94f8fc9db382a642e965339635ad6" - }, - "lubridate": { - "Package": "lubridate", - "Version": "1.9.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "generics", - "methods", - "timechange" - ], - "Hash": "680ad542fbcf801442c83a6ac5a2126c" - }, - "magrittr": { - "Package": "magrittr", - "Version": "2.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "7ce2733a9826b3aeb1775d56fd305472" - }, - "memoise": { - "Package": "memoise", - "Version": "2.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "cachem", - "rlang" - ], - "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" - }, - "microbenchmark": { - "Package": "microbenchmark", - "Version": "1.4.10", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "graphics", - "stats" - ], - "Hash": "db81b552e393ed092872cf7023469bc2" - }, - "mime": { - "Package": "mime", - "Version": "0.12", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "tools" - ], - "Hash": "18e9c28c1d3ca1560ce30658b22ce104" - }, - "miniUI": { - "Package": "miniUI", - "Version": "0.1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "htmltools", - "shiny", - "utils" - ], - "Hash": "fec5f52652d60615fdb3957b3d74324a" - }, - "openssl": { - "Package": "openssl", - "Version": "2.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "askpass" - ], - "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" - }, - "openxlsx2": { - "Package": "openxlsx2", - "Version": "1.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "Rcpp", - "grDevices", - "magrittr", - "stringi", - "utils", - "zip" - ], - "Hash": "9fa7cdc5fbdb1c8511fdde72a944db63" - }, - "pillar": { - "Package": "pillar", - "Version": "1.9.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "cli", - "fansi", - "glue", - "lifecycle", - "rlang", - "utf8", - "utils", - "vctrs" - ], - "Hash": "15da5a8412f317beeee6175fbc76f4bb" - }, - "pkgbuild": { - "Package": "pkgbuild", - "Version": "1.4.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "callr", - "cli", - "desc", - "processx" - ], - "Hash": "c0143443203205e6a2760ce553dafc24" - }, - "pkgconfig": { - "Package": "pkgconfig", - "Version": "2.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "utils" - ], - "Hash": "01f28d4278f15c76cddbea05899c5d6f" - }, - "pkgdown": { - "Package": "pkgdown", - "Version": "2.0.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bslib", - "callr", - "cli", - "desc", - "digest", - "downlit", - "fs", - "httr", - "jsonlite", - "magrittr", - "memoise", - "purrr", - "ragg", - "rlang", - "rmarkdown", - "tibble", - "whisker", - "withr", - "xml2", - "yaml" - ], - "Hash": "16fa15449c930bf3a7761d3c68f8abf9" - }, - "pkgload": { - "Package": "pkgload", - "Version": "1.3.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "crayon", - "desc", - "fs", - "glue", - "methods", - "pkgbuild", - "rlang", - "rprojroot", - "utils", - "withr" - ], - "Hash": "876c618df5ae610be84356d5d7a5d124" - }, - "praise": { - "Package": "praise", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a555924add98c99d2f411e37e7d25e9f" - }, - "prettyunits": { - "Package": "prettyunits", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7" - }, - "processx": { - "Package": "processx", - "Version": "3.8.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "ps", - "utils" - ], - "Hash": "82d48b1aec56084d9438dbf98087a7e9" - }, - "profvis": { - "Package": "profvis", - "Version": "0.3.8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "htmlwidgets", - "purrr", - "rlang", - "stringr", - "vctrs" - ], - "Hash": "aa5a3864397ce6ae03458f98618395a1" - }, - "progress": { - "Package": "progress", - "Version": "1.2.3", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", - "crayon", - "hms", - "prettyunits" - ], - "Hash": "f4625e061cb2865f111b47ff163a5ca6" - }, - "promises": { - "Package": "promises", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "Rcpp", - "fastmap", - "later", - "magrittr", - "rlang", - "stats" - ], - "Hash": "0d8a15c9d000970ada1ab21405387dee" - }, - "ps": { - "Package": "ps", - "Version": "1.7.6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "dd2b9319ee0656c8acf45c7f40c59de7" - }, - "purrr": { - "Package": "purrr", - "Version": "1.0.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "lifecycle", - "magrittr", - "rlang", - "vctrs" - ], - "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc" - }, - "ragg": { - "Package": "ragg", - "Version": "1.2.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "systemfonts", - "textshaping" - ], - "Hash": "90a1b8b7e518d7f90480d56453b4d062" - }, - "rappdirs": { - "Package": "rappdirs", - "Version": "0.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "5e3c5dc0b071b21fa128676560dbe94d" - }, - "rcmdcheck": { - "Package": "rcmdcheck", - "Version": "1.4.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "callr", - "cli", - "curl", - "desc", - "digest", - "pkgbuild", - "prettyunits", - "rprojroot", - "sessioninfo", - "utils", - "withr", - "xopen" - ], - "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" - }, - "readr": { - "Package": "readr", - "Version": "2.1.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "cli", - "clipr", - "cpp11", - "crayon", - "hms", - "lifecycle", - "methods", - "rlang", - "tibble", - "tzdb", - "utils", - "vroom" - ], - "Hash": "9de96463d2117f6ac49980577939dfb3" - }, - "rematch": { - "Package": "rematch", - "Version": "2.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "cbff1b666c6fa6d21202f07e2318d4f1" - }, - "rematch2": { - "Package": "rematch2", - "Version": "2.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "tibble" - ], - "Hash": "76c9e04c712a05848ae7a23d2f170a40" - }, - "remotes": { - "Package": "remotes", - "Version": "2.4.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods", - "stats", - "tools", - "utils" - ], - "Hash": "63d15047eb239f95160112bcadc4fcb9" - }, - "renv": { - "Package": "renv", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "utils" - ], - "Hash": "32c3f93e8360f667ca5863272ec8ba6a" - }, - "repr": { - "Package": "repr", - "Version": "1.1.6", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "base64enc", - "grDevices", - "htmltools", - "jsonlite", - "pillar", - "utils" - ], - "Hash": "fab761ee8f3554a04afef40ac53689f4" - }, - "reprex": { - "Package": "reprex", - "Version": "2.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "callr", - "cli", - "clipr", - "fs", - "glue", - "knitr", - "lifecycle", - "rlang", - "rmarkdown", - "rstudioapi", - "utils", - "withr" - ], - "Hash": "1425f91b4d5d9a8f25352c44a3d914ed" - }, - "rex": { - "Package": "rex", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "lazyeval" - ], - "Hash": "ae34cd56890607370665bee5bd17812f" - }, - "rhub": { - "Package": "rhub", - "Version": "2.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "callr", - "cli", - "curl", - "desc", - "gert", - "gitcreds", - "glue", - "jsonlite", - "pkgbuild", - "processx", - "rappdirs", - "rematch", - "rprojroot", - "utils", - "whoami" - ], - "Hash": "403efdc0d221efb38e2eccdfdc5f4b25" - }, - "rlang": { - "Package": "rlang", - "Version": "1.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" - }, - "rmarkdown": { - "Package": "rmarkdown", - "Version": "2.27", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bslib", - "evaluate", - "fontawesome", - "htmltools", - "jquerylib", - "jsonlite", - "knitr", - "methods", - "tinytex", - "tools", - "utils", - "xfun", - "yaml" - ], - "Hash": "27f9502e1cdbfa195f94e03b0f517484" - }, - "roxygen2": { - "Package": "roxygen2", - "Version": "7.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "brew", - "cli", - "commonmark", - "cpp11", - "desc", - "knitr", - "methods", - "pkgload", - "purrr", - "rlang", - "stringi", - "stringr", - "utils", - "withr", - "xml2" - ], - "Hash": "6ee25f9054a70f44d615300ed531ba8d" - }, - "rprojroot": { - "Package": "rprojroot", - "Version": "2.0.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144" - }, - "rstudioapi": { - "Package": "rstudioapi", - "Version": "0.15.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "5564500e25cffad9e22244ced1379887" - }, - "rversions": { - "Package": "rversions", - "Version": "2.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "curl", - "utils", - "xml2" - ], - "Hash": "a9881dfed103e83f9de151dc17002cd1" - }, - "sass": { - "Package": "sass", - "Version": "0.4.8", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R6", - "fs", - "htmltools", - "rappdirs", - "rlang" - ], - "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035" - }, - "sessioninfo": { - "Package": "sessioninfo", - "Version": "1.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "tools", - "utils" - ], - "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f" - }, - "shiny": { - "Package": "shiny", - "Version": "1.8.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", - "bslib", - "cachem", - "commonmark", - "crayon", - "ellipsis", - "fastmap", - "fontawesome", - "glue", - "grDevices", - "htmltools", - "httpuv", - "jsonlite", - "later", - "lifecycle", - "methods", - "mime", - "promises", - "rlang", - "sourcetools", - "tools", - "utils", - "withr", - "xtable" - ], - "Hash": "3a1f41807d648a908e3c7f0334bf85e6" - }, - "skimr": { - "Package": "skimr", - "Version": "2.1.5", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "cli", - "dplyr", - "knitr", - "magrittr", - "pillar", - "purrr", - "repr", - "rlang", - "stats", - "stringr", - "tibble", - "tidyr", - "tidyselect", - "vctrs" - ], - "Hash": "8f138ff2c8fbea9e0a523f6c399c0386" - }, - "sourcetools": { - "Package": "sourcetools", - "Version": "0.1.7-1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "5f5a7629f956619d519205ec475fe647" - }, - "spelling": { - "Package": "spelling", - "Version": "2.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "commonmark", - "hunspell", - "knitr", - "xml2" - ], - "Hash": "632e9e83d3dc774d361b9415b15642bb" - }, - "stringi": { - "Package": "stringi", - "Version": "1.8.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats", - "tools", - "utils" - ], - "Hash": "39e1144fd75428983dc3f63aa53dfa91" - }, - "stringr": { - "Package": "stringr", - "Version": "1.5.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "magrittr", - "rlang", - "stringi", - "vctrs" - ], - "Hash": "960e2ae9e09656611e0b8214ad543207" - }, - "styler": { - "Package": "styler", - "Version": "1.10.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R.cache", - "cli", - "magrittr", - "purrr", - "rlang", - "rprojroot", - "tools", - "vctrs", - "withr" - ], - "Hash": "d61238fd44fc63c8adf4565efe8eb682" - }, - "sys": { - "Package": "sys", - "Version": "3.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" - }, - "systemfonts": { - "Package": "systemfonts", - "Version": "1.0.6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" - ], - "Hash": "6d538cff441f0f1f36db2209ac7495ac" - }, - "testthat": { - "Package": "testthat", - "Version": "3.2.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "brio", - "callr", - "cli", - "desc", - "digest", - "evaluate", - "jsonlite", - "lifecycle", - "magrittr", - "methods", - "pkgload", - "praise", - "processx", - "ps", - "rlang", - "utils", - "waldo", - "withr" - ], - "Hash": "3f6e7e5e2220856ff865e4834766bf2b" - }, - "textshaping": { - "Package": "textshaping", - "Version": "0.3.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11", - "systemfonts" - ], - "Hash": "997aac9ad649e0ef3b97f96cddd5622b" - }, - "tibble": { - "Package": "tibble", - "Version": "3.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "fansi", - "lifecycle", - "magrittr", - "methods", - "pillar", - "pkgconfig", - "rlang", - "utils", - "vctrs" - ], - "Hash": "a84e2cc86d07289b3b6f5069df7a004c" - }, - "tidyr": { - "Package": "tidyr", - "Version": "1.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "cpp11", - "dplyr", - "glue", - "lifecycle", - "magrittr", - "purrr", - "rlang", - "stringr", - "tibble", - "tidyselect", - "utils", - "vctrs" - ], - "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" - }, - "tidyselect": { - "Package": "tidyselect", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "rlang", - "vctrs", - "withr" - ], - "Hash": "829f27b9c4919c16b593794a6344d6c0" - }, - "timechange": { - "Package": "timechange", - "Version": "0.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" - ], - "Hash": "c5f3c201b931cd6474d17d8700ccb1c8" - }, - "tinytex": { - "Package": "tinytex", - "Version": "0.49", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "xfun" - ], - "Hash": "5ac22900ae0f386e54f1c307eca7d843" - }, - "tzdb": { - "Package": "tzdb", - "Version": "0.4.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" - ], - "Hash": "f561504ec2897f4d46f0c7657e488ae1" - }, - "urlchecker": { - "Package": "urlchecker", - "Version": "1.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "curl", - "tools", - "xml2" - ], - "Hash": "409328b8e1253c8d729a7836fe7f7a16" - }, - "usethis": { - "Package": "usethis", - "Version": "2.2.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "clipr", - "crayon", - "curl", - "desc", - "fs", - "gert", - "gh", - "glue", - "jsonlite", - "lifecycle", - "purrr", - "rappdirs", - "rlang", - "rprojroot", - "rstudioapi", - "stats", - "utils", - "whisker", - "withr", - "yaml" - ], - "Hash": "d524fd42c517035027f866064417d7e6" - }, - "utf8": { - "Package": "utf8", - "Version": "1.2.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "62b65c52671e6665f803ff02954446e9" - }, - "vctrs": { - "Package": "vctrs", - "Version": "0.6.5", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "rlang" - ], - "Hash": "c03fa420630029418f7e6da3667aac4a" - }, - "vroom": { - "Package": "vroom", - "Version": "1.6.5", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "bit64", - "cli", - "cpp11", - "crayon", - "glue", - "hms", - "lifecycle", - "methods", - "progress", - "rlang", - "stats", - "tibble", - "tidyselect", - "tzdb", - "vctrs", - "withr" - ], - "Hash": "390f9315bc0025be03012054103d227c" - }, - "waldo": { - "Package": "waldo", - "Version": "0.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "diffobj", - "fansi", - "glue", - "methods", - "rematch2", - "rlang", - "tibble" - ], - "Hash": "c7d3fd6d29ab077cbac8f0e2751449e6" - }, - "whisker": { - "Package": "whisker", - "Version": "0.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "c6abfa47a46d281a7d5159d0a8891e88" - }, - "whoami": { - "Package": "whoami", - "Version": "1.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "httr", - "jsonlite", - "utils" - ], - "Hash": "ef0f4d9b8f2cc2ebeccae1d725b8a023" - }, - "withr": { - "Package": "withr", - "Version": "3.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics" - ], - "Hash": "07909200e8bbe90426fbfeb73e1e27aa" - }, - "xfun": { - "Package": "xfun", - "Version": "0.45", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "stats", - "tools" - ], - "Hash": "ca59c87fe305b16a9141a5874c3a7889" - }, - "xml2": { - "Package": "xml2", - "Version": "1.3.6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "methods", - "rlang" - ], - "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" - }, - "xmlparsedata": { - "Package": "xmlparsedata", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "45e4bf3c46476896e821fc0a408fb4fc" - }, - "xopen": { - "Package": "xopen", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "processx" - ], - "Hash": "6c85f015dee9cc7710ddd20f86881f58" - }, - "xtable": { - "Package": "xtable", - "Version": "1.8-4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats", - "utils" - ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" - }, - "yaml": { - "Package": "yaml", - "Version": "2.3.8", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" - }, - "zip": { - "Package": "zip", - "Version": "2.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" - } - } -} diff --git a/renv/.gitignore b/renv/.gitignore deleted file mode 100644 index 22a0d01d..00000000 --- a/renv/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -sandbox/ -library/ -local/ -cellar/ -lock/ -python/ -staging/ diff --git a/renv/activate.R b/renv/activate.R deleted file mode 100644 index 9b2e7f18..00000000 --- a/renv/activate.R +++ /dev/null @@ -1,1201 +0,0 @@ - -local({ - - # the requested version of renv - version <- "1.0.5" - attr(version, "sha") <- NULL - - # the project directory - project <- getwd() - - # use start-up diagnostics if enabled - diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") - if (diagnostics) { - start <- Sys.time() - profile <- tempfile("renv-startup-", fileext = ".Rprof") - utils::Rprof(profile) - on.exit({ - utils::Rprof(NULL) - elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) - writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) - writeLines(sprintf("- Profile: %s", profile)) - print(utils::summaryRprof(profile)) - }, add = TRUE) - } - - # figure out whether the autoloader is enabled - enabled <- local({ - - # first, check config option - override <- getOption("renv.config.autoloader.enabled") - if (!is.null(override)) - return(override) - - # if we're being run in a context where R_LIBS is already set, - # don't load -- presumably we're being run as a sub-process and - # the parent process has already set up library paths for us - rcmd <- Sys.getenv("R_CMD", unset = NA) - rlibs <- Sys.getenv("R_LIBS", unset = NA) - if (!is.na(rlibs) && !is.na(rcmd)) - return(FALSE) - - # next, check environment variables - # TODO: prefer using the configuration one in the future - envvars <- c( - "RENV_CONFIG_AUTOLOADER_ENABLED", - "RENV_AUTOLOADER_ENABLED", - "RENV_ACTIVATE_PROJECT" - ) - - for (envvar in envvars) { - envval <- Sys.getenv(envvar, unset = NA) - if (!is.na(envval)) - return(tolower(envval) %in% c("true", "t", "1")) - } - - # enable by default - TRUE - - }) - - # bail if we're not enabled - if (!enabled) { - - # if we're not enabled, we might still need to manually load - # the user profile here - profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") - if (file.exists(profile)) { - cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") - if (tolower(cfg) %in% c("true", "t", "1")) - sys.source(profile, envir = globalenv()) - } - - return(FALSE) - - } - - # avoid recursion - if (identical(getOption("renv.autoloader.running"), TRUE)) { - warning("ignoring recursive attempt to run renv autoloader") - return(invisible(TRUE)) - } - - # signal that we're loading renv during R startup - options(renv.autoloader.running = TRUE) - on.exit(options(renv.autoloader.running = NULL), add = TRUE) - - # signal that we've consented to use renv - options(renv.consent = TRUE) - - # load the 'utils' package eagerly -- this ensures that renv shims, which - # mask 'utils' packages, will come first on the search path - library(utils, lib.loc = .Library) - - # unload renv if it's already been loaded - if ("renv" %in% loadedNamespaces()) - unloadNamespace("renv") - - # load bootstrap tools - `%||%` <- function(x, y) { - if (is.null(x)) y else x - } - - catf <- function(fmt, ..., appendLF = TRUE) { - - quiet <- getOption("renv.bootstrap.quiet", default = FALSE) - if (quiet) - return(invisible()) - - msg <- sprintf(fmt, ...) - cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") - - invisible(msg) - - } - - header <- function(label, - ..., - prefix = "#", - suffix = "-", - n = min(getOption("width"), 78)) - { - label <- sprintf(label, ...) - n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) - if (n <= 0) - return(paste(prefix, label)) - - tail <- paste(rep.int(suffix, n), collapse = "") - paste0(prefix, " ", label, " ", tail) - - } - - startswith <- function(string, prefix) { - substring(string, 1, nchar(prefix)) == prefix - } - - bootstrap <- function(version, library) { - - friendly <- renv_bootstrap_version_friendly(version) - section <- header(sprintf("Bootstrapping renv %s", friendly)) - catf(section) - - # attempt to download renv - catf("- Downloading renv ... ", appendLF = FALSE) - withCallingHandlers( - tarball <- renv_bootstrap_download(version), - error = function(err) { - catf("FAILED") - stop("failed to download:\n", conditionMessage(err)) - } - ) - catf("OK") - on.exit(unlink(tarball), add = TRUE) - - # now attempt to install - catf("- Installing renv ... ", appendLF = FALSE) - withCallingHandlers( - status <- renv_bootstrap_install(version, tarball, library), - error = function(err) { - catf("FAILED") - stop("failed to install:\n", conditionMessage(err)) - } - ) - catf("OK") - - # add empty line to break up bootstrapping from normal output - catf("") - - return(invisible()) - } - - renv_bootstrap_tests_running <- function() { - getOption("renv.tests.running", default = FALSE) - } - - renv_bootstrap_repos <- function() { - - # get CRAN repository - cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") - - # check for repos override - repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) - if (!is.na(repos)) { - - # check for RSPM; if set, use a fallback repository for renv - rspm <- Sys.getenv("RSPM", unset = NA) - if (identical(rspm, repos)) - repos <- c(RSPM = rspm, CRAN = cran) - - return(repos) - - } - - # check for lockfile repositories - repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) - if (!inherits(repos, "error") && length(repos)) - return(repos) - - # retrieve current repos - repos <- getOption("repos") - - # ensure @CRAN@ entries are resolved - repos[repos == "@CRAN@"] <- cran - - # add in renv.bootstrap.repos if set - default <- c(FALLBACK = "https://cloud.r-project.org") - extra <- getOption("renv.bootstrap.repos", default = default) - repos <- c(repos, extra) - - # remove duplicates that might've snuck in - dupes <- duplicated(repos) | duplicated(names(repos)) - repos[!dupes] - - } - - renv_bootstrap_repos_lockfile <- function() { - - lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") - if (!file.exists(lockpath)) - return(NULL) - - lockfile <- tryCatch(renv_json_read(lockpath), error = identity) - if (inherits(lockfile, "error")) { - warning(lockfile) - return(NULL) - } - - repos <- lockfile$R$Repositories - if (length(repos) == 0) - return(NULL) - - keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) - vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) - names(vals) <- keys - - return(vals) - - } - - renv_bootstrap_download <- function(version) { - - sha <- attr(version, "sha", exact = TRUE) - - methods <- if (!is.null(sha)) { - - # attempting to bootstrap a development version of renv - c( - function() renv_bootstrap_download_tarball(sha), - function() renv_bootstrap_download_github(sha) - ) - - } else { - - # attempting to bootstrap a release version of renv - c( - function() renv_bootstrap_download_tarball(version), - function() renv_bootstrap_download_cran_latest(version), - function() renv_bootstrap_download_cran_archive(version) - ) - - } - - for (method in methods) { - path <- tryCatch(method(), error = identity) - if (is.character(path) && file.exists(path)) - return(path) - } - - stop("All download methods failed") - - } - - renv_bootstrap_download_impl <- function(url, destfile) { - - mode <- "wb" - - # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 - fixup <- - Sys.info()[["sysname"]] == "Windows" && - substring(url, 1L, 5L) == "file:" - - if (fixup) - mode <- "w+b" - - args <- list( - url = url, - destfile = destfile, - mode = mode, - quiet = TRUE - ) - - if ("headers" %in% names(formals(utils::download.file))) - args$headers <- renv_bootstrap_download_custom_headers(url) - - do.call(utils::download.file, args) - - } - - renv_bootstrap_download_custom_headers <- function(url) { - - headers <- getOption("renv.download.headers") - if (is.null(headers)) - return(character()) - - if (!is.function(headers)) - stopf("'renv.download.headers' is not a function") - - headers <- headers(url) - if (length(headers) == 0L) - return(character()) - - if (is.list(headers)) - headers <- unlist(headers, recursive = FALSE, use.names = TRUE) - - ok <- - is.character(headers) && - is.character(names(headers)) && - all(nzchar(names(headers))) - - if (!ok) - stop("invocation of 'renv.download.headers' did not return a named character vector") - - headers - - } - - renv_bootstrap_download_cran_latest <- function(version) { - - spec <- renv_bootstrap_download_cran_latest_find(version) - type <- spec$type - repos <- spec$repos - - baseurl <- utils::contrib.url(repos = repos, type = type) - ext <- if (identical(type, "source")) - ".tar.gz" - else if (Sys.info()[["sysname"]] == "Windows") - ".zip" - else - ".tgz" - name <- sprintf("renv_%s%s", version, ext) - url <- paste(baseurl, name, sep = "/") - - destfile <- file.path(tempdir(), name) - status <- tryCatch( - renv_bootstrap_download_impl(url, destfile), - condition = identity - ) - - if (inherits(status, "condition")) - return(FALSE) - - # report success and return - destfile - - } - - renv_bootstrap_download_cran_latest_find <- function(version) { - - # check whether binaries are supported on this system - binary <- - getOption("renv.bootstrap.binary", default = TRUE) && - !identical(.Platform$pkgType, "source") && - !identical(getOption("pkgType"), "source") && - Sys.info()[["sysname"]] %in% c("Darwin", "Windows") - - types <- c(if (binary) "binary", "source") - - # iterate over types + repositories - for (type in types) { - for (repos in renv_bootstrap_repos()) { - - # retrieve package database - db <- tryCatch( - as.data.frame( - utils::available.packages(type = type, repos = repos), - stringsAsFactors = FALSE - ), - error = identity - ) - - if (inherits(db, "error")) - next - - # check for compatible entry - entry <- db[db$Package %in% "renv" & db$Version %in% version, ] - if (nrow(entry) == 0) - next - - # found it; return spec to caller - spec <- list(entry = entry, type = type, repos = repos) - return(spec) - - } - } - - # if we got here, we failed to find renv - fmt <- "renv %s is not available from your declared package repositories" - stop(sprintf(fmt, version)) - - } - - renv_bootstrap_download_cran_archive <- function(version) { - - name <- sprintf("renv_%s.tar.gz", version) - repos <- renv_bootstrap_repos() - urls <- file.path(repos, "src/contrib/Archive/renv", name) - destfile <- file.path(tempdir(), name) - - for (url in urls) { - - status <- tryCatch( - renv_bootstrap_download_impl(url, destfile), - condition = identity - ) - - if (identical(status, 0L)) - return(destfile) - - } - - return(FALSE) - - } - - renv_bootstrap_download_tarball <- function(version) { - - # if the user has provided the path to a tarball via - # an environment variable, then use it - tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) - if (is.na(tarball)) - return() - - # allow directories - if (dir.exists(tarball)) { - name <- sprintf("renv_%s.tar.gz", version) - tarball <- file.path(tarball, name) - } - - # bail if it doesn't exist - if (!file.exists(tarball)) { - - # let the user know we weren't able to honour their request - fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." - msg <- sprintf(fmt, tarball) - warning(msg) - - # bail - return() - - } - - catf("- Using local tarball '%s'.", tarball) - tarball - - } - - renv_bootstrap_download_github <- function(version) { - - enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") - if (!identical(enabled, "TRUE")) - return(FALSE) - - # prepare download options - pat <- Sys.getenv("GITHUB_PAT") - if (nzchar(Sys.which("curl")) && nzchar(pat)) { - fmt <- "--location --fail --header \"Authorization: token %s\"" - extra <- sprintf(fmt, pat) - saved <- options("download.file.method", "download.file.extra") - options(download.file.method = "curl", download.file.extra = extra) - on.exit(do.call(base::options, saved), add = TRUE) - } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { - fmt <- "--header=\"Authorization: token %s\"" - extra <- sprintf(fmt, pat) - saved <- options("download.file.method", "download.file.extra") - options(download.file.method = "wget", download.file.extra = extra) - on.exit(do.call(base::options, saved), add = TRUE) - } - - url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) - name <- sprintf("renv_%s.tar.gz", version) - destfile <- file.path(tempdir(), name) - - status <- tryCatch( - renv_bootstrap_download_impl(url, destfile), - condition = identity - ) - - if (!identical(status, 0L)) - return(FALSE) - - renv_bootstrap_download_augment(destfile) - - return(destfile) - - } - - # Add Sha to DESCRIPTION. This is stop gap until #890, after which we - # can use renv::install() to fully capture metadata. - renv_bootstrap_download_augment <- function(destfile) { - sha <- renv_bootstrap_git_extract_sha1_tar(destfile) - if (is.null(sha)) { - return() - } - - # Untar - tempdir <- tempfile("renv-github-") - on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) - untar(destfile, exdir = tempdir) - pkgdir <- dir(tempdir, full.names = TRUE)[[1]] - - # Modify description - desc_path <- file.path(pkgdir, "DESCRIPTION") - desc_lines <- readLines(desc_path) - remotes_fields <- c( - "RemoteType: github", - "RemoteHost: api.github.com", - "RemoteRepo: renv", - "RemoteUsername: rstudio", - "RemotePkgRef: rstudio/renv", - paste("RemoteRef: ", sha), - paste("RemoteSha: ", sha) - ) - writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) - - # Re-tar - local({ - old <- setwd(tempdir) - on.exit(setwd(old), add = TRUE) - - tar(destfile, compression = "gzip") - }) - invisible() - } - - # Extract the commit hash from a git archive. Git archives include the SHA1 - # hash as the comment field of the tarball pax extended header - # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) - # For GitHub archives this should be the first header after the default one - # (512 byte) header. - renv_bootstrap_git_extract_sha1_tar <- function(bundle) { - - # open the bundle for reading - # We use gzcon for everything because (from ?gzcon) - # > Reading from a connection which does not supply a 'gzip' magic - # > header is equivalent to reading from the original connection - conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) - on.exit(close(conn)) - - # The default pax header is 512 bytes long and the first pax extended header - # with the comment should be 51 bytes long - # `52 comment=` (11 chars) + 40 byte SHA1 hash - len <- 0x200 + 0x33 - res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) - - if (grepl("^52 comment=", res)) { - sub("52 comment=", "", res) - } else { - NULL - } - } - - renv_bootstrap_install <- function(version, tarball, library) { - - # attempt to install it into project library - dir.create(library, showWarnings = FALSE, recursive = TRUE) - output <- renv_bootstrap_install_impl(library, tarball) - - # check for successful install - status <- attr(output, "status") - if (is.null(status) || identical(status, 0L)) - return(status) - - # an error occurred; report it - header <- "installation of renv failed" - lines <- paste(rep.int("=", nchar(header)), collapse = "") - text <- paste(c(header, lines, output), collapse = "\n") - stop(text) - - } - - renv_bootstrap_install_impl <- function(library, tarball) { - - # invoke using system2 so we can capture and report output - bin <- R.home("bin") - exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" - R <- file.path(bin, exe) - - args <- c( - "--vanilla", "CMD", "INSTALL", "--no-multiarch", - "-l", shQuote(path.expand(library)), - shQuote(path.expand(tarball)) - ) - - system2(R, args, stdout = TRUE, stderr = TRUE) - - } - - renv_bootstrap_platform_prefix <- function() { - - # construct version prefix - version <- paste(R.version$major, R.version$minor, sep = ".") - prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") - - # include SVN revision for development versions of R - # (to avoid sharing platform-specific artefacts with released versions of R) - devel <- - identical(R.version[["status"]], "Under development (unstable)") || - identical(R.version[["nickname"]], "Unsuffered Consequences") - - if (devel) - prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") - - # build list of path components - components <- c(prefix, R.version$platform) - - # include prefix if provided by user - prefix <- renv_bootstrap_platform_prefix_impl() - if (!is.na(prefix) && nzchar(prefix)) - components <- c(prefix, components) - - # build prefix - paste(components, collapse = "/") - - } - - renv_bootstrap_platform_prefix_impl <- function() { - - # if an explicit prefix has been supplied, use it - prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) - if (!is.na(prefix)) - return(prefix) - - # if the user has requested an automatic prefix, generate it - auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) - if (auto %in% c("TRUE", "True", "true", "1")) - return(renv_bootstrap_platform_prefix_auto()) - - # empty string on failure - "" - - } - - renv_bootstrap_platform_prefix_auto <- function() { - - prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) - if (inherits(prefix, "error") || prefix %in% "unknown") { - - msg <- paste( - "failed to infer current operating system", - "please file a bug report at https://github.com/rstudio/renv/issues", - sep = "; " - ) - - warning(msg) - - } - - prefix - - } - - renv_bootstrap_platform_os <- function() { - - sysinfo <- Sys.info() - sysname <- sysinfo[["sysname"]] - - # handle Windows + macOS up front - if (sysname == "Windows") - return("windows") - else if (sysname == "Darwin") - return("macos") - - # check for os-release files - for (file in c("/etc/os-release", "/usr/lib/os-release")) - if (file.exists(file)) - return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) - - # check for redhat-release files - if (file.exists("/etc/redhat-release")) - return(renv_bootstrap_platform_os_via_redhat_release()) - - "unknown" - - } - - renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { - - # read /etc/os-release - release <- utils::read.table( - file = file, - sep = "=", - quote = c("\"", "'"), - col.names = c("Key", "Value"), - comment.char = "#", - stringsAsFactors = FALSE - ) - - vars <- as.list(release$Value) - names(vars) <- release$Key - - # get os name - os <- tolower(sysinfo[["sysname"]]) - - # read id - id <- "unknown" - for (field in c("ID", "ID_LIKE")) { - if (field %in% names(vars) && nzchar(vars[[field]])) { - id <- vars[[field]] - break - } - } - - # read version - version <- "unknown" - for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { - if (field %in% names(vars) && nzchar(vars[[field]])) { - version <- vars[[field]] - break - } - } - - # join together - paste(c(os, id, version), collapse = "-") - - } - - renv_bootstrap_platform_os_via_redhat_release <- function() { - - # read /etc/redhat-release - contents <- readLines("/etc/redhat-release", warn = FALSE) - - # infer id - id <- if (grepl("centos", contents, ignore.case = TRUE)) - "centos" - else if (grepl("redhat", contents, ignore.case = TRUE)) - "redhat" - else - "unknown" - - # try to find a version component (very hacky) - version <- "unknown" - - parts <- strsplit(contents, "[[:space:]]")[[1L]] - for (part in parts) { - - nv <- tryCatch(numeric_version(part), error = identity) - if (inherits(nv, "error")) - next - - version <- nv[1, 1] - break - - } - - paste(c("linux", id, version), collapse = "-") - - } - - renv_bootstrap_library_root_name <- function(project) { - - # use project name as-is if requested - asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") - if (asis) - return(basename(project)) - - # otherwise, disambiguate based on project's path - id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) - paste(basename(project), id, sep = "-") - - } - - renv_bootstrap_library_root <- function(project) { - - prefix <- renv_bootstrap_profile_prefix() - - path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) - if (!is.na(path)) - return(paste(c(path, prefix), collapse = "/")) - - path <- renv_bootstrap_library_root_impl(project) - if (!is.null(path)) { - name <- renv_bootstrap_library_root_name(project) - return(paste(c(path, prefix, name), collapse = "/")) - } - - renv_bootstrap_paths_renv("library", project = project) - - } - - renv_bootstrap_library_root_impl <- function(project) { - - root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) - if (!is.na(root)) - return(root) - - type <- renv_bootstrap_project_type(project) - if (identical(type, "package")) { - userdir <- renv_bootstrap_user_dir() - return(file.path(userdir, "library")) - } - - } - - renv_bootstrap_validate_version <- function(version, description = NULL) { - - # resolve description file - # - # avoid passing lib.loc to `packageDescription()` below, since R will - # use the loaded version of the package by default anyhow. note that - # this function should only be called after 'renv' is loaded - # https://github.com/rstudio/renv/issues/1625 - description <- description %||% packageDescription("renv") - - # check whether requested version 'version' matches loaded version of renv - sha <- attr(version, "sha", exact = TRUE) - valid <- if (!is.null(sha)) - renv_bootstrap_validate_version_dev(sha, description) - else - renv_bootstrap_validate_version_release(version, description) - - if (valid) - return(TRUE) - - # the loaded version of renv doesn't match the requested version; - # give the user instructions on how to proceed - remote <- if (!is.null(description[["RemoteSha"]])) { - paste("rstudio/renv", description[["RemoteSha"]], sep = "@") - } else { - paste("renv", description[["Version"]], sep = "@") - } - - # display both loaded version + sha if available - friendly <- renv_bootstrap_version_friendly( - version = description[["Version"]], - sha = description[["RemoteSha"]] - ) - - fmt <- paste( - "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - sep = "\n" - ) - catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) - - FALSE - - } - - renv_bootstrap_validate_version_dev <- function(version, description) { - expected <- description[["RemoteSha"]] - is.character(expected) && startswith(expected, version) - } - - renv_bootstrap_validate_version_release <- function(version, description) { - expected <- description[["Version"]] - is.character(expected) && identical(expected, version) - } - - renv_bootstrap_hash_text <- function(text) { - - hashfile <- tempfile("renv-hash-") - on.exit(unlink(hashfile), add = TRUE) - - writeLines(text, con = hashfile) - tools::md5sum(hashfile) - - } - - renv_bootstrap_load <- function(project, libpath, version) { - - # try to load renv from the project library - if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) - return(FALSE) - - # warn if the version of renv loaded does not match - renv_bootstrap_validate_version(version) - - # execute renv load hooks, if any - hooks <- getHook("renv::autoload") - for (hook in hooks) - if (is.function(hook)) - tryCatch(hook(), error = warnify) - - # load the project - renv::load(project) - - TRUE - - } - - renv_bootstrap_profile_load <- function(project) { - - # if RENV_PROFILE is already set, just use that - profile <- Sys.getenv("RENV_PROFILE", unset = NA) - if (!is.na(profile) && nzchar(profile)) - return(profile) - - # check for a profile file (nothing to do if it doesn't exist) - path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) - if (!file.exists(path)) - return(NULL) - - # read the profile, and set it if it exists - contents <- readLines(path, warn = FALSE) - if (length(contents) == 0L) - return(NULL) - - # set RENV_PROFILE - profile <- contents[[1L]] - if (!profile %in% c("", "default")) - Sys.setenv(RENV_PROFILE = profile) - - profile - - } - - renv_bootstrap_profile_prefix <- function() { - profile <- renv_bootstrap_profile_get() - if (!is.null(profile)) - return(file.path("profiles", profile, "renv")) - } - - renv_bootstrap_profile_get <- function() { - profile <- Sys.getenv("RENV_PROFILE", unset = "") - renv_bootstrap_profile_normalize(profile) - } - - renv_bootstrap_profile_set <- function(profile) { - profile <- renv_bootstrap_profile_normalize(profile) - if (is.null(profile)) - Sys.unsetenv("RENV_PROFILE") - else - Sys.setenv(RENV_PROFILE = profile) - } - - renv_bootstrap_profile_normalize <- function(profile) { - - if (is.null(profile) || profile %in% c("", "default")) - return(NULL) - - profile - - } - - renv_bootstrap_path_absolute <- function(path) { - - substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( - substr(path, 1L, 1L) %in% c(letters, LETTERS) && - substr(path, 2L, 3L) %in% c(":/", ":\\") - ) - - } - - renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { - renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") - root <- if (renv_bootstrap_path_absolute(renv)) NULL else project - prefix <- if (profile) renv_bootstrap_profile_prefix() - components <- c(root, renv, prefix, ...) - paste(components, collapse = "/") - } - - renv_bootstrap_project_type <- function(path) { - - descpath <- file.path(path, "DESCRIPTION") - if (!file.exists(descpath)) - return("unknown") - - desc <- tryCatch( - read.dcf(descpath, all = TRUE), - error = identity - ) - - if (inherits(desc, "error")) - return("unknown") - - type <- desc$Type - if (!is.null(type)) - return(tolower(type)) - - package <- desc$Package - if (!is.null(package)) - return("package") - - "unknown" - - } - - renv_bootstrap_user_dir <- function() { - dir <- renv_bootstrap_user_dir_impl() - path.expand(chartr("\\", "/", dir)) - } - - renv_bootstrap_user_dir_impl <- function() { - - # use local override if set - override <- getOption("renv.userdir.override") - if (!is.null(override)) - return(override) - - # use R_user_dir if available - tools <- asNamespace("tools") - if (is.function(tools$R_user_dir)) - return(tools$R_user_dir("renv", "cache")) - - # try using our own backfill for older versions of R - envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") - for (envvar in envvars) { - root <- Sys.getenv(envvar, unset = NA) - if (!is.na(root)) - return(file.path(root, "R/renv")) - } - - # use platform-specific default fallbacks - if (Sys.info()[["sysname"]] == "Windows") - file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") - else if (Sys.info()[["sysname"]] == "Darwin") - "~/Library/Caches/org.R-project.R/R/renv" - else - "~/.cache/R/renv" - - } - - renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { - sha <- sha %||% attr(version, "sha", exact = TRUE) - parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) - paste(parts, collapse = "") - } - - renv_bootstrap_exec <- function(project, libpath, version) { - if (!renv_bootstrap_load(project, libpath, version)) - renv_bootstrap_run(version, libpath) - } - - renv_bootstrap_run <- function(version, libpath) { - - # perform bootstrap - bootstrap(version, libpath) - - # exit early if we're just testing bootstrap - if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) - return(TRUE) - - # try again to load - if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - return(renv::load(project = getwd())) - } - - # failed to download or load renv; warn the user - msg <- c( - "Failed to find an renv installation: the project will not be loaded.", - "Use `renv::activate()` to re-initialize the project." - ) - - warning(paste(msg, collapse = "\n"), call. = FALSE) - - } - - renv_json_read <- function(file = NULL, text = NULL) { - - jlerr <- NULL - - # if jsonlite is loaded, use that instead - if ("jsonlite" %in% loadedNamespaces()) { - - json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) - if (!inherits(json, "error")) - return(json) - - jlerr <- json - - } - - # otherwise, fall back to the default JSON reader - json <- tryCatch(renv_json_read_default(file, text), error = identity) - if (!inherits(json, "error")) - return(json) - - # report an error - if (!is.null(jlerr)) - stop(jlerr) - else - stop(json) - - } - - renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - jsonlite::fromJSON(txt = text, simplifyVector = FALSE) - } - - renv_json_read_default <- function(file = NULL, text = NULL) { - - # find strings in the JSON - text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' - locs <- gregexpr(pattern, text, perl = TRUE)[[1]] - - # if any are found, replace them with placeholders - replaced <- text - strings <- character() - replacements <- character() - - if (!identical(c(locs), -1L)) { - - # get the string values - starts <- locs - ends <- locs + attr(locs, "match.length") - 1L - strings <- substring(text, starts, ends) - - # only keep those requiring escaping - strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) - - # compute replacements - replacements <- sprintf('"\032%i\032"', seq_along(strings)) - - # replace the strings - mapply(function(string, replacement) { - replaced <<- sub(string, replacement, replaced, fixed = TRUE) - }, strings, replacements) - - } - - # transform the JSON into something the R parser understands - transformed <- replaced - transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) - transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) - transformed <- gsub("[]}]", ")", transformed, perl = TRUE) - transformed <- gsub(":", "=", transformed, fixed = TRUE) - text <- paste(transformed, collapse = "\n") - - # parse it - json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] - - # construct map between source strings, replaced strings - map <- as.character(parse(text = strings)) - names(map) <- as.character(parse(text = replacements)) - - # convert to list - map <- as.list(map) - - # remap strings in object - remapped <- renv_json_read_remap(json, map) - - # evaluate - eval(remapped, envir = baseenv()) - - } - - renv_json_read_remap <- function(json, map) { - - # fix names - if (!is.null(names(json))) { - lhs <- match(names(json), names(map), nomatch = 0L) - rhs <- match(names(map), names(json), nomatch = 0L) - names(json)[rhs] <- map[lhs] - } - - # fix values - if (is.character(json)) - return(map[[json]] %||% json) - - # handle true, false, null - if (is.name(json)) { - text <- as.character(json) - if (text == "true") - return(TRUE) - else if (text == "false") - return(FALSE) - else if (text == "null") - return(NULL) - } - - # recurse - if (is.recursive(json)) { - for (i in seq_along(json)) { - json[i] <- list(renv_json_read_remap(json[[i]], map)) - } - } - - json - - } - - # load the renv profile, if any - renv_bootstrap_profile_load(project) - - # construct path to library root - root <- renv_bootstrap_library_root(project) - - # construct library prefix for platform - prefix <- renv_bootstrap_platform_prefix() - - # construct full libpath - libpath <- file.path(root, prefix) - - # run bootstrap code - renv_bootstrap_exec(project, libpath, version) - - invisible() - -}) diff --git a/renv/profiles/dev/renv.lock b/renv/profiles/dev/renv.lock deleted file mode 100644 index 478be64c..00000000 --- a/renv/profiles/dev/renv.lock +++ /dev/null @@ -1,1465 +0,0 @@ -{ - "R": { - "Version": "4.2.0", - "Repositories": [ - { - "Name": "CRAN", - "URL": "https://cran.rstudio.com" - } - ] - }, - "Packages": { - "R6": { - "Package": "R6", - "Version": "2.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "470851b6d5d0ac559e9d01bb352b4021", - "Requirements": [] - }, - "REDCapR": { - "Package": "REDCapR", - "Version": "1.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "e76c401b631961c865b89bb5a4ea3b97", - "Requirements": [ - "checkmate", - "dplyr", - "httr", - "jsonlite", - "magrittr", - "readr", - "rlang", - "tibble", - "tidyr" - ] - }, - "Rcpp": { - "Package": "Rcpp", - "Version": "1.0.9", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "e9c08b94391e9f3f97355841229124f2", - "Requirements": [] - }, - "askpass": { - "Package": "askpass", - "Version": "1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "e8a22846fff485f0be3770c2da758713", - "Requirements": [ - "sys" - ] - }, - "backports": { - "Package": "backports", - "Version": "1.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "c39fbec8a30d23e721980b8afb31984c", - "Requirements": [] - }, - "base64enc": { - "Package": "base64enc", - "Version": "0.1-3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "543776ae6848fde2f48ff3816d0628bc", - "Requirements": [] - }, - "bit": { - "Package": "bit", - "Version": "4.0.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f36715f14d94678eea9933af927bc15d", - "Requirements": [] - }, - "bit64": { - "Package": "bit64", - "Version": "4.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9fe98599ca456d6552421db0d6772d8f", - "Requirements": [ - "bit" - ] - }, - "brew": { - "Package": "brew", - "Version": "1.0-7", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "38875ea52350ff4b4c03849fc69736c8", - "Requirements": [] - }, - "brio": { - "Package": "brio", - "Version": "1.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "976cf154dfb043c012d87cddd8bca363", - "Requirements": [] - }, - "bslib": { - "Package": "bslib", - "Version": "0.4.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "be5ee090716ce1671be6cd5d7c34d091", - "Requirements": [ - "cachem", - "htmltools", - "jquerylib", - "jsonlite", - "memoise", - "rlang", - "sass" - ] - }, - "cachem": { - "Package": "cachem", - "Version": "1.0.6", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "648c5b3d71e6a37e3043617489a0a0e9", - "Requirements": [ - "fastmap", - "rlang" - ] - }, - "callr": { - "Package": "callr", - "Version": "3.7.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "358689cac9fe93b1bb3a19088d2dbed8", - "Requirements": [ - "R6", - "processx" - ] - }, - "checkmate": { - "Package": "checkmate", - "Version": "2.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "147e4db6909d8814bb30f671b49d7e06", - "Requirements": [ - "backports" - ] - }, - "cli": { - "Package": "cli", - "Version": "3.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "0d297d01734d2bcea40197bd4971a764", - "Requirements": [] - }, - "clipr": { - "Package": "clipr", - "Version": "0.8.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", - "Requirements": [] - }, - "clisymbols": { - "Package": "clisymbols", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "96c01552bfd5661b9bbdefbc762f4bcd", - "Requirements": [] - }, - "codetools": { - "Package": "codetools", - "Version": "0.2-18", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "019388fc48e48b3da0d3a76ff94608a8", - "Requirements": [] - }, - "commonmark": { - "Package": "commonmark", - "Version": "1.8.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "2ba81b120c1655ab696c935ef33ea716", - "Requirements": [] - }, - "covr": { - "Package": "covr", - "Version": "3.6.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a861cee34fbb4b107a73dd414ef56724", - "Requirements": [ - "crayon", - "digest", - "httr", - "jsonlite", - "rex", - "withr", - "yaml" - ] - }, - "cpp11": { - "Package": "cpp11", - "Version": "0.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "fa53ce256cd280f468c080a58ea5ba8c", - "Requirements": [] - }, - "crayon": { - "Package": "crayon", - "Version": "1.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8dc45fd8a1ee067a92b85ef274e66d6a", - "Requirements": [] - }, - "credentials": { - "Package": "credentials", - "Version": "1.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "93762d0a34d78e6a025efdbfb5c6bb41", - "Requirements": [ - "askpass", - "curl", - "jsonlite", - "openssl", - "sys" - ] - }, - "curl": { - "Package": "curl", - "Version": "4.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "022c42d49c28e95d69ca60446dbabf88", - "Requirements": [] - }, - "cyclocomp": { - "Package": "cyclocomp", - "Version": "1.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "53cbed70a2f7472d48fb6aef08442f25", - "Requirements": [ - "callr", - "crayon", - "desc", - "remotes", - "withr" - ] - }, - "desc": { - "Package": "desc", - "Version": "1.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", - "Requirements": [ - "R6", - "cli", - "rprojroot" - ] - }, - "devtools": { - "Package": "devtools", - "Version": "2.4.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "d6ad91ae6533b84d227bb0b5262c111f", - "Requirements": [ - "cli", - "desc", - "ellipsis", - "fs", - "lifecycle", - "memoise", - "miniUI", - "pkgbuild", - "pkgdown", - "pkgload", - "profvis", - "rcmdcheck", - "remotes", - "rlang", - "roxygen2", - "rversions", - "sessioninfo", - "testthat", - "urlchecker", - "usethis", - "withr" - ] - }, - "diffobj": { - "Package": "diffobj", - "Version": "0.3.5", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8", - "Requirements": [ - "crayon" - ] - }, - "digest": { - "Package": "digest", - "Version": "0.6.29", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "cf6b206a045a684728c3267ef7596190", - "Requirements": [] - }, - "downlit": { - "Package": "downlit", - "Version": "0.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "79bf3f66590752ffbba20f8d2da94c7c", - "Requirements": [ - "brio", - "desc", - "digest", - "evaluate", - "fansi", - "memoise", - "rlang", - "vctrs", - "withr", - "yaml" - ] - }, - "dplyr": { - "Package": "dplyr", - "Version": "1.0.10", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "539412282059f7f0c07295723d23f987", - "Requirements": [ - "R6", - "generics", - "glue", - "lifecycle", - "magrittr", - "pillar", - "rlang", - "tibble", - "tidyselect", - "vctrs" - ] - }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", - "Requirements": [ - "rlang" - ] - }, - "evaluate": { - "Package": "evaluate", - "Version": "0.16", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9a3d3c345f8a5648abe61608aaa29518", - "Requirements": [] - }, - "fansi": { - "Package": "fansi", - "Version": "1.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "83a8afdbe71839506baa9f90eebad7ec", - "Requirements": [] - }, - "fastmap": { - "Package": "fastmap", - "Version": "1.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", - "Requirements": [] - }, - "fontawesome": { - "Package": "fontawesome", - "Version": "0.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a36c4a3eade472039a3ec8cb824e6dc4", - "Requirements": [ - "htmltools", - "rlang" - ] - }, - "fs": { - "Package": "fs", - "Version": "1.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "7c89603d81793f0d5486d91ab1fc6f1d", - "Requirements": [] - }, - "generics": { - "Package": "generics", - "Version": "0.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "15e9634c0fcd294799e9b2e929ed1b86", - "Requirements": [] - }, - "gert": { - "Package": "gert", - "Version": "1.8.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "4bdd6588a3cbde071c7de6d07b66f1d3", - "Requirements": [ - "askpass", - "credentials", - "openssl", - "rstudioapi", - "sys", - "zip" - ] - }, - "gh": { - "Package": "gh", - "Version": "1.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b6a12054ee13dce0f6696c019c10e539", - "Requirements": [ - "cli", - "gitcreds", - "httr", - "ini", - "jsonlite" - ] - }, - "gitcreds": { - "Package": "gitcreds", - "Version": "0.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe", - "Requirements": [] - }, - "glue": { - "Package": "glue", - "Version": "1.6.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", - "Requirements": [] - }, - "goodpractice": { - "Package": "goodpractice", - "Version": "1.0.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "0f6da9489ee2bc6197a4a4e845b5a217", - "Requirements": [ - "clisymbols", - "covr", - "crayon", - "cyclocomp", - "desc", - "jsonlite", - "lintr", - "praise", - "rcmdcheck", - "rstudioapi", - "whoami", - "withr", - "xml2", - "xmlparsedata" - ] - }, - "highr": { - "Package": "highr", - "Version": "0.9", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8eb36c8125038e648e5d111c0d7b2ed4", - "Requirements": [ - "xfun" - ] - }, - "hms": { - "Package": "hms", - "Version": "1.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "41100392191e1244b887878b533eea91", - "Requirements": [ - "ellipsis", - "lifecycle", - "pkgconfig", - "rlang", - "vctrs" - ] - }, - "htmltools": { - "Package": "htmltools", - "Version": "0.5.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6496090a9e00f8354b811d1a2d47b566", - "Requirements": [ - "base64enc", - "digest", - "fastmap", - "rlang" - ] - }, - "htmlwidgets": { - "Package": "htmlwidgets", - "Version": "1.5.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb", - "Requirements": [ - "htmltools", - "jsonlite", - "yaml" - ] - }, - "httpuv": { - "Package": "httpuv", - "Version": "1.6.6", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "fd090e236ae2dc0f0cdf33a9ec83afb6", - "Requirements": [ - "R6", - "Rcpp", - "later", - "promises" - ] - }, - "httr": { - "Package": "httr", - "Version": "1.4.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "57557fac46471f0dbbf44705cc6a5c8c", - "Requirements": [ - "R6", - "curl", - "jsonlite", - "mime", - "openssl" - ] - }, - "hunspell": { - "Package": "hunspell", - "Version": "3.0.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "656219b6f3f605499d7cdbe208656639", - "Requirements": [ - "Rcpp", - "digest" - ] - }, - "ini": { - "Package": "ini", - "Version": "0.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6154ec2223172bce8162d4153cda21f7", - "Requirements": [] - }, - "jquerylib": { - "Package": "jquerylib", - "Version": "0.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "5aab57a3bd297eee1c1d862735972182", - "Requirements": [ - "htmltools" - ] - }, - "jsonlite": { - "Package": "jsonlite", - "Version": "1.8.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "d07e729b27b372429d42d24d503613a0", - "Requirements": [] - }, - "knitr": { - "Package": "knitr", - "Version": "1.40", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "caea8b0f899a0b1738444b9bc47067e7", - "Requirements": [ - "evaluate", - "highr", - "stringr", - "xfun", - "yaml" - ] - }, - "later": { - "Package": "later", - "Version": "1.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e", - "Requirements": [ - "Rcpp", - "rlang" - ] - }, - "lazyeval": { - "Package": "lazyeval", - "Version": "0.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "d908914ae53b04d4c0c0fd72ecc35370", - "Requirements": [] - }, - "lifecycle": { - "Package": "lifecycle", - "Version": "1.0.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "25f74670fa7d3277fe3ad8c1712a699f", - "Requirements": [ - "glue", - "rlang" - ] - }, - "lintr": { - "Package": "lintr", - "Version": "3.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "1214604176fb93fdcac030fc5d2177d9", - "Requirements": [ - "backports", - "codetools", - "crayon", - "cyclocomp", - "digest", - "glue", - "jsonlite", - "knitr", - "rex", - "xml2", - "xmlparsedata" - ] - }, - "magrittr": { - "Package": "magrittr", - "Version": "2.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "7ce2733a9826b3aeb1775d56fd305472", - "Requirements": [] - }, - "memoise": { - "Package": "memoise", - "Version": "2.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c", - "Requirements": [ - "cachem", - "rlang" - ] - }, - "mime": { - "Package": "mime", - "Version": "0.12", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "18e9c28c1d3ca1560ce30658b22ce104", - "Requirements": [] - }, - "miniUI": { - "Package": "miniUI", - "Version": "0.1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "fec5f52652d60615fdb3957b3d74324a", - "Requirements": [ - "htmltools", - "shiny" - ] - }, - "openssl": { - "Package": "openssl", - "Version": "2.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b9621e75c0652041002a19609fb23c5a", - "Requirements": [ - "askpass" - ] - }, - "pillar": { - "Package": "pillar", - "Version": "1.8.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f2316df30902c81729ae9de95ad5a608", - "Requirements": [ - "cli", - "fansi", - "glue", - "lifecycle", - "rlang", - "utf8", - "vctrs" - ] - }, - "pkgbuild": { - "Package": "pkgbuild", - "Version": "1.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "66d2adfed274daf81ccfe77d974c3b9b", - "Requirements": [ - "R6", - "callr", - "cli", - "crayon", - "desc", - "prettyunits", - "rprojroot", - "withr" - ] - }, - "pkgconfig": { - "Package": "pkgconfig", - "Version": "2.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "01f28d4278f15c76cddbea05899c5d6f", - "Requirements": [] - }, - "pkgdown": { - "Package": "pkgdown", - "Version": "2.0.6", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f958d0b2a5dabc5ffd414f062b1ffbe7", - "Requirements": [ - "bslib", - "callr", - "cli", - "desc", - "digest", - "downlit", - "fs", - "httr", - "jsonlite", - "magrittr", - "memoise", - "purrr", - "ragg", - "rlang", - "rmarkdown", - "tibble", - "whisker", - "withr", - "xml2", - "yaml" - ] - }, - "pkgload": { - "Package": "pkgload", - "Version": "1.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "4b20f937a363c78a5730265c1925f54a", - "Requirements": [ - "cli", - "crayon", - "desc", - "fs", - "glue", - "rlang", - "rprojroot", - "withr" - ] - }, - "praise": { - "Package": "praise", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a555924add98c99d2f411e37e7d25e9f", - "Requirements": [] - }, - "prettyunits": { - "Package": "prettyunits", - "Version": "1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", - "Requirements": [] - }, - "processx": { - "Package": "processx", - "Version": "3.7.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f91df0f5f31ffdf88bc0b624f5ebab0f", - "Requirements": [ - "R6", - "ps" - ] - }, - "profvis": { - "Package": "profvis", - "Version": "0.3.7", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "e9d21e79848e02e524bea6f5bd53e7e4", - "Requirements": [ - "htmlwidgets", - "stringr" - ] - }, - "progress": { - "Package": "progress", - "Version": "1.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061", - "Requirements": [ - "R6", - "crayon", - "hms", - "prettyunits" - ] - }, - "promises": { - "Package": "promises", - "Version": "1.2.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "4ab2c43adb4d4699cf3690acd378d75d", - "Requirements": [ - "R6", - "Rcpp", - "later", - "magrittr", - "rlang" - ] - }, - "ps": { - "Package": "ps", - "Version": "1.7.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8b93531308c01ad0e56d9eadcc0c4fcd", - "Requirements": [] - }, - "purrr": { - "Package": "purrr", - "Version": "0.3.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "97def703420c8ab10d8f0e6c72101e02", - "Requirements": [ - "magrittr", - "rlang" - ] - }, - "ragg": { - "Package": "ragg", - "Version": "1.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "14932bb6f2739c771ca4ceaba6b4248e", - "Requirements": [ - "systemfonts", - "textshaping" - ] - }, - "rappdirs": { - "Package": "rappdirs", - "Version": "0.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "5e3c5dc0b071b21fa128676560dbe94d", - "Requirements": [] - }, - "rcmdcheck": { - "Package": "rcmdcheck", - "Version": "1.4.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4", - "Requirements": [ - "R6", - "callr", - "cli", - "curl", - "desc", - "digest", - "pkgbuild", - "prettyunits", - "rprojroot", - "sessioninfo", - "withr", - "xopen" - ] - }, - "readr": { - "Package": "readr", - "Version": "2.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9c59de1357dc209868b5feb5c9f0fe2f", - "Requirements": [ - "R6", - "cli", - "clipr", - "cpp11", - "crayon", - "hms", - "lifecycle", - "rlang", - "tibble", - "tzdb", - "vroom" - ] - }, - "rematch2": { - "Package": "rematch2", - "Version": "2.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "76c9e04c712a05848ae7a23d2f170a40", - "Requirements": [ - "tibble" - ] - }, - "remotes": { - "Package": "remotes", - "Version": "2.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "227045be9aee47e6dda9bb38ac870d67", - "Requirements": [] - }, - "renv": { - "Package": "renv", - "Version": "0.15.5", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6a38294e7d12f5d8e656b08c5bd8ae34", - "Requirements": [] - }, - "rex": { - "Package": "rex", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "ae34cd56890607370665bee5bd17812f", - "Requirements": [ - "lazyeval" - ] - }, - "rlang": { - "Package": "rlang", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "971c3d698fc06dabdac6bc4bcda72dc4", - "Requirements": [] - }, - "rmarkdown": { - "Package": "rmarkdown", - "Version": "2.16", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "0f3eaa1547e2c6880d4de1c043ac6826", - "Requirements": [ - "bslib", - "evaluate", - "htmltools", - "jquerylib", - "jsonlite", - "knitr", - "stringr", - "tinytex", - "xfun", - "yaml" - ] - }, - "roxygen2": { - "Package": "roxygen2", - "Version": "7.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "da1f278262e563c835345872f2fef537", - "Requirements": [ - "R6", - "brew", - "cli", - "commonmark", - "cpp11", - "desc", - "digest", - "knitr", - "pkgload", - "purrr", - "rlang", - "stringi", - "stringr", - "withr", - "xml2" - ] - }, - "rprojroot": { - "Package": "rprojroot", - "Version": "2.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "1de7ab598047a87bba48434ba35d497d", - "Requirements": [] - }, - "rstudioapi": { - "Package": "rstudioapi", - "Version": "0.14", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "690bd2acc42a9166ce34845884459320", - "Requirements": [] - }, - "rversions": { - "Package": "rversions", - "Version": "2.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a9881dfed103e83f9de151dc17002cd1", - "Requirements": [ - "curl", - "xml2" - ] - }, - "sass": { - "Package": "sass", - "Version": "0.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "1b191143d7d3444d504277843f3a95fe", - "Requirements": [ - "R6", - "fs", - "htmltools", - "rappdirs", - "rlang" - ] - }, - "sessioninfo": { - "Package": "sessioninfo", - "Version": "1.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", - "Requirements": [ - "cli" - ] - }, - "shiny": { - "Package": "shiny", - "Version": "1.7.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "4f7970a3edb0a153ac6b376785a1944a", - "Requirements": [ - "R6", - "bslib", - "cachem", - "commonmark", - "crayon", - "ellipsis", - "fastmap", - "fontawesome", - "glue", - "htmltools", - "httpuv", - "jsonlite", - "later", - "lifecycle", - "mime", - "promises", - "rlang", - "sourcetools", - "withr", - "xtable" - ] - }, - "sourcetools": { - "Package": "sourcetools", - "Version": "0.1.7", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "947e4e02a79effa5d512473e10f41797", - "Requirements": [] - }, - "spelling": { - "Package": "spelling", - "Version": "2.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b8c899a5c83f0d897286550481c91798", - "Requirements": [ - "commonmark", - "hunspell", - "knitr", - "xml2" - ] - }, - "stringi": { - "Package": "stringi", - "Version": "1.7.8", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a68b980681bcbc84c7a67003fa796bfb", - "Requirements": [] - }, - "stringr": { - "Package": "stringr", - "Version": "1.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a66ad12140cd34d4f9dfcc19e84fc2a5", - "Requirements": [ - "glue", - "magrittr", - "stringi" - ] - }, - "sys": { - "Package": "sys", - "Version": "3.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b227d13e29222b4574486cfcbde077fa", - "Requirements": [] - }, - "systemfonts": { - "Package": "systemfonts", - "Version": "1.0.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "90b28393209827327de889f49935140a", - "Requirements": [ - "cpp11" - ] - }, - "testthat": { - "Package": "testthat", - "Version": "3.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f76c2a02d0fdc24aa7a47ea34261a6e3", - "Requirements": [ - "R6", - "brio", - "callr", - "cli", - "crayon", - "desc", - "digest", - "ellipsis", - "evaluate", - "jsonlite", - "lifecycle", - "magrittr", - "pkgload", - "praise", - "processx", - "ps", - "rlang", - "waldo", - "withr" - ] - }, - "textshaping": { - "Package": "textshaping", - "Version": "0.3.6", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "1ab6223d3670fac7143202cb6a2d43d5", - "Requirements": [ - "cpp11", - "systemfonts" - ] - }, - "tibble": { - "Package": "tibble", - "Version": "3.1.8", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "56b6934ef0f8c68225949a8672fe1a8f", - "Requirements": [ - "fansi", - "lifecycle", - "magrittr", - "pillar", - "pkgconfig", - "rlang", - "vctrs" - ] - }, - "tidyr": { - "Package": "tidyr", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "cdb403db0de33ccd1b6f53b83736efa8", - "Requirements": [ - "cpp11", - "dplyr", - "ellipsis", - "glue", - "lifecycle", - "magrittr", - "purrr", - "rlang", - "tibble", - "tidyselect", - "vctrs" - ] - }, - "tidyselect": { - "Package": "tidyselect", - "Version": "1.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "17f6da8cfd7002760a859915ce7eef8f", - "Requirements": [ - "ellipsis", - "glue", - "purrr", - "rlang", - "vctrs" - ] - }, - "tinytex": { - "Package": "tinytex", - "Version": "0.41", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6edfe5df6431a724b4254c0591e34ab3", - "Requirements": [ - "xfun" - ] - }, - "tzdb": { - "Package": "tzdb", - "Version": "0.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e", - "Requirements": [ - "cpp11" - ] - }, - "urlchecker": { - "Package": "urlchecker", - "Version": "1.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "409328b8e1253c8d729a7836fe7f7a16", - "Requirements": [ - "cli", - "curl", - "xml2" - ] - }, - "usethis": { - "Package": "usethis", - "Version": "2.1.6", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a67a22c201832b12c036cc059f1d137d", - "Requirements": [ - "cli", - "clipr", - "crayon", - "curl", - "desc", - "fs", - "gert", - "gh", - "glue", - "jsonlite", - "lifecycle", - "purrr", - "rappdirs", - "rlang", - "rprojroot", - "rstudioapi", - "whisker", - "withr", - "yaml" - ] - }, - "utf8": { - "Package": "utf8", - "Version": "1.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "c9c462b759a5cc844ae25b5942654d13", - "Requirements": [] - }, - "vctrs": { - "Package": "vctrs", - "Version": "0.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8b54f22e2a58c4f275479c92ce041a57", - "Requirements": [ - "cli", - "glue", - "rlang" - ] - }, - "vroom": { - "Package": "vroom", - "Version": "1.5.7", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "976507b5a105bc3bdf6a5a5f29e0684f", - "Requirements": [ - "bit64", - "cli", - "cpp11", - "crayon", - "glue", - "hms", - "lifecycle", - "progress", - "rlang", - "tibble", - "tidyselect", - "tzdb", - "vctrs", - "withr" - ] - }, - "waldo": { - "Package": "waldo", - "Version": "0.4.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "035fba89d0c86e2113120f93301b98ad", - "Requirements": [ - "cli", - "diffobj", - "fansi", - "glue", - "rematch2", - "rlang", - "tibble" - ] - }, - "whisker": { - "Package": "whisker", - "Version": "0.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "ca970b96d894e90397ed20637a0c1bbe", - "Requirements": [] - }, - "whoami": { - "Package": "whoami", - "Version": "1.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "ef0f4d9b8f2cc2ebeccae1d725b8a023", - "Requirements": [ - "httr", - "jsonlite" - ] - }, - "withr": { - "Package": "withr", - "Version": "2.5.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "c0e49a9760983e81e55cdd9be92e7182", - "Requirements": [] - }, - "xfun": { - "Package": "xfun", - "Version": "0.33", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "1a666f915cd65072f4ccf5b2888d5d39", - "Requirements": [] - }, - "xml2": { - "Package": "xml2", - "Version": "1.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "40682ed6a969ea5abfd351eb67833adc", - "Requirements": [] - }, - "xmlparsedata": { - "Package": "xmlparsedata", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "45e4bf3c46476896e821fc0a408fb4fc", - "Requirements": [] - }, - "xopen": { - "Package": "xopen", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6c85f015dee9cc7710ddd20f86881f58", - "Requirements": [ - "processx" - ] - }, - "xtable": { - "Package": "xtable", - "Version": "1.8-4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", - "Requirements": [] - }, - "yaml": { - "Package": "yaml", - "Version": "2.3.5", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "458bb38374d73bf83b1bb85e353da200", - "Requirements": [] - }, - "zip": { - "Package": "zip", - "Version": "2.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "a7e91189fa51d9029a30eba3831ce53f", - "Requirements": [] - } - } -} diff --git a/renv/profiles/dev/renv/.gitignore b/renv/profiles/dev/renv/.gitignore deleted file mode 100644 index 275e4ca3..00000000 --- a/renv/profiles/dev/renv/.gitignore +++ /dev/null @@ -1,6 +0,0 @@ -library/ -local/ -cellar/ -lock/ -python/ -staging/ diff --git a/renv/settings.dcf b/renv/settings.dcf deleted file mode 100644 index 0ca4d87e..00000000 --- a/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: -package.dependency.fields: Imports, Depends, LinkingTo -r.version: 4.2.0 -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE diff --git a/renv/settings.json b/renv/settings.json deleted file mode 100644 index 08d0def7..00000000 --- a/renv/settings.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "bioconductor.version": [], - "external.libraries": [], - "ignored.packages": [], - "package.dependency.fields": [ - "Imports", - "Depends", - "LinkingTo" - ], - "ppm.enabled": null, - "ppm.ignored.urls": [], - "r.version": "4.4.0", - "snapshot.type": "implicit", - "use.cache": true, - "vcs.ignore.cellar": true, - "vcs.ignore.library": true, - "vcs.ignore.local": true, - "vcs.manage.ignores": true -} diff --git a/tests/testthat/test-read_redcap.R b/tests/testthat/test-read_redcap.R index 769b0d53..59f1d762 100644 --- a/tests/testthat/test-read_redcap.R +++ b/tests/testthat/test-read_redcap.R @@ -680,5 +680,4 @@ test_that("get_repeat_event_types() works", { ) expect_equal(out, expected_out) - }) diff --git a/utility/cli_message_examples_reprex.md b/utility/cli_message_examples_reprex.md index 4234a231..2413a8d8 100644 --- a/utility/cli_message_examples_reprex.md +++ b/utility/cli_message_examples_reprex.md @@ -34,13 +34,9 @@ read_redcap(letters[1:3], classic_token) read_redcap("https://www.google.com", classic_token) #> Error in `read_redcap()`: #> ✖ The REDCapR export operation was not successful. -#> ! An unexpected error occured. -#> ℹ This means that you probably discovered a bug! -#> ℹ Please consider submitting a bug report here: -#> . -#> Caused by error in `redcap_metadata_read()`: -#> ! The REDCapR metadata export operation was not successful. The error message was: -#>

404 Not Found

+#> ! The URL returned the HTTP error code 405 (POST Method not allowed). +#> ℹ Are you sure the URI points to an active REDCap API endpoint? +#> ℹ URI: `https://www.google.com` read_redcap("https://www.google.comm", classic_token) #> Error in `read_redcap()`: @@ -63,13 +59,13 @@ read_redcap(redcap_uri, letters[1:3]) read_redcap(redcap_uri, "") #> Error in `read_redcap()`: -#> ✖ The token is an empty string, not a valid 32-character hexademical -#> value. +#> ✖ The token is an empty string, which is not allowed. #> ℹ API token: `` read_redcap(redcap_uri, "CC0CE44238EF65C5DA26A55DD749AF7") # 31 hex characters #> Error in `read_redcap()`: -#> ✖ The token is not a valid 32-character hexademical value. +#> ✖ The token does not conform with the regex +#> `^([0-9A-Fa-f]{32})(?:\n)?$`. #> ℹ API token: `CC0CE44238EF65C5DA26A55DD749AF7` read_redcap(redcap_uri, "CC0CE44238EF65C5DA26A55DD749AF7A") # will be rejected by server @@ -259,7 +255,7 @@ withr::with_tempdir({ }) #> Error: #> ✖ File -#> ''/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmp1QPC0p/file5c744dd73619/temp.csv'' +#> ''/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/Rtmph4LQ3Z/filee5aa7b9bea48/temp.csv'' #> already exists. #> ℹ Overwriting files is disabled by default. Set `overwrite = TRUE` to overwrite #> existing file. @@ -300,25 +296,26 @@ withr::with_tempdir({ write_redcap_xlsx(file = filepath) }) #> Warning in write_redcap_xlsx(., file = filepath): ! No extension provided for `file`: -#> '/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmp1QPC0p/file5c7456597c2b/temp' +#> '/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/Rtmph4LQ3Z/filee5aa11455c98/temp' #> ℹ The extension '.xlsx' will be appended to the file name. # Printed supertibble read_redcap(Sys.getenv("REDCAP_URI"), Sys.getenv("REDCAPTIDIER_CLASSIC_API")) %>% suppressWarnings() -#> # A REDCapTidieR Supertibble with 9 instruments -#> redcap_form_name redcap_form_label redcap_data redcap_metadata structure -#> -#> 1 nonrepeated Nonrepeated nonrepea… -#> 2 nonrepeated2 Nonrepeated2 nonrepea… -#> 3 repeated Repeated repeating -#> 4 data_field_types Data Field Types nonrepea… -#> 5 text_input_validation… Text Input Valid… nonrepea… -#> 6 api_no_access API No Access nonrepea… -#> 7 api_no_access_2 API No Access 2 nonrepea… -#> 8 survey Survey nonrepea… -#> 9 repeat_survey Repeat Survey repeating +#> # A REDCapTidieR Supertibble with 10 instruments +#> redcap_form_name redcap_form_label redcap_data redcap_metadata structure +#> +#> 1 nonrepeated Nonrepeated nonrepea… +#> 2 nonrepeated2 Nonrepeated2 nonrepea… +#> 3 repeated Repeated repeating +#> 4 data_field_types Data Field Types nonrepea… +#> 5 text_input_validatio… Text Input Valid… nonrepea… +#> 6 api_no_access API No Access nonrepea… +#> 7 api_no_access_2 API No Access 2 nonrepea… +#> 8 survey Survey nonrepea… +#> 9 repeat_survey Repeat Survey repeating +#> 10 labelled_vignette Labelled Vignette nonrepea… #> # ℹ 5 more variables: data_rows , data_cols , data_size , #> # data_na_pct , form_complete_pct @@ -343,4 +340,4 @@ read_redcap(redcap_uri, Sys.getenv("REDCAPTIDIER_MDC_API")) #> # data_na_pct , form_complete_pct ``` -Created on 2024-04-10 with [reprex v2.1.0](https://reprex.tidyverse.org) +Created on 2024-10-16 with [reprex v2.1.0](https://reprex.tidyverse.org) diff --git a/utility/microbenchmark_results.csv b/utility/microbenchmark_results.csv index a7186b18..d572548a 100644 --- a/utility/microbenchmark_results.csv +++ b/utility/microbenchmark_results.csv @@ -1,42 +1,42 @@ min,lq,mean,median,uq,max,neval,description,source -1.15,1.15,1.15,1.15,1.15,1.15,1,simple static (read-only) test project,ouhsc -1.7,1.7,1.7,1.7,1.7,1.7,1,longitudinal (read-only) ARM test project,ouhsc -0.83,0.83,0.83,0.83,0.83,0.83,1,simple write data,ouhsc -1.79,1.79,1.79,1.79,1.79,1.79,1,Russian Characters,ouhsc -3.37,3.37,3.37,3.37,3.37,3.37,1,"super-wide --3,000 columns",ouhsc -1,1,1,1,1,1,1,static (not longitudinal) survey test project,ouhsc -0.82,0.82,0.82,0.82,0.82,0.82,1,"Clinical Trial (Fake) --Read-only, contributed by @higgi13425",ouhsc -0.77,0.77,0.77,0.77,0.77,0.77,1,nonnumeric record_id,ouhsc -0.94,0.94,0.94,0.94,0.94,0.94,1,DAG Read,ouhsc -0.82,0.82,0.82,0.82,0.82,0.82,1,potentially problematic values,ouhsc -0.81,0.81,0.81,0.81,0.81,0.81,1,Repeating Instruments,ouhsc -0.81,0.81,0.81,0.81,0.81,0.81,1,simple write metadata,ouhsc -0.81,0.81,0.81,0.81,0.81,0.81,1,DAG Write -admin,ouhsc -0.81,0.81,0.81,0.81,0.81,0.81,1,DAG Write -group A,ouhsc -129.61,129.61,129.61,129.61,129.61,129.61,1,"super-wide #3--35,000 columns",ouhsc -0.82,0.82,0.82,0.82,0.82,0.82,1,Repeating Instruments --Sparse,ouhsc -0.8,0.8,0.8,0.8,0.8,0.8,1,Delete Single Arm,ouhsc -1.29,1.29,1.29,1.29,1.29,1.29,1,Delete Multiple Arm,ouhsc -1.55,1.55,1.55,1.55,1.55,1.55,1,longitudinal single arm,ouhsc -0.78,0.78,0.78,0.78,0.78,0.78,1,decimal comma and dot,ouhsc -0.82,0.82,0.82,0.82,0.82,0.82,1,decimal comma,ouhsc -0.81,0.81,0.81,0.81,0.81,0.81,1,decimal dot,ouhsc -0.87,0.87,0.87,0.87,0.87,0.87,1,Validation Types,ouhsc -0.81,0.81,0.81,0.81,0.81,0.81,1,Blank for Gray Status,ouhsc -0.97,0.97,0.97,0.97,0.97,0.97,1,Checkboxes 1,ouhsc -0.83,0.83,0.83,0.83,0.83,0.83,1,Vignette: Longitudinal & Repeating Measures,ouhsc -1.11,1.11,1.11,1.11,1.11,1.11,1,classic,redcaptidier -0.98,0.98,0.98,0.98,0.98,0.98,1,classic no repeat,redcaptidier -1.7,1.7,1.7,1.7,1.7,1.7,1,longitudinal,redcaptidier -1.67,1.67,1.67,1.67,1.67,1.67,1,longitudinal no arms,redcaptidier -1.51,1.51,1.51,1.51,1.51,1.51,1,longitudinal no repeat,redcaptidier -1.96,1.96,1.96,1.96,1.96,1.96,1,deep dive vignette,redcaptidier -0.99,0.99,0.99,0.99,0.99,0.99,1,repeat first instrument,redcaptidier -1.51,1.51,1.51,1.51,1.51,1.51,1,repeat event,redcaptidier -1.04,1.04,1.04,1.04,1.04,1.04,1,restricted access,redcaptidier -0.97,0.97,0.97,0.97,0.97,0.97,1,large sparse db,redcaptidier -1.13,1.13,1.13,1.13,1.13,1.13,1,data access groups,redcaptidier -1.78,1.78,1.78,1.78,1.78,1.78,1,longitudinal data access groups,redcaptidier -2.06,2.06,2.06,2.06,2.06,2.06,1,mixed structure repeat no repeat,redcaptidier -4.62,4.62,4.62,4.62,4.62,4.62,1,prodigy db,redcaptidier -5.26,5.26,5.26,5.26,5.26,5.26,1,cart comprehensive db,redcaptidier +0.96,0.96,0.96,0.96,0.96,0.96,1,simple static (read-only) test project,ouhsc +2.35,2.35,2.35,2.35,2.35,2.35,1,longitudinal (read-only) ARM test project,ouhsc +0.99,0.99,0.99,0.99,0.99,0.99,1,simple write data,ouhsc +4.29,4.29,4.29,4.29,4.29,4.29,1,Russian Characters,ouhsc +6.67,6.67,6.67,6.67,6.67,6.67,1,"super-wide --3,000 columns",ouhsc +1.72,1.72,1.72,1.72,1.72,1.72,1,static (not longitudinal) survey test project,ouhsc +1.43,1.43,1.43,1.43,1.43,1.43,1,"Clinical Trial (Fake) --Read-only, contributed by @higgi13425",ouhsc +1.12,1.12,1.12,1.12,1.12,1.12,1,nonnumeric record_id,ouhsc +0.97,0.97,0.97,0.97,0.97,0.97,1,DAG Read,ouhsc +0.9,0.9,0.9,0.9,0.9,0.9,1,potentially problematic values,ouhsc +1.13,1.13,1.13,1.13,1.13,1.13,1,simple write metadata,ouhsc +0.89,0.89,0.89,0.89,0.89,0.89,1,DAG Write -admin,ouhsc +0.95,0.95,0.95,0.95,0.95,0.95,1,DAG Write -group A,ouhsc +1278.89,1278.89,1278.89,1278.89,1278.89,1278.89,1,"super-wide #3--35,000 columns",ouhsc +0.99,0.99,0.99,0.99,0.99,0.99,1,Repeating Instruments --Sparse,ouhsc +1.1,1.1,1.1,1.1,1.1,1.1,1,Delete Single Arm,ouhsc +2.35,2.35,2.35,2.35,2.35,2.35,1,Delete Multiple Arm,ouhsc +2.13,2.13,2.13,2.13,2.13,2.13,1,longitudinal single arm,ouhsc +1.25,1.25,1.25,1.25,1.25,1.25,1,decimal comma and dot,ouhsc +1.32,1.32,1.32,1.32,1.32,1.32,1,decimal comma,ouhsc +1.09,1.09,1.09,1.09,1.09,1.09,1,decimal dot,ouhsc +1.21,1.21,1.21,1.21,1.21,1.21,1,Validation Types,ouhsc +0.99,0.99,0.99,0.99,0.99,0.99,1,Blank for Gray Status,ouhsc +1.32,1.32,1.32,1.32,1.32,1.32,1,Checkboxes 1,ouhsc +1.13,1.13,1.13,1.13,1.13,1.13,1,Vignette: Longitudinal & Repeating Measures,ouhsc +3.01,3.01,3.01,3.01,3.01,3.01,1,classic,redcaptidier +3.34,3.34,3.34,3.34,3.34,3.34,1,classic no repeat,redcaptidier +3.1,3.1,3.1,3.1,3.1,3.1,1,longitudinal,redcaptidier +2.88,2.88,2.88,2.88,2.88,2.88,1,longitudinal no arms,redcaptidier +3.5,3.5,3.5,3.5,3.5,3.5,1,longitudinal no repeat,redcaptidier +5.16,5.16,5.16,5.16,5.16,5.16,1,deep dive vignette,redcaptidier +2.8,2.8,2.8,2.8,2.8,2.8,1,repeat first instrument,redcaptidier +4.69,4.69,4.69,4.69,4.69,4.69,1,repeat event,redcaptidier +2.42,2.42,2.42,2.42,2.42,2.42,1,restricted access,redcaptidier +1.99,1.99,1.99,1.99,1.99,1.99,1,large sparse db,redcaptidier +1.63,1.63,1.63,1.63,1.63,1.63,1,data access groups,redcaptidier +3.62,3.62,3.62,3.62,3.62,3.62,1,longitudinal data access groups,redcaptidier +3.16,3.16,3.16,3.16,3.16,3.16,1,mixed structure repeat no repeat,redcaptidier +11.29,11.29,11.29,11.29,11.29,11.29,1,prodigy db,redcaptidier +15.8,15.8,15.8,15.8,15.8,15.8,1,cart comprehensive db,redcaptidier +34.07,34.07,34.07,34.07,34.07,34.07,1,bmt outcomes db,redcaptidier diff --git a/utility/refresh.R b/utility/refresh.R index 82518bda..9117db43 100644 --- a/utility/refresh.R +++ b/utility/refresh.R @@ -64,10 +64,10 @@ devtools::check( # Equivalent of R-hub incoming = TRUE ) # Approx matches to https://cran.r-project.org/web/checks/check_flavors.html -rhub::rhub_check(platforms = c("linux", "windows", "ubuntu-next", "ubuntu-release")) -devtools::check_win_devel(email = "porterej@chop.edu") # CRAN submission policies encourage the development version +rhub::rhub_check(platforms = c("linux", "windows", "ubuntu-next", "ubuntu-release")) # These will be available in GitHub Actions +devtools::check_win_devel(email = "hannar1@chop.edu") # CRAN submission policies encourage the development version # Note: Must be off of VPN -# revdepcheck::revdep_check(num_workers = 4) # Deprecated +# To run reverse dependency check, manually trigger the "Revere dependency check" workflow in GitHub Actions # Careful, the last question ultimately uploads it to CRAN, where you can't delete/reverse your decision. # Run as not CRAN to build full vignettes # withr::with_envvar( diff --git a/utility/test_creds.R b/utility/test_creds.R index 4f8fbf1b..849df456 100644 --- a/utility/test_creds.R +++ b/utility/test_creds.R @@ -9,12 +9,13 @@ ouhsc_creds <- readr::read_csv(file = "utility/redcapr.example.credentials", ski select(redcap_uri, token, comment) # Remove identified APIs that don't work -ouhsc_creds <- ouhsc_creds[-c(5,6,10,15,19),] +ouhsc_creds <- ouhsc_creds[-c(5,6,10,14,15,19),] # Empty rows (dataframe with 0 rows, 0 columns) # Single Column (dataframe with 0 rows, 0 columns) # Missing/invalid token, "---" (REDCapR errors as well) # Potentially problematic dictionary (dataframe with 0 rows, 0 columns) # super-wide #2--5,785 columns (dataframe with 0 rows, 0 columns) +# repeat instrument, no longer a working api key # Load REDCapTidieR and CGTI creds redcaptidier_creds <- tibble::tribble( diff --git a/vignettes/REDCapTidieR.Rmd b/vignettes/REDCapTidieR.Rmd index d70be3bd..c31cecff 100644 --- a/vignettes/REDCapTidieR.Rmd +++ b/vignettes/REDCapTidieR.Rmd @@ -26,7 +26,7 @@ redcap_uri <- Sys.getenv("REDCAP_URI") token <- Sys.getenv("SUPERHEROES_REDCAP_API") ``` -[REDCap](https://www.project-redcap.org/) is an electronic data capture software that is widely used in the academic research community. The [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package streamlines calls to the REDCap API from an R environment. One of REDCapR's main uses is to [import](glossary.html#import) [records](glossary.html#record) from a REDCap [project](glossary.html#project). This works well for simple projects, however becomes ugly when complex databases that include [longitudinal](glossary.html#longitudinal-project) structure and/or [repeating](glossary.html#repeating) [instruments](glossary.html#instrument) are involved. +[REDCap](https://projectredcap.org/) is an electronic data capture software that is widely used in the academic research community. The [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package streamlines calls to the REDCap API from an R environment. One of REDCapR's main uses is to [import](glossary.html#import) [records](glossary.html#record) from a REDCap [project](glossary.html#project). This works well for simple projects, however becomes ugly when complex databases that include [longitudinal](glossary.html#longitudinal-project) structure and/or [repeating](glossary.html#repeating) [instruments](glossary.html#instrument) are involved. The REDCapTidieR package aims to make the life of analysts who deal with complex REDCap databases easier. It builds upon **REDCapR** to make its output **tidier**. Instead of [one large data frame that contains all the data from your project](glossary.html#block-matrix), you get to work with a set of [tidy](glossary.html#tidy) [tibbles](glossary.html#tibble), one for each REDCap [instrument](glossary.html#instrument).