From 9bb6fd083167a6550f70b807bfc339df656960a0 Mon Sep 17 00:00:00 2001 From: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> Date: Mon, 10 Jun 2024 09:15:17 +0100 Subject: [PATCH] Closes #221 #222 #231 - remove renv, update PR template, remove non-ascii chars (#233) * #221 remove renv * #222 updated PR template * #231 remove non-ascii chars --- .Rbuildignore | 2 - .Rprofile | 48 - .github/pull_request_template.md | 18 +- LICENSE.md | 32 +- R/convert_etdrs_to_logmar.R | 2 +- R/convert_logmar_to_etdrs.R | 2 +- README.md | 4 +- inst/WORDLIST | 3 +- man/convert_etdrs_to_logmar.Rd | 2 +- man/convert_logmar_to_etdrs.Rd | 2 +- renv.lock | 1701 ------------------------ renv/.gitignore | 8 - renv/activate.R | 1181 ----------------- renv/profiles/4.1/renv.lock | 1701 ------------------------ renv/profiles/4.1/renv/.gitignore | 7 - renv/profiles/4.1/renv/settings.json | 25 - renv/profiles/4.2/renv.lock | 1785 -------------------------- renv/profiles/4.2/renv/.gitignore | 7 - renv/profiles/4.2/renv/settings.json | 25 - renv/profiles/4.3/renv.lock | 1785 -------------------------- renv/profiles/4.3/renv/.gitignore | 7 - renv/profiles/4.3/renv/settings.json | 25 - renv/settings.json | 24 - 23 files changed, 32 insertions(+), 8364 deletions(-) delete mode 100644 .Rprofile delete mode 100644 renv.lock delete mode 100644 renv/.gitignore delete mode 100644 renv/activate.R delete mode 100644 renv/profiles/4.1/renv.lock delete mode 100644 renv/profiles/4.1/renv/.gitignore delete mode 100644 renv/profiles/4.1/renv/settings.json delete mode 100644 renv/profiles/4.2/renv.lock delete mode 100644 renv/profiles/4.2/renv/.gitignore delete mode 100644 renv/profiles/4.2/renv/settings.json delete mode 100644 renv/profiles/4.3/renv.lock delete mode 100644 renv/profiles/4.3/renv/.gitignore delete mode 100644 renv/profiles/4.3/renv/settings.json delete mode 100644 renv/settings.json diff --git a/.Rbuildignore b/.Rbuildignore index 1656ec68..90bf411e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,3 @@ -^renv$ -^renv\.lock$ ^.*\.Rproj$ ^.*\.lycheeignore$ ^\.Rproj\.user$ diff --git a/.Rprofile b/.Rprofile deleted file mode 100644 index d059c2fc..00000000 --- a/.Rprofile +++ /dev/null @@ -1,48 +0,0 @@ -# Set renv profile base on R version. -.get_dependencies <- function(project_dir) { - - admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE) - adm_dev_suggests <- if(length(admdev_loc) != 0) { - renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests")) - } else { - data.frame(Packages = character(0)) - } - suggests_packages <- renv:::renv_dependencies_discover_description(project_dir, fields = "Suggests") - - packages <- names( - renv:::renv_package_dependencies( - unique(c( - project_dir, - adm_dev_suggests[["Package"]], - suggests_packages[["Package"]], - c("staged.dependencies", "renv", "styler") - )) - ) - ) - packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))] -} - -options(renv.snapshot.filter = .get_dependencies) - -.renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") -if (!file.exists("./renv/profile")) { - if (.renv_profile %in% c("4.1", "4.2", "4.3")) { - message("Set renv profile to `", .renv_profile, "`") - Sys.setenv("RENV_PROFILE" = .renv_profile) - } else { - message("This repository do not contains the renv profile for your R version.") - } -} else { - message( - "Using renv profile from `renv/profile` file.\n", - "The `", readLines("./renv/profile"), "` profile will be used." - ) -} - -if (Sys.getenv("GITHUB_ACTIONS") != "") { - options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest")) - Sys.setenv("RENV_AUTOLOADER_ENABLED" = FALSE) -} -Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE) -Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE) -source("renv/activate.R") diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 88626f9e..178752ee 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,18 +1,18 @@ -Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent. +Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral family codebase remains robust and consistent. Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `main` branch until you have checked off each task. -- [ ] Place Closes # into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update) -- [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files -- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html) +- [ ] Place Closes # into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update). +- [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files. +- [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios) - [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)? -- [ ] Update to all relevant roxygen headers and examples. -- [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately +- [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions] +- [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately. - [ ] Address any updates needed for vignettes and/or templates -- [ ] Update `NEWS.md` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers) +- [ ] Update `NEWS.md` under the header `# admiralophtha (development version)` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers) - [ ] Build admiralophtha site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiralophtha/reference/index.html)" page. -- [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()` -- [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()` +- [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`. +- [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`. - [ ] Link the issue so that it closes after successful merging. - [ ] Address all merge conflicts and resolve appropriately. - [ ] Pat yourself on the back for a job well done! Much love to your accomplishment! diff --git a/LICENSE.md b/LICENSE.md index 37d7bd9f..afd77eb2 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -8,55 +8,55 @@ _<>_ #### 1. Definitions -“License” shall mean the terms and conditions for use, reproduction, and +"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. -“Licensor” shall mean the copyright owner or entity authorized by the copyright +"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. -“Legal Entity” shall mean the union of the acting entity and all other entities +"Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. -For the purposes of this definition, “control” means **(i)** the power, direct or +For the purposes of this definition, "control" means **(i)** the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or **(ii)** ownership of fifty percent (50%) or more of the outstanding shares, or **(iii)** beneficial ownership of such entity. -“You” (or “Your”) shall mean an individual or Legal Entity exercising +"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. -“Source” form shall mean the preferred form for making modifications, including +"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. -“Object” form shall mean any form resulting from mechanical transformation or +"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. -“Work” shall mean the work of authorship, whether in Source or Object form, made +"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). -“Derivative Works” shall mean any work, whether in Source or Object form, that +"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. -“Contribution” shall mean any work of authorship, including the original version +"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, -“submitted” means any form of electronic, verbal, or written communication sent +"submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright -owner as “Not a Contribution.” +owner as "Not a Contribution." -“Contributor” shall mean Licensor and any individual or Legal Entity on behalf +"Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. @@ -97,7 +97,7 @@ changed the files; and all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and -* **(d)** If the Work includes a “NOTICE” text file as part of its distribution, then any +* **(d)** If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the @@ -136,7 +136,7 @@ reproducing the content of the NOTICE file. #### 7. Disclaimer of Warranty Unless required by applicable law or agreed to in writing, Licensor provides the -Work (and each Contributor provides its Contributions) on an “AS IS” BASIS, +Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are @@ -176,7 +176,7 @@ notice, with the fields enclosed by brackets `[]` replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on -the same “printed page” as the copyright notice for easier identification within +the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright 2021 F. Hoffmann-La Roche AG and GlaxoSmithKline LLC diff --git a/R/convert_etdrs_to_logmar.R b/R/convert_etdrs_to_logmar.R index 3022e032..d208ddbd 100644 --- a/R/convert_etdrs_to_logmar.R +++ b/R/convert_etdrs_to_logmar.R @@ -9,7 +9,7 @@ #' #' Source for conversion formula: #' Beck, R.W., et al. A computerized method of visual acuity testing. -#' American Journal of Ophthalmology, 135(2), pp.194–205. +#' American Journal of Ophthalmology, 135(2), pp.194-205. #' doi:https://doi.org/10.1016/s0002-9394(02)01825-1. #' #' @author Rachel Linacre diff --git a/R/convert_logmar_to_etdrs.R b/R/convert_logmar_to_etdrs.R index ecdb56de..1c966cd3 100644 --- a/R/convert_logmar_to_etdrs.R +++ b/R/convert_logmar_to_etdrs.R @@ -9,7 +9,7 @@ #' #' Source for conversion formula: #' Beck, R.W., et al. A computerized method of visual acuity testing. -#' American Journal of Ophthalmology, 135(2), pp.194–205. +#' American Journal of Ophthalmology, 135(2), pp.194-205. #' doi:https://doi.org/10.1016/s0002-9394(02)01825-1. #' #' @author Nandini R Thampi diff --git a/README.md b/README.md index 6c166f8c..49c73733 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,7 @@ remotes::install_github("pharmaverse/admiralophtha", ref = "devel") ## R Versions -Here’s a summary of our strategy for this package related to R versions: +Here's a summary of our strategy for this package related to R versions: * R versions for developers and users will follow the same as `{admiral}` core package. @@ -58,7 +58,7 @@ developer community: * [Slack](https://pharmaverse.slack.com/) - for informal discussions, Q\&A and building our user community. If you - don’t have access, use this + don't have access, use this [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A) to join the pharmaverse Slack workspace * [GitHub diff --git a/inst/WORDLIST b/inst/WORDLIST index 1afc3bb3..f4746a2b 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -41,7 +41,7 @@ Onboarding README SDTM TAs -Template’ +Template' USUBJIDs adae adam @@ -58,7 +58,6 @@ https onboarding paramcds pharmaverse -renv repo studyeye tribble diff --git a/man/convert_etdrs_to_logmar.Rd b/man/convert_etdrs_to_logmar.Rd index 12352158..92397952 100644 --- a/man/convert_etdrs_to_logmar.Rd +++ b/man/convert_etdrs_to_logmar.Rd @@ -20,7 +20,7 @@ ETDRS value converted to logMAR as logMAR = -0.02 * ETDRS + 1.7 Source for conversion formula: Beck, R.W., et al. A computerized method of visual acuity testing. -American Journal of Ophthalmology, 135(2), pp.194–205. +American Journal of Ophthalmology, 135(2), pp.194-205. doi:https://doi.org/10.1016/s0002-9394(02)01825-1. } \examples{ diff --git a/man/convert_logmar_to_etdrs.Rd b/man/convert_logmar_to_etdrs.Rd index 15da6bfe..692e727d 100644 --- a/man/convert_logmar_to_etdrs.Rd +++ b/man/convert_logmar_to_etdrs.Rd @@ -20,7 +20,7 @@ logMAR value converted to ETDRS as ETDRS = -(logMAR - 1.7) / 0.02 Source for conversion formula: Beck, R.W., et al. A computerized method of visual acuity testing. -American Journal of Ophthalmology, 135(2), pp.194–205. +American Journal of Ophthalmology, 135(2), pp.194-205. doi:https://doi.org/10.1016/s0002-9394(02)01825-1. } \examples{ diff --git a/renv.lock b/renv.lock deleted file mode 100644 index 5801ed10..00000000 --- a/renv.lock +++ /dev/null @@ -1,1701 +0,0 @@ -{ - "R": { - "Version": "4.1.3", - "Repositories": [ - { - "Name": "CRAN", - "URL": "https://packagemanager.posit.co/cran/latest" - }, - { - "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2022-03-10" - } - ] - }, - "Packages": { - "DT": { - "Package": "DT", - "Version": "0.21", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "crosstalk", - "htmltools", - "htmlwidgets", - "jquerylib", - "jsonlite", - "magrittr", - "promises" - ], - "Hash": "45fa28dbf288cd606e13ca35d3d72437" - }, - "R.cache": { - "Package": "R.cache", - "Version": "0.15.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - 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"Version": "1.0.5", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "45e4bf3c46476896e821fc0a408fb4fc" - }, - "xopen": { - "Package": "xopen", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "processx" - ], - "Hash": "6c85f015dee9cc7710ddd20f86881f58" - }, - "xtable": { - "Package": "xtable", - "Version": "1.8-4", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "stats", - "utils" - ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" - }, - "yaml": { - "Package": "yaml", - "Version": "2.3.5", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "458bb38374d73bf83b1bb85e353da200" - }, - "zip": { - "Package": "zip", - "Version": "2.2.0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "c7eef2996ac270a18c2715c997a727c5" - } - } -} diff --git a/renv/.gitignore b/renv/.gitignore deleted file mode 100644 index 2649d0a0..00000000 --- a/renv/.gitignore +++ /dev/null @@ -1,8 +0,0 @@ -cellar/ -sandbox/ -library/ -local/ -lock/ -python/ -staging/ -profile diff --git a/renv/activate.R b/renv/activate.R deleted file mode 100644 index cc742fc9..00000000 --- a/renv/activate.R +++ /dev/null @@ -1,1181 +0,0 @@ - -local({ - - # the requested version of renv - version <- "1.0.0" - attr(version, "sha") <- NULL - - # the project directory - project <- getwd() - - # 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) - - # 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 - - }) - - if (!enabled) - 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 - description <- description %||% { - path <- getNamespaceInfo("renv", "path") - packageDescription("renv", lib.loc = dirname(path)) - } - - # 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 = warning) - - # 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, sha = NULL) { - sha <- sha %||% attr(version, "sha", exact = TRUE) - parts <- c(version, sprintf("[sha: %s]", substring(sha, 1L, 7L))) - paste(parts, collapse = " ") - } - - 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_bootstrap_in_rstudio <- function() { - commandArgs()[[1]] == "RStudio" - } - - renv_json_read <- function(file = NULL, text = NULL) { - - jlerr <- NULL - - # if jsonlite is loaded, use that instead - if ("jsonlite" %in% loadedNamespaces()) { - - json <- catch(renv_json_read_jsonlite(file, text)) - if (!inherits(json, "error")) - return(json) - - jlerr <- json - - } - - # otherwise, fall back to the default JSON reader - json <- catch(renv_json_read_default(file, text)) - 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 %||% read(file), 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 %||% read(file), 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_remap(json, map) - - # evaluate - eval(remapped, envir = baseenv()) - - } - - renv_json_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_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) - - # attempt to load - if (renv_bootstrap_load(project, libpath, version)) - return(TRUE) - - if (renv_bootstrap_in_rstudio()) { - setHook("rstudio.sessionInit", function(...) { - renv_bootstrap_run(version, libpath) - - # Work around buglet in RStudio if hook uses readline - tryCatch( - { - tools <- as.environment("tools:rstudio") - tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE) - }, - error = function(cnd) {} - ) - }) - } else { - renv_bootstrap_run(version, libpath) - } - - invisible() - -}) diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock deleted file mode 100644 index 5801ed10..00000000 --- a/renv/profiles/4.1/renv.lock +++ /dev/null @@ -1,1701 +0,0 @@ -{ - "R": { - "Version": "4.1.3", - "Repositories": [ - { - "Name": "CRAN", - "URL": "https://packagemanager.posit.co/cran/latest" - }, - { - "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2022-03-10" - } - ] - }, - "Packages": { - "DT": { - "Package": "DT", - "Version": "0.21", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "crosstalk", - "htmltools", - "htmlwidgets", - "jquerylib", - 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