From 7a18182f0d852946f8faeba40e44b6bd3093d15b Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 14:29:27 +0100 Subject: [PATCH 1/9] Add a rig project for the R test environment The tests/ R environment moves from renv to rig projects. Several worktrees setting up their R environment at once hang for tens of minutes on renv's shared cache and lock, and every R start in tests/ pays the renv autoloader. rig proj sync installs binaries without running R or taking renv's lock. rproj.toml is imported from renv.lock (renv itself dropped) and pins R 4.6.x. rproj.lock is solved for Windows, macOS arm64, glibc Linux and source; every package resolves to a P3M binary on the three OS targets. .rvenvlib holds rig's generated activation shim and must be committed. Nothing reads these files yet. --- tests/.gitignore | 7 + tests/.rvenvlib/.gitignore | 3 + tests/.rvenvlib/rvenv/DESCRIPTION | 14 + tests/.rvenvlib/rvenv/LICENSE | 2 + tests/.rvenvlib/rvenv/Meta/package.rds | Bin 0 -> 727 bytes tests/.rvenvlib/rvenv/NAMESPACE | 2 + tests/.rvenvlib/rvenv/R/rvenv | 204 + tests/rproj.lock | 11220 +++++++++++++++++++++++ tests/rproj.toml | 157 + 9 files changed, 11609 insertions(+) create mode 100644 tests/.rvenvlib/.gitignore create mode 100644 tests/.rvenvlib/rvenv/DESCRIPTION create mode 100644 tests/.rvenvlib/rvenv/LICENSE create mode 100644 tests/.rvenvlib/rvenv/Meta/package.rds create mode 100644 tests/.rvenvlib/rvenv/NAMESPACE create mode 100644 tests/.rvenvlib/rvenv/R/rvenv create mode 100644 tests/rproj.lock create mode 100644 tests/rproj.toml diff --git a/tests/.gitignore b/tests/.gitignore index b50374b5ecc..bba21ab1cd6 100644 --- a/tests/.gitignore +++ b/tests/.gitignore @@ -9,3 +9,10 @@ venv.bak/ bin/ /.luarc.json + +# rig rvenv start +# Everything in .rvenv is machine-specific output of `rig proj sync`; it can +# be deleted and rebuilt at any time. The committed rvenv shim package lives +# in .rvenvlib instead. +/.rvenv/ +# rig rvenv end diff --git a/tests/.rvenvlib/.gitignore b/tests/.rvenvlib/.gitignore new file mode 100644 index 00000000000..857aa3c7296 --- /dev/null +++ b/tests/.rvenvlib/.gitignore @@ -0,0 +1,3 @@ +# Managed by rig. Everything in .rvenvlib must be committed, so this +# overrides ignore rules from elsewhere, e.g. *.rds. +!* diff --git a/tests/.rvenvlib/rvenv/DESCRIPTION b/tests/.rvenvlib/rvenv/DESCRIPTION new file mode 100644 index 00000000000..0229b6428eb --- /dev/null +++ b/tests/.rvenvlib/rvenv/DESCRIPTION @@ -0,0 +1,14 @@ +Package: rvenv +Title: Project Library Activation Shim +Version: 0.1.0 +Author: Gabor Csardi +Maintainer: Gabor Csardi +Description: Loaded automatically via R_DEFAULT_PACKAGES from a project's + .Renviron file. Points the library path at the project library, as an + absolute path, so that child R processes inherit it, and warns if the + project has not been synced yet. This package is generated and installed + by rig, the R installation manager; do not edit it. +License: MIT + file LICENSE +Encoding: UTF-8 +Depends: R (>= 3.0.0) +Built: R 4.0.0; ; 2020-04-24 00:00:00 UTC; unix diff --git a/tests/.rvenvlib/rvenv/LICENSE b/tests/.rvenvlib/rvenv/LICENSE new file mode 100644 index 00000000000..864864336ba --- /dev/null +++ b/tests/.rvenvlib/rvenv/LICENSE @@ -0,0 +1,2 @@ +YEAR: 2026 +COPYRIGHT HOLDER: Gabor Csardi diff --git a/tests/.rvenvlib/rvenv/Meta/package.rds b/tests/.rvenvlib/rvenv/Meta/package.rds new file mode 100644 index 0000000000000000000000000000000000000000..4c4f443d824c812bb6e66d80f8258211b613798e GIT binary patch literal 727 zcmV;|0x10-iwFP!000001JzT{bJ9Q*4iF1P9Xs~m(RXpIW1ETCgCn*h0_`x;mI>f^ z>nzC<)+W2m?t=2qt1n@s%vUeYz>jfCSmK2uJzXCzjr)Q`Gy<~FBE?)GNs<*T8G+!s(>-gA`=jeYtNpok z-W|eJiWCUU*LA*Bb->39kOGrfk%o<|}R zC6a}v`T0Xo0v*sRoUtT=AoC2VQd9xsGb)(|rqP{8@SRAG=rl`^N3uy~7@P|Y6G}O# z6%Uc=ifRu=Go~<2ctc_e_!(19CDEA>7>{wKQ3o33!6qw^EI!Pu5A5E$Eh*s`KsF%~ zc^(?&Re7cpPcM2Sc%AD4{a(9!Iqcddjz?!l?`#tTI5<6lx1R6$uMBn&z;R|bp$QGY z;UD?OM~!3f{rC9~#-nx<7M%TX9Jh?;OExekDOLEfdCjVWHB)K7^%axvyk zYoTXC8moRmu$lN$i#+U56-qYOcP`aF3n^DNV6DqT5iuUy?GBw&9x0pr(}E=$KYrpY zWHaHK*(l-rI2)8TW}hOvFd@pas~B)ExK=BrX?ndZP-A zDe70Y)s+85ngSmyx|`iITZ5R}UKcerW&Qt5at6*;0B3`x^XFPPTe}^f?yw#72BY59 zWpNchKo3+N?W_yOXot~n!A0*Z*UYxVoN?N`o58GW2ze&t=~hJ Jz-+z-007z7Qzrlb literal 0 HcmV?d00001 diff --git a/tests/.rvenvlib/rvenv/NAMESPACE b/tests/.rvenvlib/rvenv/NAMESPACE new file mode 100644 index 00000000000..67d101bfe19 --- /dev/null +++ b/tests/.rvenvlib/rvenv/NAMESPACE @@ -0,0 +1,2 @@ +# This package intentionally exports nothing. All of its behavior happens in +# .onLoad(), see R/rvenv.R. diff --git a/tests/.rvenvlib/rvenv/R/rvenv b/tests/.rvenvlib/rvenv/R/rvenv new file mode 100644 index 00000000000..849870f03fe --- /dev/null +++ b/tests/.rvenvlib/rvenv/R/rvenv @@ -0,0 +1,204 @@ +# This package is loaded from a project's .Renviron, via +# +# R_DEFAULT_PACKAGES=rvenv,datasets,utils,grDevices,graphics,stats,methods +# +# It is the "in-session activation" leg of a rig project: it makes the +# project's `.rvenv/lib` library work in R sessions that rig did not start, +# e.g. in RStudio, Positron or VS Code. We deliberately do not use a project +# `.Rprofile` for this, because that would shadow the user's own +# `~/.Rprofile` entirely. +# +# `.Renviron` sets `R_LIBS_USER` to `.rvenvlib`, this package's own library, +# which is the one R has to be able to load a package from at startup. +# Switching it to the project library is this file's job. The path in +# `.Renviron` is *relative*, because the file is committed to version control +# and has to work from any clone location, while `.onLoad()` receives an +# already-resolved absolute `libname` -- so this is also where the relative +# path becomes an absolute one. That matters for child processes (callr, +# parallel, `R CMD`, `Rscript` from a subdirectory): they inherit the +# environment variable, not our `.libPaths()` call, so a child started in a +# subdirectory would otherwise look for `/.rvenvlib`. +# +# This file is committed (`rig proj init` writes it once, into +# `.rvenvlib/rvenv/R/rvenv`) and so is not re-written by `rig proj sync` on an +# already-init'ed project. It is therefore kept to the one thing that has to +# work even before a project has ever been synced: if there is no project +# library yet, put the session back the way it would have been outside the +# project. Everything else -- the R-version check, setting up the active +# environment, the "not synced" warning -- lives in `.rvenv/onload.R` +# instead, which `rig proj sync` rewrites every time, so fixes there reach +# already-init'ed projects on their next sync, with no `rig proj init` (or +# `rig` upgrade) required. + +.onLoad <- function(libname, pkgname) { + # libname is `/.rvenvlib`, this package's own library. `venv`, used + # throughout this file, is `/.rvenv`, the machine-specific + # environment `rig proj sync` builds -- the same path the RVENV + # environment variable holds when a wrapper script started R. + root <- normalizePath(dirname(libname), mustWork = FALSE) + venv <- file.path(root, ".rvenv") + lib <- file.path(venv, "lib") + + # Whether a parent process activated this project already. Note that this + # does *not* mean there is nothing to do: a child process started in the + # project root reads the project .Renviron itself, which sets R_LIBS_USER + # back to the relative `.rvenv/lib`, and a grandchild started from a + # subdirectory would then look for the wrong directory. So the variables + # below are re-asserted unconditionally, and only the parts that are not + # idempotent -- re-reading the user's .Renviron and warning about an + # unsynced project -- are skipped. + activated <- identical( + normalizePath(Sys.getenv("RVENV"), mustWork = FALSE), + venv + ) + + # Re-read the user's own .Renviron first: the project .Renviron shadows it + # rather than merging with it, so without this the user's variables are + # empty in this session. Our own variables are set after it, so they win. + # Not in a child process: there the parent's environment, including + # whatever it deliberately changed, is what should survive. + home_renv <- path.expand("~/.Renviron") + if (!activated && file.exists(home_renv)) readRenviron(home_renv) + + # `lib` may not exist: `rig proj sync` creates it, and this package does + # not, because it must not write to the project. There is nothing to + # activate then, and leaving R_LIBS_USER pointing at `/.rvenvlib` would + # leave the session with no user library at all: `install.packages()` would + # want to write into rig's own directory. So put the library path back to + # what a session outside the project would have had, and only warn. + # `file.exists()` rather than `dir.exists()`, which is R >= 3.2.0. + if (!file.exists(lib)) { + restore_r_libs_user(libname, lib) + Sys.unsetenv("R_DEFAULT_PACKAGES") + # One warning per project is enough; child processes are quiet. RVENV is + # not set in this code path -- nothing was activated -- so the "did a + # parent already do this?" flag is a separate variable here. + warned <- identical( + normalizePath(Sys.getenv("RVENV_UNSYNCED"), mustWork = FALSE), + venv + ) + Sys.setenv(RVENV_UNSYNCED = venv) + if (!activated && !warned) warn_unsynced(venv, lib) + return(invisible()) + } + + # The rest of activation is machine-specific and rewritten by every + # `rig proj sync`, so it lives outside this committed file. Sourced with + # `local = TRUE`: it runs in this call's own frame, so it reuses + # `root`/`venv`/`lib`/`libname`/`activated` above directly, and any + # functions it defines still resolve `restore_r_libs_user()` / + # `warn_unsynced()` below by lexical scoping. + onload <- file.path(venv, "onload.R") + if (file.exists(onload)) { + source(onload, local = TRUE) + } + + invisible() +} + +# Warns unless the project library was installed from the current lock file. +# `rig proj sync` copies the lock file it installed from to +# `.rvenv/lib/.synced`. A copy rather than a hash, so that both sides only +# need to read files: base R has no sha256, and md5 would mean one more +# dependency on the rig side. +warn_unsynced <- function(venv, lib) { + stamp <- file.path(lib, ".synced") + lock <- file.path(dirname(venv), "rproj.lock") + synced <- FALSE + if (file.exists(stamp) && file.exists(lock)) { + synced <- identical( + readLines(stamp, warn = FALSE), + readLines(lock, warn = FALSE) + ) + } + if (!synced) { + packageStartupMessage("! Project is not synced. Run: rig proj sync") + } + invisible() +} + +# Undoes what the project `.Renviron` did to `R_LIBS_USER`, for a project +# that has no library yet. `.Renviron` pointed it at `/.rvenvlib`, this +# package's own library, only to get R far enough to load this package, and +# `libname` is that directory. If the user's own `~/.Renviron` (re-read +# above) set `R_LIBS_USER`, that value is now in place and is what we keep; +# otherwise the value R had before `.Renviron` is restored. `R_LIBS`, +# `R_LIBS_SITE` and `RVENV` are untouched in this code path, so there is +# nothing to undo there. +restore_r_libs_user <- function(libname, lib) { + sep <- .Platform$path.sep + # The shim's own library, and the project library that is not there. Either + # one can be what R_LIBS_USER points at now (`.Renviron`, or a `rig proj` + # wrapper), and `RVENV_R_LIBS_USER` can hold the latter too, recorded by + # `.Renviron` in a child of a session that was activated by a wrapper. + reject <- normalizePath(c(libname, lib), mustWork = FALSE) + keep <- function(x) { + x <- unlist(strsplit(x, sep, fixed = TRUE)) + x <- x[nzchar(x) & x != "NULL"] + x[!normalizePath(x, mustWork = FALSE) %in% reject] + } + + user <- paste(keep(Sys.getenv("R_LIBS_USER")), collapse = sep) + if (!nzchar(user)) user <- paste(keep(default_r_libs_user()), collapse = sep) + if (nzchar(user)) { + Sys.setenv(R_LIBS_USER = user) + } else { + Sys.unsetenv("R_LIBS_USER") + } + + # Same as R's own startup code, in `/library/base/R/Rprofile`: + # R_LIBS first, then R_LIBS_USER, with the site and system libraries added + # by `.libPaths()` itself. This also drops `/.rvenvlib`, which + # `.Renviron` put on the path at startup. + .libPaths(c(keep(Sys.getenv("R_LIBS")), keep(user))) + + invisible() +} + +# The `R_LIBS_USER` the session would have had without the project, i.e. +# what R itself had set by the time the project `.Renviron` was read, which +# that file recorded in `RVENV_R_LIBS_USER` before overwriting the real +# variable. It is still the *unexpanded* value from the R installation's +# `etc/Renviron`, e.g. `%U` or `~/R/%p-library/%v`: R only expands the +# `%`-specs later, in its own profile, after `.Renviron` files are read. So +# expand it with the running R's own expander, which knows exactly the specs +# that R's own `etc/Renviron` uses -- `%U` for instance is only understood +# from R 4.2.0 on, but older installations do not use it either. Should that +# function ever go away, an unexpanded path is still better than pointing the +# user at rig's directory. +# +# Empty when the project was set up by a rig older than this shim, or if the +# R installation does not set `R_LIBS_USER` at all; the caller then only +# drops the shim's own library from the path. +# +# On a rig-managed R installation the user library may hold several named +# libraries (`rig library`), in `__` subdirectories, with the active one +# named in a `___default` file. rig's `Rprofile` hook resolves that before the +# default packages are loaded, but it did so for `/.rvenvlib` in this +# session, so we resolve it here too. Unlike that hook, we never create a +# directory. +default_r_libs_user <- function() { + spec <- Sys.getenv("RVENV_R_LIBS_USER") + if (!nzchar(spec) || spec == "NULL") return("") + + expander <- ".expand_R_libs_env_var" + if (exists(expander, envir = asNamespace("base"), inherits = FALSE)) { + spec <- get(expander, envir = asNamespace("base"))(spec) + } + + sep <- .Platform$path.sep + libs <- unlist(strsplit(spec, sep, fixed = TRUE)) + libs[1L] <- resolve_named_library(libs[1L]) + paste(libs, collapse = sep) +} + +# `/__` if `` is a rig user library with a named library +# other than `main` selected, `` otherwise. See `default_r_libs_user()`. +resolve_named_library <- function(lib) { + deffile <- file.path(lib, "___default") + if (!file.exists(deffile)) return(lib) + def <- readLines(deffile, warn = FALSE)[1L] + if (is.na(def) || !nzchar(def) || def == "main") return(lib) + named <- file.path(lib, paste0("__", def)) + if (file.exists(named)) named else lib +} diff --git a/tests/rproj.lock b/tests/rproj.lock new file mode 100644 index 00000000000..f2f5aee3436 --- /dev/null +++ b/tests/rproj.lock @@ -0,0 +1,11220 @@ +version = 7 + +[[tool.rig.repository]] +name = "bioc" +metadata = "https://ppm-bioc.r-pkg.org/%v" + +[[tool.rig.repository]] +name = "cran" +metadata = "https://ppm.r-pkg.org" + +[[targets]] +r_version = "4.6" +platform = "aarch64-apple-darwin" +bioc-version = "3.23" + +[[targets.direct_dependencies]] +name = "AsioHeaders" +constraint = ">= 1.30.2-1, << 2.0.0.0" + +[[targets.direct_dependencies]] +name = "DBI" +constraint = ">= 1.3.0, << 2.0.0" + +[[targets.direct_dependencies]] +name 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-0,0 +1,157 @@ +[project] +name = "tests" +version = "0.1.0" +type = "project" + +[dependencies] +AsioHeaders = "^1.30.2-1" +DBI = "^1.3.0" +DT = "^0.34.0" +R = ">= 4.6" +R6 = "^2.6.1" +RColorBrewer = "^1.1-3" +RSQLite = "^3.53.3" +Rcpp = "^1.1.2" +S7 = "^0.2.2" +V8 = "^8.2.0" +askpass = "^1.2.1" +backports = "^1.5.1" +base64enc = "^0.1-6" +bigD = "^0.3.1" +bit = "^4.6.0" +bit64 = "^4.8.6" +bitops = "^1.1-0" +blob = "^1.3.0" +brio = "^1.1.5" +broom = "^1.0.13" +bsicons = "^0.1.2" +bslib = "^0.12.0" +cachem = "^1.1.0" +callr = "^3.8.0" +cellranger = "^1.1.0" +chromote = "^0.5.1" +cli = "^3.6.6" +clipr = "^0.8.1" +colorspace = "^2.1-3" +colourpicker = "^1.3.0" +commonmark = "^2.0.0" +conflicted = "^1.2.0" +cpp11 = "^0.5.5" +crayon = "^1.5.3" +crosstalk = "^1.2.2" +curl = "^8.0.0" +"data.table" = "^1.18.6.1" +dbplyr = "^2.6.0" +desc = "^1.4.3" +digest = "^0.6.39" +downlit = "^0.4.5" +dplyr = "^1.2.1" +dtplyr = "^1.3.3" +evaluate = "^1.0.5" +fansi = "^1.0.7" +farver = "^2.1.2" +fastmap = "^1.2.0" +flextable = "^0.10.0" +fontBitstreamVera = "^0.1.1" +fontLiberation = "^0.1.0" +fontawesome = "^0.5.3" +fontquiver = "^0.2.1" +forcats = "^1.0.1" +fs = "^2.1.0" +gargle = "^1.6.1" +gdtools = "^0.5.2" +generics = "^0.1.4" +ggExtra = "^0.11.0" +ggplot2 = "^4.0.3" +glue = "^1.8.1" +googledrive = "^2.1.2" +googlesheets4 = "^1.1.2" +gt = "^1.3.0" +gtable = "^0.3.6" +haven = "^2.5.5" +highr = "^0.12" +hms = "^1.1.4" +htmltools = "^0.5.9" +htmlwidgets = "^1.6.4" +httpuv = "^1.6.17" +httr = "^1.4.9" +ids = "^1.0.1" +isoband = "^0.3.0" +jquerylib = "^0.1.4" +jsonlite = "^2.0.0" +juicyjuice = "^0.1.0" +kableExtra = "^1.4.1" +knitr = "^1.52" +labeling = "^0.4.3" +later = "^1.4.8" +lazyeval = "^0.2.3" +lifecycle = "^1.0.5" +litedown = "^0.11" +lubridate = "^1.9.5" +magrittr = "^2.0.5" +markdown = "^2.0" +memoise = "^2.0.1" +mime = "^0.13" +miniUI = "^0.1.2" +modelr = "^0.1.11" +officer = "^0.7.6" +openssl = "^2.4.2" +otel = "^0.2.0" +pillar = "^1.11.1" +pkgconfig = "^2.0.3" +prettyunits = "^1.2.0" +processx = "^3.9.0" +progress = "^1.2.3" +promises = "^1.5.0" +ps = "^1.9.3" +purrr = "^1.2.2" +ragg = "^1.5.2" +rappdirs = "^0.3.4" +reactR = "^0.6.1" +reactable = "^0.4.5" +readr = "^2.2.0" +readxl = "^1.5.0" +rematch = "^2.0.0" +rematch2 = "^2.1.2" +reprex = "^2.1.1" +rlang = "^1.3.0" +rmarkdown = "^2.32" +rstudioapi = "^0.19.0" +rvest = "^1.0.5" +sass = "^0.4.10" +scales = "^1.4.0" +selectr = "^0.6-0" +shiny = "^1.14.0" +shinyjs = "^2.1.1" +sourcetools = "^0.1.7-2" +stringi = "^1.8.9" +stringr = "^1.6.0" +svglite = "^2.2.2" +sys = "^3.4.3" +systemfonts = "^1.3.2" +textshaping = "^1.0.5" +tibble = "^3.3.1" +tidyr = "^1.3.2" +tidyselect = "^1.2.1" +tidyverse = "^2.0.0" +timechange = "^0.4.0" +tinytex = "^0.60" +tzdb = "^0.5.0" +utf8 = "^1.2.6" +uuid = "^1.2-2" +vctrs = "^0.7.3" +viridisLite = "^0.4.3" +vroom = "^1.7.1" +webshot2 = "^0.1.2" +websocket = "^1.4.4" +withr = "^3.0.3" +xfun = "^0.60" +xml2 = "^1.6.0" +xtable = "^1.8-8" +yaml = "^2.3.12" +zip = "^3.0.2" + +# Solve for R 4.6.x on every platform: the lock records "4.6", so CI's setup-r +# patch release and a contributor's patch release both satisfy it. +[tool.rig] +r-versions = ["4.6"] From 548a46afbd75918ade7c1e4df422949a0f0b8e4d Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 14:42:01 +0100 Subject: [PATCH 2/9] Use the rig project for the R test environment configure-test-env now runs rig proj sync, then installs the dev rmarkdown and knitr from r-universe into the project library. The install has to name both the library and the exact R version: rig's default target is the default R's user library, which the project library would shadow anyway. run-tests points QUARTO_R at tests/.rvenv/bin. Quarto resolves Rscript from QUARTO_R first, and the wrapper sets the R version and project library itself, so R subprocesses started outside tests/ no longer need a per-fixture .Rprofile. writeTestsRenvProfile and its two callers go. tests/.Rprofile is deleted rather than left unused: it activated renv in every R started in tests/, which is where the setup hangs came from. tests/.Renviron is rig's committed hook for IDEs and a bare Rscript in tests/. Every sync rewrites it with LF line endings, so it is checked out as LF to stay unmodified under core.autocrlf. DESCRIPTION and .renvignore only served renv's dependency discovery; rproj.toml is now the manifest. --- .gitattributes | 3 + .luarc.json | 2 +- tests/.Renviron | 26 + tests/.Rprofile | 1 - tests/.renvignore | 49 - tests/DESCRIPTION | 28 - tests/configure-test-env.ps1 | 28 +- tests/configure-test-env.sh | 28 +- tests/renv.lock | 5676 ----------------- tests/renv/.gitignore | 7 - tests/renv/activate.R | 1438 ----- tests/renv/settings.json | 18 - tests/run-tests.ps1 | 20 + tests/run-tests.sh | 14 + .../render-embed-website-rerender.test.ts | 5 +- tests/unit/preview-subdir-knitr-cwd.test.ts | 13 +- tests/utils.ts | 15 +- 17 files changed, 111 insertions(+), 7260 deletions(-) create mode 100644 tests/.Renviron delete mode 100644 tests/.Rprofile delete mode 100644 tests/.renvignore delete mode 100644 tests/DESCRIPTION delete mode 100644 tests/renv.lock delete mode 100644 tests/renv/.gitignore delete mode 100644 tests/renv/activate.R delete mode 100644 tests/renv/settings.json diff --git a/.gitattributes b/.gitattributes index 9cc408d197c..de67889b191 100644 --- a/.gitattributes +++ b/.gitattributes @@ -48,3 +48,6 @@ tools/codemod/** text eol=lf *.otf binary +# rig proj sync rewrites this file with LF line endings; a CRLF checkout +# would then show it as modified after every sync. +tests/.Renviron text eol=lf diff --git a/.luarc.json b/.luarc.json index 516c6636c7f..c2529dfed45 100644 --- a/.luarc.json +++ b/.luarc.json @@ -19,5 +19,5 @@ "Lua.runtime.version": "Lua 5.3", "Lua.workspace.checkThirdParty": false, "Lua.workspace.library": ["src/resources/lua-types"], - "Lua.workspace.ignoreDir": ["tests/renv", ".vscode", "**/node_modules/*"] + "Lua.workspace.ignoreDir": ["tests/.rvenv", ".vscode", "**/node_modules/*"] } diff --git a/tests/.Renviron b/tests/.Renviron new file mode 100644 index 00000000000..30ebb4b29a4 --- /dev/null +++ b/tests/.Renviron @@ -0,0 +1,26 @@ +# rig rvenv start +# Managed by rig (rig proj init). rig rewrites the lines between the +# `rig rvenv` markers, put your own settings outside of them. Settings after +# this block that set R_LIBS_USER or R_DEFAULT_PACKAGES break the project +# setup. +# +# R_LIBS_USER names rig's own library, not the project library: it only has to +# get R far enough to load the `rvenv` package below. That package points +# R_LIBS_USER at the project library, as an absolute path, so that child R +# processes started from a subdirectory still see it. The path here is +# deliberately relative, because this file is committed to version control. +# +# RVENV_R_LIBS_USER keeps the R_LIBS_USER this R installation had set by the +# time this file is read, so that the `rvenv` package can put it back if the +# project has no library yet. It is still unexpanded at this point, e.g. `%U`; +# R expands the %-specs later, and so does the package. The value is quoted +# because R drops unquoted backslashes, which would break Windows paths. +# +# R_DEFAULT_PACKAGES replaces R's default package list rather than adding to +# it, so the whole list has to be spelled out. +# +# Note that `R --vanilla` ignores this file entirely. +RVENV_R_LIBS_USER="${R_LIBS_USER}" +R_LIBS_USER=.rvenvlib +R_DEFAULT_PACKAGES=rvenv,datasets,utils,grDevices,graphics,stats,methods +# rig rvenv end diff --git a/tests/.Rprofile b/tests/.Rprofile deleted file mode 100644 index 81b960f5c6a..00000000000 --- a/tests/.Rprofile +++ /dev/null @@ -1 +0,0 @@ -source("renv/activate.R") diff --git a/tests/.renvignore b/tests/.renvignore deleted file mode 100644 index 33066e69566..00000000000 --- a/tests/.renvignore +++ /dev/null @@ -1,49 +0,0 @@ -# Python Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# skip folders with no R to speed up dependencies detection - -/integration/ -/smoke/ -/unit/ - -_extensions/ - -# skip files with no R code to speed up dependencies detection -*.ts -*.js -*.yml -*.css -*.py -*.json -*.sh -*.ps1 -*.toml -*.csl -*.bib -*.mp4 -*.png -*.jpg -*.jpeg -*.svg -*.woff -*.tex -*.cls -*.sty -*.lua -*.theme -*.xml -*.gz -*.html -*.xls -*.pdf -*.eps -*.dtd -*.ent -*.mod diff --git a/tests/DESCRIPTION b/tests/DESCRIPTION deleted file mode 100644 index fa24171bfc1..00000000000 --- a/tests/DESCRIPTION +++ /dev/null @@ -1,28 +0,0 @@ -Type: tests -Description: Quarto tests projects -Depends: - bsicons, - bslib, - colorspace, - DBI, - downlit, - dplyr, - DT, - flextable, - ggExtra, - ggplot2, - gt, - kableExtra, - knitr, - openssl, - renv, - rmarkdown, - RSQLite, - scales, - shiny, - stats, - tibble, - tidyverse, - tinytex, - webshot2, - yaml diff --git a/tests/configure-test-env.ps1 b/tests/configure-test-env.ps1 index c5ba764ce63..eed9280e7df 100644 --- a/tests/configure-test-env.ps1 +++ b/tests/configure-test-env.ps1 @@ -1,15 +1,27 @@ # Check R environment --- Write-Host -ForegroundColor green ">>>> Configuring R environment" -try { $null = gcm Rscript -ea stop; $r=$true} catch { - Write-Host -ForegroundColor red "No Rscript found in PATH - Check your PATH or install R and add to PATH" +try { $null = gcm rig -ea stop; $rig=$true } catch { + Write-Host -ForegroundColor red "No rig found in PATH - the R test environment is a rig project (rproj.toml). Install rig 0.11.1 or later: https://github.com/r-lib/rig" } -If ($r) { - Write-Host -ForegroundColor green " > Restoring renv project" - Rscript -e 'renv::restore()' - Write-Host -ForegroundColor green " > Installing dev knitr and rmarkdown" - Rscript -e "install.packages('rmarkdown', repos = c('https://rstudio.r-universe.dev', getOption('repos')))" - Rscript -e "install.packages('knitr', repos = c('https://yihui.r-universe.dev', getOption('repos')))" +If ($rig) { + Write-Host -ForegroundColor green " > Syncing R packages from rproj.lock" + rig proj sync + If ($LASTEXITCODE -ne 0) { + Write-Host -ForegroundColor red "rig proj sync failed - R tests will run without the locked packages" + } Else { + # Installs on top of the lock must target the project library and the + # exact R the sync used; rig's default is the default R's user library. + $rVersion = (Select-String -Path .rvenv/rvenv.cfg -Pattern '^r-version = (.+)$').Matches[0].Groups[1].Value.Trim() + $rLib = (Resolve-Path .rvenv/lib).Path + Write-Host -ForegroundColor green " > Installing dev knitr and rmarkdown" + foreach ($dev in @(@('rmarkdown', 'https://rstudio.r-universe.dev'), @('knitr', 'https://yihui.r-universe.dev'))) { + rig pkg install --r-version $rVersion --library $rLib --with-repos $dev[1] $dev[0] + If ($LASTEXITCODE -ne 0) { + Write-Host -ForegroundColor yellow "Dev $($dev[0]) not installed - tests use the locked version" + } + } + } } # Check python test environment --- diff --git a/tests/configure-test-env.sh b/tests/configure-test-env.sh index 0c67327ed51..a1e492acb4a 100755 --- a/tests/configure-test-env.sh +++ b/tests/configure-test-env.sh @@ -1,17 +1,27 @@ # Check R environment --- echo ">>>> Configuring R environment" -r_exists=$(command -v Rscript) +rig_exists=$(command -v rig) -if [ -z $r_exists ] -then - echo "No Rscript found in PATH - Check your PATH or install R and add to PATH." +if [ -z "$rig_exists" ] +then + echo "No rig found in PATH - the R test environment is a rig project (rproj.toml). Install rig 0.11.1 or later: https://github.com/r-lib/rig" else - echo " > Restoring renv project" - Rscript -e 'renv::restore()' - echo " > Installing dev knitr and rmarkdown" - Rscript -e "install.packages('rmarkdown', repos = c('https://rstudio.r-universe.dev', getOption('repos')))" - Rscript -e "install.packages('knitr', repos = c('https://yihui.r-universe.dev', getOption('repos')))" + echo " > Syncing R packages from rproj.lock" + if rig proj sync + then + # Installs on top of the lock must target the project library and the + # exact R the sync used; rig's default is the default R's user library. + r_version=$(sed -n 's/^r-version = //p' .rvenv/rvenv.cfg | tr -d '\r') + r_lib="$(cd .rvenv/lib && pwd)" + echo " > Installing dev knitr and rmarkdown" + rig pkg install --r-version "$r_version" --library "$r_lib" --with-repos https://rstudio.r-universe.dev rmarkdown \ + || echo "Dev rmarkdown not installed - tests use the locked version" + rig pkg install --r-version "$r_version" --library "$r_lib" --with-repos https://yihui.r-universe.dev knitr \ + || echo "Dev knitr not installed - tests use the locked version" + else + echo "rig proj sync failed - R tests will run without the locked packages" + fi fi diff --git a/tests/renv.lock b/tests/renv.lock deleted file mode 100644 index c5757a46f1a..00000000000 --- a/tests/renv.lock +++ /dev/null @@ -1,5676 +0,0 @@ -{ - "R": { - "Version": "4.6.1", - "Repositories": [ - { - "Name": "P3M", - "URL": "https://packagemanager.posit.co/cran/latest" - }, - { - "Name": "CRAN", - "URL": "https://cloud.r-project.org" - } - ] - }, - "Packages": { - "AsioHeaders": { - "Package": "AsioHeaders", - "Version": "1.30.2-1", - "Source": "Repository", - "Type": "Package", - "Title": "'Asio' C++ Header Files", - "Date": "2025-04-15", - "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Christopher M.\", \"Kohlhoff\", role = \"aut\", comment = \"Author of Asio\"))", - "Description": "'Asio' is a cross-platform C++ library for network and low-level I/O programming that provides developers with a consistent asynchronous model using a modern C++ approach. It is also included in Boost but requires linking when used with Boost. Standalone it can be used header-only (provided a recent compiler). 'Asio' is written and maintained by Christopher M. Kohlhoff, and released under the 'Boost Software License', Version 1.0.", - "Copyright": "file inst/COPYRIGHTS", - "License": "BSL-1.0", - "URL": "https://github.com/eddelbuettel/asioheaders, https://dirk.eddelbuettel.com/code/asioheaders.html", - "BugReports": "https://github.com/eddelbuettel/asioheaders/issues", - "NeedsCompilation": "no", - "Author": "Dirk Eddelbuettel [aut, cre] (), Christopher M. Kohlhoff [aut] (Author of Asio)", - "Maintainer": "Dirk Eddelbuettel ", - "Repository": "P3M", - "Encoding": "UTF-8" - }, - "DBI": { - "Package": "DBI", - "Version": "1.3.0", - "Source": "Repository", - "Title": "R Database Interface", - "Date": "2026-02-11", - "Authors@R": "c( person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\") )", - "Description": "A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.", - "License": "LGPL (>= 2.1)", - "URL": "https://dbi.r-dbi.org, https://github.com/r-dbi/DBI", - "BugReports": "https://github.com/r-dbi/DBI/issues", - "Depends": [ - "methods", - "R (>= 3.0.0)" - ], - "Suggests": [ - "arrow", - "blob", - "callr", - "covr", - "DBItest (>= 1.8.2)", - "dbplyr", - "downlit", - "dplyr", - "glue", - "hms", - "knitr", - "magrittr", - "nanoarrow (>= 0.3.0.1)", - "otel", - "otelsdk", - "RMariaDB", - "rmarkdown", - "rprojroot", - "RSQLite (>= 1.1-2)", - "testthat (>= 3.0.0)", - "vctrs", - "xml2" - ], - "VignetteBuilder": "knitr", - "Config/autostyle/scope": "line_breaks", - "Config/autostyle/strict": "false", - "Config/Needs/check": "r-dbi/DBItest", - "Config/Needs/website": "r-dbi/DBItest, r-dbi/dbitemplate, adbi, AzureKusto, bigrquery, DatabaseConnector, dittodb, duckdb, implyr, lazysf, odbc, pool, RAthena, IMSMWU/RClickhouse, RH2, RJDBC, RMariaDB, RMySQL, RPostgres, RPostgreSQL, RPresto, RSQLite, sergeant, sparklyr, withr", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3.9000", - "NeedsCompilation": "no", - "Author": "R Special Interest Group on Databases (R-SIG-DB) [aut], Hadley Wickham [aut], Kirill Müller [aut, cre] (ORCID: ), R Consortium [fnd]", - "Maintainer": "Kirill Müller ", - "Repository": "P3M" - }, - "DT": { - "Package": "DT", - "Version": "0.34.0", - "Source": "Repository", - "Type": "Package", - "Title": "A Wrapper of the JavaScript Library 'DataTables'", - "Authors@R": "c( person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Xianying\", \"Tan\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Maximilian\", \"Girlich\", role = \"ctb\"), person(\"Greg\", \"Freedman Ellis\", role = \"ctb\"), person(\"Johannes\", \"Rauh\", role = \"ctb\"), person(\"SpryMedia Limited\", role = c(\"ctb\", \"cph\"), comment = \"DataTables in htmlwidgets/lib\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js in htmlwidgets/lib\"), person(\"Leon\", \"Gersen\", role = c(\"ctb\", \"cph\"), comment = \"noUiSlider in htmlwidgets/lib\"), person(\"Bartek\", \"Szopka\", role = c(\"ctb\", \"cph\"), comment = \"jquery.highlight.js in htmlwidgets/lib\"), person(\"Alex\", \"Pickering\", role = \"ctb\"), person(\"William\", \"Holmes\", role = \"ctb\"), person(\"Mikko\", \"Marttila\", role = \"ctb\"), person(\"Andres\", \"Quintero\", role = \"ctb\"), person(\"Stéphane\", \"Laurent\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/rstudio/DT", - "BugReports": "https://github.com/rstudio/DT/issues", - "Imports": [ - "crosstalk", - "htmltools (>= 0.3.6)", - "htmlwidgets (>= 1.3)", - "jquerylib", - "jsonlite (>= 0.9.16)", - "magrittr", - "promises" - ], - "Suggests": [ - "bslib", - "future", - "httpuv", - "knitr (>= 1.8)", - "rmarkdown", - "shiny (>= 1.6)", - "testit", - "tibble" - ], - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Yihui Xie [aut], Joe Cheng [aut], Xianying Tan [aut], Garrick Aden-Buie [aut, cre] (ORCID: ), JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), Alex Pickering [ctb], William Holmes [ctb], Mikko Marttila [ctb], Andres Quintero [ctb], Stéphane Laurent [ctb], Posit Software, PBC [cph, fnd]", - "Maintainer": "Garrick Aden-Buie ", - "Repository": "P3M" - }, - "R6": { - "Package": "R6", - "Version": "2.6.1", - "Source": "Repository", - "Title": "Encapsulated Classes with Reference Semantics", - "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. 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Richard\", \"Hipp\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(\"Dan\", \"Kennedy\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(\"Joe\", \"Mistachkin\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(, \"SQLite Authors\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(\"Liam\", \"Healy\", role = \"ctb\", comment = \"for the included SQLite sources\"), person(\"R Consortium\", role = \"fnd\"), person(, \"RStudio\", role = \"cph\") )", - "Description": "Embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine and for various extensions is included. System libraries will never be consulted because this package relies on static linking for the plugins it includes; this also ensures a consistent experience across all installations. Optionally, when libcurl is available at build time, an experimental HTTP/HTTPS virtual file system (VFS) can be enabled to allow read-only access to remote immutable SQLite database files via URIs.", - "License": "LGPL (>= 2.1)", - "URL": "https://rsqlite.r-dbi.org, https://github.com/r-dbi/RSQLite", - "BugReports": "https://github.com/r-dbi/RSQLite/issues", - "Depends": [ - "R (>= 3.1.0)" - ], - "Imports": [ - "bit64", - "blob (>= 1.2.0)", - "DBI (>= 1.2.0)", - "memoise", - "methods", - "pkgconfig", - "rlang" - ], - "Suggests": [ - "callr", - "cli", - "DBItest (>= 1.8.0)", - "decor", - "gert", - "gh", - "hms", - "httpuv", - "knitr", - "magrittr", - "rmarkdown", - "rvest", - "testthat (>= 3.0.0)", - "withr", - "xml2" - ], - "LinkingTo": [ - "cpp11 (>= 0.4.0)" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "r-dbi/dbitemplate", - "Config/autostyle/scope": "line_breaks", - "Config/autostyle/strict": "false", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "Collate": "'SQLiteConnection.R' 'SQLKeywords_SQLiteConnection.R' 'SQLiteDriver.R' 'SQLite.R' 'SQLiteResult.R' 'coerce.R' 'compatRowNames.R' 'copy.R' 'cpp11.R' 'datasetsDb.R' 'dbAppendTable_SQLiteConnection.R' 'dbBeginTransaction.R' 'dbBegin_SQLiteConnection.R' 'dbBind_SQLiteResult.R' 'dbClearResult_SQLiteResult.R' 'dbColumnInfo_SQLiteResult.R' 'dbCommit_SQLiteConnection.R' 'dbConnect_SQLiteConnection.R' 'dbConnect_SQLiteDriver.R' 'dbDataType_SQLiteConnection.R' 'dbDataType_SQLiteDriver.R' 'dbDisconnect_SQLiteConnection.R' 'dbExistsTable_SQLiteConnection_Id.R' 'dbExistsTable_SQLiteConnection_character.R' 'dbFetch_SQLiteResult.R' 'dbGetException_SQLiteConnection.R' 'dbGetInfo_SQLiteConnection.R' 'dbGetInfo_SQLiteDriver.R' 'dbGetPreparedQuery.R' 'dbGetPreparedQuery_SQLiteConnection_character_data.frame.R' 'dbGetRowCount_SQLiteResult.R' 'dbGetRowsAffected_SQLiteResult.R' 'dbGetStatement_SQLiteResult.R' 'dbHasCompleted_SQLiteResult.R' 'dbIsValid_SQLiteConnection.R' 'dbIsValid_SQLiteDriver.R' 'dbIsValid_SQLiteResult.R' 'dbListObjects_SQLiteConnection.R' 'dbListResults_SQLiteConnection.R' 'dbListTables_SQLiteConnection.R' 'dbQuoteIdentifier_SQLiteConnection_SQL.R' 'dbQuoteIdentifier_SQLiteConnection_character.R' 'dbReadTable_SQLiteConnection_character.R' 'dbRemoveTable_SQLiteConnection_character.R' 'dbRollback_SQLiteConnection.R' 'dbSendPreparedQuery.R' 'dbSendPreparedQuery_SQLiteConnection_character_data.frame.R' 'dbSendQuery_SQLiteConnection_character.R' 'dbUnloadDriver_SQLiteDriver.R' 'dbUnquoteIdentifier_SQLiteConnection_SQL.R' 'dbWriteTable_SQLiteConnection_character_character.R' 'dbWriteTable_SQLiteConnection_character_data.frame.R' 'db_bind.R' 'deprecated.R' 'export.R' 'fetch_SQLiteResult.R' 'httpvfs.R' 'httpvfs_config.R' 'import-standalone-check_suggested.R' 'import-standalone-purrr.R' 'initExtension.R' 'initRegExp.R' 'isSQLKeyword_SQLiteConnection_character.R' 'make.db.names_SQLiteConnection_character.R' 'pkgconfig.R' 'show_SQLiteConnection.R' 'sqlData_SQLiteConnection.R' 'table.R' 'transactions.R' 'utils.R' 'version.R' 'zzz.R'", - "Config/roxygen2/version": "8.0.0.9000", - "NeedsCompilation": "yes", - "Author": "Kirill Müller [aut, cre] (ORCID: ), Hadley Wickham [aut], David A. James [aut], Seth Falcon [aut], D. Richard Hipp [ctb] (for the included SQLite sources), Dan Kennedy [ctb] (for the included SQLite sources), Joe Mistachkin [ctb] (for the included SQLite sources), SQLite Authors [ctb] (for the included SQLite sources), Liam Healy [ctb] (for the included SQLite sources), R Consortium [fnd], RStudio [cph]", - "Maintainer": "Kirill Müller ", - "Repository": "P3M" - }, - "Rcpp": { - "Package": "Rcpp", - "Version": "1.1.2", - "Source": "Repository", - "Title": "Seamless R and C++ Integration", - "Date": "2026-07-01", - "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", - "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at , the paper by Eddelbuettel and Francois (2011, ), the book by Eddelbuettel (2013, ) and the paper by Eddelbuettel and Balamuta (2018, ); see 'citation(\"Rcpp\")' for details.", - "Depends": [ - "R (>= 3.5.0)" - ], - "Imports": [ - "methods", - "utils" - ], - "Suggests": [ - "tinytest", - "inline", - "rbenchmark", - "pkgKitten (>= 0.1.2)" - ], - "URL": "https://www.rcpp.org, https://dirk.eddelbuettel.com/code/rcpp.html, https://github.com/RcppCore/Rcpp", - "License": "GPL (>= 2)", - "BugReports": "https://github.com/RcppCore/Rcpp/issues", - "RoxygenNote": "6.1.1", - "Encoding": "UTF-8", - "VignetteBuilder": "Rcpp", - "NeedsCompilation": "yes", - "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), JJ Allaire [aut] (ORCID: ), Kevin Ushey [aut] (ORCID: ), Qiang Kou [aut] (ORCID: ), Nathan Russell [aut], Iñaki Ucar [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), John Chambers [aut]", - "Maintainer": "Dirk Eddelbuettel ", - "Repository": "P3M" - }, - "S7": { - "Package": "S7", - "Version": "0.2.2", - "Source": "Repository", - "Title": "An Object Oriented System Meant to Become a Successor to S3 and S4", - "Authors@R": "c( person(\"Object-Oriented Programming Working Group\", role = \"cph\"), person(\"Davis\", \"Vaughan\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"Will\", \"Landau\", role = \"aut\"), person(\"Michael\", \"Lawrence\", role = \"aut\"), person(\"Martin\", \"Maechler\", role = \"aut\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Luke\", \"Tierney\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")) )", - "Description": "A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.", - "License": "MIT + file LICENSE", - "URL": "https://rconsortium.github.io/S7/, https://github.com/RConsortium/S7", - "BugReports": "https://github.com/RConsortium/S7/issues", - "Depends": [ - "R (>= 3.5.0)" - ], - "Imports": [ - "utils" - ], - "Suggests": [ - "bench", - "callr", - "covr", - "knitr", - "methods", - "rmarkdown", - "testthat (>= 3.2.0)", - "tibble" - ], - "VignetteBuilder": "knitr", - "Config/build/compilation-database": "true", - "Config/Needs/website": "sloop", - "Config/testthat/edition": "3", - "Config/testthat/parallel": "TRUE", - "Config/testthat/start-first": "external-generic", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3", - "NeedsCompilation": "yes", - "Author": "Object-Oriented Programming Working Group [cph], Davis Vaughan [aut], Jim Hester [aut] (ORCID: ), Tomasz Kalinowski [aut], Will Landau [aut], Michael Lawrence [aut], Martin Maechler [aut] (ORCID: ), Luke Tierney [aut], Hadley Wickham [aut, cre] (ORCID: )", - "Maintainer": "Hadley Wickham ", - "Repository": "P3M" - }, - "V8": { - "Package": "V8", - "Version": "8.2.0", - "Source": "Repository", - "Type": "Package", - "Title": "Embedded JavaScript and WebAssembly Engine for R", - "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"George\", \"Stagg\", role = \"ctb\", comment = c(ORCID = \"0009-0006-3173-9846\")), person(\"Jan Marvin\", \"Garbuszus\", role = \"ctb\"))", - "Description": "An R interface to V8 : Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 or NodeJS when built as a shared library.", - "License": "MIT + file LICENSE", - "URL": "https://jeroen.r-universe.dev/V8", - "BugReports": "https://github.com/jeroen/v8/issues", - "SystemRequirements": "On Linux you can build against libv8-dev (Debian) or v8-devel (Fedora). 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Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.", - "License": "MIT + file LICENSE", - "URL": "https://r-lib.r-universe.dev/askpass", - "BugReports": "https://github.com/r-lib/askpass/issues", - "Encoding": "UTF-8", - "Imports": [ - "sys (>= 2.1)" - ], - "RoxygenNote": "7.2.3", - "Suggests": [ - "testthat" - ], - "Language": "en-US", - "NeedsCompilation": "yes", - "Author": "Jeroen Ooms [aut, cre] ()", - "Maintainer": "Jeroen Ooms ", - "Repository": "P3M" - }, - "backports": { - "Package": "backports", - "Version": "1.5.1", - "Source": "Repository", - "Type": "Package", - "Title": "Reimplementations of Functions Introduced Since R-3.0.0", - "Authors@R": "c( person(\"Michel\", \"Lang\", NULL, \"michellang@gmail.com\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Duncan\", \"Murdoch\", NULL, \"murdoch.duncan@gmail.com\", role = c(\"aut\")), person(\"R Core Team\", role = \"aut\"))", - "Maintainer": "Michel Lang ", - "Description": "Functions introduced or changed since R v3.0.0 are re-implemented in this package. 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It support ANSI colors and text styles as well.", - "License": "MIT + file LICENSE", - "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli", - "BugReports": "https://github.com/r-lib/cli/issues", - "Depends": [ - "R (>= 3.4)" - ], - "Imports": [ - "utils" - ], - "Suggests": [ - "callr", - "covr", - "crayon", - "digest", - "glue (>= 1.6.0)", - "grDevices", - "htmltools", - "htmlwidgets", - "knitr", - "methods", - "processx", - "ps (>= 1.3.4.9000)", - "rlang (>= 1.0.2.9003)", - "rmarkdown", - "rprojroot", - "rstudioapi", - "testthat (>= 3.2.0)", - "tibble", - "whoami", - "withr" - ], - "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs", - "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2025-04-25", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2.9000", - "NeedsCompilation": "yes", - "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", - "Maintainer": "Gábor Csárdi ", - "Repository": "P3M" - }, - "clipr": { - "Package": "clipr", - "Version": "0.8.1", - "Source": "Repository", - "Type": "Package", - "Title": "Read and Write from the System Clipboard", - "Authors@R": "c( person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4387-3384\")), person(\"Louis\", \"Maddox\", role = \"ctb\"), person(\"Steve\", \"Simpson\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\") )", - "Description": "Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.", - "License": "GPL-3", - "URL": "https://github.com/mdlincoln/clipr, http://matthewlincoln.net/clipr/", - "BugReports": "https://github.com/mdlincoln/clipr/issues", - "Imports": [ - "utils" - ], - "Suggests": [ - "covr", - "knitr", - "rmarkdown", - "rstudioapi (>= 0.5)", - "testthat (>= 2.0.0)" - ], - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "Language": "en-US", - "RoxygenNote": "7.3.3", - "SystemRequirements": "xclip (https://github.com/astrand/xclip) or xsel (http://www.vergenet.net/~conrad/software/xsel/) for accessing the X11 clipboard, or wl-clipboard (https://github.com/bugaevc/wl-clipboard) for systems using Wayland.", - "NeedsCompilation": "no", - "Author": "Matthew Lincoln [aut, cre] (ORCID: ), Louis Maddox [ctb], Steve Simpson [ctb], Jennifer Bryan [ctb]", - "Maintainer": "Matthew Lincoln ", - "Repository": "P3M" - }, - "colorspace": { - "Package": "colorspace", - "Version": "2.1-3", - "Source": "Repository", - "Date": "2026-07-10", - "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", - "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", - "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", - "Depends": [ - "R (>= 3.0.0)", - "methods" - ], - "Imports": [ - "graphics", - "grDevices", - "stats" - ], - "Suggests": [ - "datasets", - "utils", - "KernSmooth", - "MASS", - "kernlab", - "mvtnorm", - "vcd", - "tcltk", - "shiny", - "shinyjs", - "ggplot2", - "dplyr", - "scales", - "grid", - "png", - "jpeg", - "knitr", - "rmarkdown", - "RColorBrewer", - "rcartocolor", - "scico", - "viridis", - "wesanderson" - ], - "VignetteBuilder": "knitr", - "License": "BSD_3_clause + file LICENSE", - "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", - "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", - "LazyData": "yes", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Ross Ihaka [aut], Paul Murrell [aut] (ORCID: ), Kurt Hornik [aut] (ORCID: ), Jason C. Fisher [aut] (ORCID: ), Reto Stauffer [aut] (ORCID: ), Claus O. Wilke [aut] (ORCID: ), Claire D. McWhite [aut] (ORCID: ), Achim Zeileis [aut, cre] (ORCID: )", - "Maintainer": "Achim Zeileis ", - "Repository": "P3M" - }, - "colourpicker": { - "Package": "colourpicker", - "Version": "1.3.0", - "Source": "Repository", - "Title": "A Colour Picker Tool for Shiny and for Selecting Colours in Plots", - "Authors@R": "c( person(\"Dean\", \"Attali\", email = \"daattali@gmail.com\", role = c(\"aut\", \"cre\"), comment= c(ORCID=\"0000-0002-5645-3493\")), person(\"David\", \"Griswold\", email=\"novachild@gmail.com\", role = \"ctb\") )", - "Description": "A colour picker that can be used as an input in 'Shiny' apps or Rmarkdown documents. The colour picker supports alpha opacity, custom colour palettes, and many more options. A Plot Colour Helper tool is available as an 'RStudio' Addin, which helps you pick colours to use in your plots. A more generic Colour Picker 'RStudio' Addin is also provided to let you select colours to use in your R code.", - "URL": "https://github.com/daattali/colourpicker, https://daattali.com/shiny/colourInput/", - "BugReports": "https://github.com/daattali/colourpicker/issues", - "Depends": [ - "R (>= 3.1.0)" - ], - "Imports": [ - "ggplot2", - "htmltools", - "htmlwidgets (>= 0.7)", - "jsonlite", - "miniUI (>= 0.1.1)", - "shiny (>= 0.11.1)", - "shinyjs (>= 2.0.0)", - "utils" - ], - "Suggests": [ - "knitr (>= 1.7)", - "rmarkdown", - "rstudioapi (>= 0.5)", - "shinydisconnect" - ], - "License": "MIT + file LICENSE", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "NeedsCompilation": "no", - "Author": "Dean Attali [aut, cre] (), David Griswold [ctb]", - "Maintainer": "Dean Attali ", - "Repository": "P3M" - }, - "commonmark": { - "Package": "commonmark", - "Version": "2.0.0", - "Source": "Repository", - "Type": "Package", - "Title": "High Performance CommonMark and Github Markdown Rendering in R", - "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", - "Description": "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.", - "License": "BSD_2_clause + file LICENSE", - "URL": "https://docs.ropensci.org/commonmark/ https://ropensci.r-universe.dev/commonmark", - "BugReports": "https://github.com/r-lib/commonmark/issues", - "Suggests": [ - "curl", - "testthat", - "xml2" - ], - "RoxygenNote": "7.3.2", - "Language": "en-US", - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Author": "Jeroen Ooms [aut, cre] (ORCID: ), John MacFarlane [cph] (Author of cmark)", - "Maintainer": "Jeroen Ooms ", - "Repository": "P3M" - }, - "conflicted": { - "Package": "conflicted", - "Version": "1.2.0", - "Source": "Repository", - "Title": "An Alternative Conflict Resolution Strategy", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", - "Description": "R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.", - "License": "MIT + file LICENSE", - "URL": "https://conflicted.r-lib.org/, https://github.com/r-lib/conflicted", - "BugReports": "https://github.com/r-lib/conflicted/issues", - "Depends": [ - "R (>= 3.2)" - ], - "Imports": [ - "cli (>= 3.4.0)", - "memoise", - "rlang (>= 1.0.0)" - ], - "Suggests": [ - "callr", - "covr", - "dplyr", - "Matrix", - "methods", - "pkgload", - "testthat (>= 3.0.0)", - "withr" - ], - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", - "Maintainer": "Hadley Wickham ", - "Repository": "P3M" - }, - "cpp11": { - "Package": "cpp11", - "Version": "0.5.5", - "Source": "Repository", - "Title": "A C++11 Interface for R's C Interface", - "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", - "License": "MIT + file LICENSE", - "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", - "BugReports": "https://github.com/r-lib/cpp11/issues", - "Depends": [ - "R (>= 4.0.0)" - ], - "Suggests": [ - "bench", - "brio", - "callr", - "cli", - "covr", - "decor", - "desc", - "ggplot2", - "glue", - "knitr", - "lobstr", - "mockery", - "progress", - "rmarkdown", - "scales", - "Rcpp", - "testthat (>= 3.2.0)", - "tibble", - "utils", - "vctrs", - "withr" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3", - "NeedsCompilation": "no", - "Author": "Davis Vaughan [aut, cre] (ORCID: ), Jim Hester [aut] (ORCID: ), Romain François [aut] (ORCID: ), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", - "Maintainer": "Davis Vaughan ", - "Repository": "P3M" - }, - "crayon": { - "Package": "crayon", - "Version": "1.5.3", - "Source": "Repository", - "Title": "Colored Terminal Output", - "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", - "License": "MIT + file LICENSE", - "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", - "BugReports": "https://github.com/r-lib/crayon/issues", - "Imports": [ - "grDevices", - "methods", - "utils" - ], - "Suggests": [ - "mockery", - "rstudioapi", - "testthat", - "withr" - ], - "Config/Needs/website": "tidyverse/tidytemplate", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", - "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", - "NeedsCompilation": "no", - "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", - "Maintainer": "Gábor Csárdi ", - "Repository": "P3M" - }, - "crosstalk": { - "Package": "crosstalk", - "Version": "1.2.2", - "Source": "Repository", - "Type": "Package", - "Title": "Inter-Widget Interactivity for HTML Widgets", - "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(, \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(, \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", - "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). 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The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.", - "License": "MIT + file LICENSE", - "URL": "https://gt.rstudio.com, https://github.com/rstudio/gt", - "BugReports": "https://github.com/rstudio/gt/issues", - "Depends": [ - "R (>= 4.1.0)" - ], - "Imports": [ - "base64enc (>= 0.1-3)", - "bigD (>= 0.2)", - "bitops (>= 1.0-7)", - "cli (>= 3.6.3)", - "commonmark (>= 1.9.1)", - "dplyr (>= 1.1.4)", - "fs (>= 1.6.4)", - "glue (>= 1.8.0)", - "htmltools (>= 0.5.8.1)", - "htmlwidgets (>= 1.6.4)", - "juicyjuice (>= 0.1.0)", - "magrittr (>= 2.0.3)", - "markdown (>= 1.13)", - "reactable (>= 0.4.4)", - "rlang (>= 1.1.4)", - "sass (>= 0.4.9)", - "scales (>= 1.3.0)", - "tidyselect (>= 1.2.1)", - "vctrs", - "xml2 (>= 1.3.6)" - ], - "Suggests": [ - "bit64", - "farver", - "fontawesome (>= 0.5.2)", - "ggplot2", - "grid", - "gtable (>= 0.3.6)", - "katex (>= 1.4.1)", - "knitr", - "lubridate", - "magick", - "paletteer", - "RColorBrewer", - "rmarkdown (>= 2.20)", - "rsvg", - "rvest", - "shiny (>= 1.9.1)", - "testthat (>= 3.1.9)", - "tidyr (>= 1.0.0)", - "webshot2 (>= 0.1.0)", - "withr" - ], - "Config/Needs/coverage": "officer", - "Config/Needs/website": "quarto", - "ByteCompile": "true", - "Config/testthat/edition": "3", - "Config/testthat/parallel": "true", - "Encoding": "UTF-8", - "LazyData": "true", - "RoxygenNote": "7.3.3", - "NeedsCompilation": "no", - "Author": "Richard Iannone [aut, cre] (ORCID: ), Joe Cheng [aut], Barret Schloerke [aut] (ORCID: ), Shannon Haughton [aut], Ellis Hughes [aut] (ORCID: ), Alexandra Lauer [aut] (ORCID: ), Romain François [aut], JooYoung Seo [aut] (ORCID: ), Ken Brevoort [aut] (ORCID: ), Olivier Roy [aut], Posit Software, PBC [cph, fnd]", - "Maintainer": "Richard Iannone ", - "Repository": "P3M" - }, - "gtable": { - "Package": "gtable", - "Version": "0.3.6", - "Source": "Repository", - "Title": "Arrange 'Grobs' in Tables", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Tools to make it easier to work with \"tables\" of 'grobs'. The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.", - "License": "MIT + file LICENSE", - "URL": "https://gtable.r-lib.org, https://github.com/r-lib/gtable", - "BugReports": "https://github.com/r-lib/gtable/issues", - "Depends": [ - "R (>= 4.0)" - ], - "Imports": [ - "cli", - "glue", - "grid", - "lifecycle", - "rlang (>= 1.1.0)", - "stats" - ], - "Suggests": [ - "covr", - "ggplot2", - "knitr", - "profvis", - "rmarkdown", - "testthat (>= 3.0.0)" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2024-10-25", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", - "Maintainer": "Thomas Lin Pedersen ", - "Repository": "P3M" - }, - "haven": { - "Package": "haven", - "Version": "2.5.5", - "Source": "Repository", - "Title": "Import and Export 'SPSS', 'Stata' and 'SAS' Files", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Evan\", \"Miller\", role = c(\"aut\", \"cph\"), comment = \"Author of included ReadStat code\"), person(\"Danny\", \"Smith\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Import foreign statistical formats into R via the embedded 'ReadStat' C library, .", - "License": "MIT + file LICENSE", - "URL": "https://haven.tidyverse.org, https://github.com/tidyverse/haven, https://github.com/WizardMac/ReadStat", - "BugReports": "https://github.com/tidyverse/haven/issues", - "Depends": [ - "R (>= 3.6)" - ], - "Imports": [ - "cli (>= 3.0.0)", - "forcats (>= 0.2.0)", - "hms", - "lifecycle", - "methods", - "readr (>= 0.1.0)", - "rlang (>= 0.4.0)", - "tibble", - "tidyselect", - "vctrs (>= 0.3.0)" - ], - "Suggests": [ - "covr", - "crayon", - "fs", - "knitr", - "pillar (>= 1.4.0)", - "rmarkdown", - "testthat (>= 3.0.0)", - "utf8" - ], - "LinkingTo": [ - "cpp11" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "SystemRequirements": "GNU make, zlib: zlib1g-dev (deb), zlib-devel (rpm)", - "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), Danny Smith [aut], Posit Software, PBC [cph, fnd]", - "Maintainer": "Hadley Wickham ", - "Repository": "P3M" - }, - "highr": { - "Package": "highr", - "Version": "0.12", - "Source": "Repository", - "Type": "Package", - "Title": "Syntax Highlighting for R Source Code", - "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )", - "Description": "Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package ().", - "Depends": [ - "R (>= 3.3.0)" - ], - "Imports": [ - "xfun (>= 0.18)" - ], - "Suggests": [ - "knitr", - "markdown", - "testit" - ], - "License": "GPL", - "URL": "https://github.com/yihui/highr", - "BugReports": "https://github.com/yihui/highr/issues", - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3", - "NeedsCompilation": "no", - "Author": "Yihui Xie [aut, cre] (ORCID: ), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", - "Maintainer": "Yihui Xie ", - "Repository": "P3M" - }, - "hms": { - "Package": "hms", - "Version": "1.1.4", - "Source": "Repository", - "Title": "Pretty Time of Day", - "Date": "2025-10-11", - "Authors@R": "c( person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\"), person(\"Posit Software, PBC\", role = \"fnd\", comment = c(ROR = \"03wc8by49\")) )", - "Description": "Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.", - "License": "MIT + file LICENSE", - "URL": "https://hms.tidyverse.org/, https://github.com/tidyverse/hms", - "BugReports": "https://github.com/tidyverse/hms/issues", - "Imports": [ - "cli", - "lifecycle", - "methods", - "pkgconfig", - "rlang (>= 1.0.2)", - "vctrs (>= 0.3.8)" - ], - "Suggests": [ - "crayon", - "lubridate", - "pillar (>= 1.1.0)", - "testthat (>= 3.0.0)" - ], - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3.9000", - "NeedsCompilation": "no", - "Author": "Kirill Müller [aut, cre] (ORCID: ), R Consortium [fnd], Posit Software, PBC [fnd] (ROR: )", - "Maintainer": "Kirill Müller ", - "Repository": "P3M" - }, - "htmltools": { - "Package": "htmltools", - "Version": "0.5.9", - "Source": "Repository", - "Type": "Package", - "Title": "Tools for HTML", - "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Yihui\", \"Xie\", , \"yihui@posit.co\", role = \"aut\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Tools for HTML generation and output.", - "License": "GPL (>= 2)", - "URL": "https://github.com/rstudio/htmltools, https://rstudio.github.io/htmltools/", - "BugReports": "https://github.com/rstudio/htmltools/issues", - "Depends": [ - "R (>= 2.14.1)" - ], - "Imports": [ - "base64enc", - "digest", - "fastmap (>= 1.1.0)", - "grDevices", - "rlang (>= 1.0.0)", - "utils" - ], - "Suggests": [ - "Cairo", - "markdown", - "ragg", - "shiny", - "testthat", - "withr" - ], - "Enhances": [ - "knitr" - ], - "Config/Needs/check": "knitr", - "Config/Needs/website": "rstudio/quillt, bench", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3", - "Collate": "'colors.R' 'fill.R' 'html_dependency.R' 'html_escape.R' 'html_print.R' 'htmltools-package.R' 'images.R' 'known_tags.R' 'selector.R' 'staticimports.R' 'tag_query.R' 'utils.R' 'tags.R' 'template.R'", - "NeedsCompilation": "yes", - "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (ORCID: ), Barret Schloerke [aut] (ORCID: ), Winston Chang [aut] (ORCID: ), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]", - "Maintainer": "Carson Sievert ", - "Repository": "P3M" - }, - "htmlwidgets": { - "Package": "htmlwidgets", - "Version": "1.6.4", - "Source": "Repository", - "Type": "Package", - "Title": "HTML Widgets for R", - "Authors@R": "c( person(\"Ramnath\", \"Vaidyanathan\", role = c(\"aut\", \"cph\")), person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Kenton\", \"Russell\", role = c(\"aut\", \"cph\")), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/ramnathv/htmlwidgets", - "BugReports": "https://github.com/ramnathv/htmlwidgets/issues", - "Imports": [ - "grDevices", - "htmltools (>= 0.5.7)", - "jsonlite (>= 0.9.16)", - "knitr (>= 1.8)", - "rmarkdown", - "yaml" - ], - "Suggests": [ - "testthat" - ], - "Enhances": [ - "shiny (>= 1.1)" - ], - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "NeedsCompilation": "no", - "Author": "Ramnath Vaidyanathan [aut, cph], Yihui Xie [aut], JJ Allaire [aut], Joe Cheng [aut], Carson Sievert [aut, cre] (), Kenton Russell [aut, cph], Ellis Hughes [ctb], Posit Software, PBC [cph, fnd]", - "Maintainer": "Carson Sievert ", - "Repository": "P3M" - }, - "httpuv": { - "Package": "httpuv", - "Version": "1.6.17", - "Source": "Repository", - "Type": "Package", - "Title": "HTTP and WebSocket Server Library", - "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Hector\", \"Corrada Bravo\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Andrzej\", \"Krzemienski\", role = \"cph\", comment = \"optional.hpp\"), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file\"), person(\"Niels\", \"Provos\", role = \"cph\", comment = \"libuv subcomponent: tree.h\"), person(\"Internet Systems Consortium, Inc.\", role = \"cph\", comment = \"libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c\"), person(\"Alexander\", \"Chemeris\", role = \"cph\", comment = \"libuv subcomponent: stdint-msvc2008.h (from msinttypes)\"), person(\"Google, Inc.\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Sony Mobile Communcations AB\", role = \"cph\", comment = \"libuv subcomponent: pthread-fixes.c\"), person(\"Berkeley Software Design Inc.\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Kenneth\", \"MacKay\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016)\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Steve\", \"Reid\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"James\", \"Brown\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"Bob\", \"Trower\", role = \"aut\", comment = \"base64 implementation\"), person(\"Alexander\", \"Peslyak\", role = \"aut\", comment = \"MD5 implementation\"), person(\"Trantor Standard Systems\", role = \"cph\", comment = \"base64 implementation\"), person(\"Igor\", \"Sysoev\", role = \"cph\", comment = \"http-parser\") )", - "Description": "Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)", - "License": "GPL (>= 2) | file LICENSE", - "URL": "https://rstudio.github.io/httpuv/, https://github.com/rstudio/httpuv", - "BugReports": "https://github.com/rstudio/httpuv/issues", - "Depends": [ - "R (>= 2.15.1)" - ], - "Imports": [ - "later (>= 0.8.0)", - "promises", - "R6", - "Rcpp (>= 1.0.7)", - "utils" - ], - "Suggests": [ - "callr", - "curl", - "jsonlite", - "testthat (>= 3.0.0)", - "websocket" - ], - "LinkingTo": [ - "later", - "Rcpp" - ], - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2025-07-01", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3", - "SystemRequirements": "GNU make, zlib", - "Collate": "'RcppExports.R' 'httpuv-package.R' 'httpuv.R' 'random_port.R' 'server.R' 'staticServer.R' 'static_paths.R' 'utils.R'", - "NeedsCompilation": "yes", - "Author": "Joe Cheng [aut], Winston Chang [aut, cre], Posit, PBC [cph, fnd] (ROR: ), Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph] (optional.hpp), libuv project contributors [cph] (libuv library, see src/libuv/AUTHORS file), Joyent, Inc. and other Node contributors [cph] (libuv library, see src/libuv/AUTHORS file; and http-parser library, see src/http-parser/AUTHORS file), Niels Provos [cph] (libuv subcomponent: tree.h), Internet Systems Consortium, Inc. [cph] (libuv subcomponent: inet_pton and inet_ntop, contained in src/libuv/src/inet.c), Alexander Chemeris [cph] (libuv subcomponent: stdint-msvc2008.h (from msinttypes)), Google, Inc. [cph] (libuv subcomponent: pthread-fixes.c), Sony Mobile Communcations AB [cph] (libuv subcomponent: pthread-fixes.c), Berkeley Software Design Inc. [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Kenneth MacKay [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016) [cph] (libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c), Steve Reid [aut] (SHA-1 implementation), James Brown [aut] (SHA-1 implementation), Bob Trower [aut] (base64 implementation), Alexander Peslyak [aut] (MD5 implementation), Trantor Standard Systems [cph] (base64 implementation), Igor Sysoev [cph] (http-parser)", - "Maintainer": "Winston Chang ", - "Repository": "P3M" - }, - "httr": { - "Package": "httr", - "Version": "1.4.9", - "Source": "Repository", - "Title": "Tools for Working with URLs and HTTP", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", - "License": "MIT + file LICENSE", - "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", - "BugReports": "https://github.com/r-lib/httr/issues", - "Depends": [ - "R (>= 3.6)" - ], - "Imports": [ - "curl (>= 5.1.0)", - "jsonlite", - "mime", - "openssl (>= 0.8)", - "R6" - ], - "Suggests": [ - "covr", - "httpuv", - "jpeg", - "knitr", - "png", - "readr", - "rmarkdown", - "testthat (>= 0.8.0)", - "xml2" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/roxygen2/version": "8.1.0", - "Encoding": "UTF-8", - "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", - "Maintainer": "Hadley Wickham ", - "Repository": "P3M" - }, - "ids": { - "Package": "ids", - "Version": "1.0.1", - "Source": "Repository", - "Title": "Generate Random Identifiers", - "Authors@R": "person(\"Rich\", \"FitzJohn\", role = c(\"aut\", \"cre\"), email = \"rich.fitzjohn@gmail.com\")", - "Description": "Generate random or human readable and pronounceable identifiers.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/richfitz/ids", - "BugReports": "https://github.com/richfitz/ids/issues", - "Imports": [ - "openssl", - "uuid" - ], - "Suggests": [ - "knitr", - "rcorpora", - "rmarkdown", - "testthat" - ], - "RoxygenNote": "6.0.1", - "VignetteBuilder": "knitr", - "NeedsCompilation": "no", - "Author": "Rich FitzJohn [aut, cre]", - "Maintainer": "Rich FitzJohn ", - "Repository": "P3M", - "Encoding": "UTF-8" - }, - "isoband": { - "Package": "isoband", - "Version": "0.3.0", - "Source": "Repository", - "Title": "Generate Isolines and Isobands from Regularly Spaced Elevation Grids", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", - "Description": "A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.", - "License": "MIT + file LICENSE", - "URL": "https://isoband.r-lib.org, https://github.com/r-lib/isoband", - "BugReports": "https://github.com/r-lib/isoband/issues", - "Imports": [ - "cli", - "grid", - "rlang", - "utils" - ], - "Suggests": [ - "covr", - "ggplot2", - "knitr", - "magick", - "bench", - "rmarkdown", - "sf", - "testthat (>= 3.0.0)", - "xml2" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2025-12-05", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3", - "Config/build/compilation-database": "true", - "LinkingTo": [ - "cpp11" - ], - "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut] (ORCID: ), Claus O. Wilke [aut] (Original author, ORCID: ), Thomas Lin Pedersen [aut, cre] (ORCID: ), Posit, PBC [cph, fnd] (ROR: )", - "Maintainer": "Thomas Lin Pedersen ", - "Repository": "P3M" - }, - "jquerylib": { - "Package": "jquerylib", - "Version": "0.1.4", - "Source": "Repository", - "Title": "Obtain 'jQuery' as an HTML Dependency Object", - "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )", - "Description": "Obtain any major version of 'jQuery' () and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.", - "License": "MIT + file LICENSE", - "Encoding": "UTF-8", - "Config/testthat/edition": "3", - "RoxygenNote": "7.0.2", - "Imports": [ - "htmltools" - ], - "Suggests": [ - "testthat" - ], - "NeedsCompilation": "no", - "Author": "Carson Sievert [aut, cre] (), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)", - "Maintainer": "Carson Sievert ", - "Repository": "P3M" - }, - "jsonlite": { - "Package": "jsonlite", - "Version": "2.0.0", - "Source": "Repository", - "Title": "A Simple and Robust JSON Parser and Generator for R", - "License": "MIT + file LICENSE", - "Depends": [ - "methods" - ], - "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))", - "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805", - "BugReports": "https://github.com/jeroen/jsonlite/issues", - "Maintainer": "Jeroen Ooms ", - "VignetteBuilder": "knitr, R.rsp", - "Description": "A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.", - "Suggests": [ - "httr", - "vctrs", - "testthat", - "knitr", - "rmarkdown", - "R.rsp", - "sf" - ], - "RoxygenNote": "7.3.2", - "Encoding": "UTF-8", - "NeedsCompilation": "yes", - "Author": "Jeroen Ooms [aut, cre] (), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", - "Repository": "CRAN" - }, - "juicyjuice": { - "Package": "juicyjuice", - "Version": "0.1.0", - "Source": "Repository", - "Title": "Inline CSS Properties into HTML Tags Using 'juice'", - "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"riannone@me.com\", c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Automattic\", role = c(\"cph\"), comment = \"juice library\"), person(\"juice contributors\", role = c(\"ctb\"), comment = \"juice library\") )", - "Description": "There are occasions where you need a piece of HTML with integrated styles. A prime example of this is HTML email. This transformation involves moving the CSS and associated formatting instructions from the style block in the head of your document into the body of the HTML. Many prominent email clients require integrated styles in HTML email; otherwise a received HTML email will be displayed without any styling. This package will quickly and precisely perform these CSS transformations when given HTML text and it does so by using the JavaScript 'juice' library.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/rich-iannone/juicyjuice", - "BugReports": "https://github.com/rich-iannone/juicyjuice/issues", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.1", - "Imports": [ - "V8 (>= 4.2.0)" - ], - "Suggests": [ - "testthat (>= 3.0.0)" - ], - "Config/testthat/edition": "3", - "NeedsCompilation": "no", - "Author": "Richard Iannone [aut, cre, cph] (), Automattic [cph] (juice library), juice contributors [ctb] (juice library)", - "Maintainer": "Richard Iannone ", - "Repository": "P3M" - }, - "kableExtra": { - "Package": "kableExtra", - "Version": "1.4.1", - "Source": "Repository", - "Type": "Package", - "Title": "Construct Complex Table with 'kable' and Pipe Syntax", - "Authors@R": "c( person('Hao', 'Zhu', email = 'haozhu233@gmail.com', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3386-6076')), person('Thomas', 'Travison', role = 'ctb'), person('Timothy', 'Tsai', role = 'ctb'), person('Will', 'Beasley', email = 'wibeasley@hotmail.com', role = 'ctb'), person('Yihui', 'Xie', email = 'xie@yihui.name', role = 'ctb'), person('GuangChuang', 'Yu', email = 'guangchuangyu@gmail.com', role = 'ctb'), person('Stéphane', 'Laurent', role = 'ctb'), person('Rob', 'Shepherd', role = 'ctb'), person('Yoni', 'Sidi', role = 'ctb'), person('Brian', 'Salzer', role = 'ctb'), person('George', 'Gui', role = 'ctb'), person('Yeliang', 'Fan', role = 'ctb'), person('Duncan', 'Murdoch', role = 'ctb'), person('Vincent', 'Arel-Bundock', role = 'ctb'), person('Bill', 'Evans', role = 'ctb') )", - "Description": "Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.", - "License": "MIT + file LICENSE", - "URL": "https://haozhu233.github.io/kableExtra/, https://github.com/haozhu233/kableExtra", - "BugReports": "https://github.com/haozhu233/kableExtra/issues", - "Depends": [ - "R (>= 3.1.0)" - ], - "Imports": [ - "knitr (>= 1.33)", - "magrittr", - "stringr (>= 1.0)", - "xml2 (>= 1.1.1)", - "rmarkdown (>= 1.6.0)", - "scales", - "viridisLite", - "stats", - "grDevices", - "htmltools", - "rstudioapi", - "tools", - "digest", - "graphics", - "svglite" - ], - "Suggests": [ - "testthat", - "magick", - "tinytex", - "formattable", - "sparkline", - "webshot2" - ], - "Config/testthat/edition": "3", - "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Language": "en-US", - "NeedsCompilation": "no", - "Author": "Hao Zhu [aut, cre] (ORCID: ), Thomas Travison [ctb], Timothy Tsai [ctb], Will Beasley [ctb], Yihui Xie [ctb], GuangChuang Yu [ctb], Stéphane Laurent [ctb], Rob Shepherd [ctb], Yoni Sidi [ctb], Brian Salzer [ctb], George Gui [ctb], Yeliang Fan [ctb], Duncan Murdoch [ctb], Vincent Arel-Bundock [ctb], Bill Evans [ctb]", - "Maintainer": "Hao Zhu ", - "Repository": "P3M" - }, - "knitr": { - "Package": "knitr", - "Version": "1.52", - "Source": "Repository", - "Type": "Package", - "Title": "A General-Purpose Package for Dynamic Report Generation in R", - "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de\"), person(\"Aron\", \"Atkins\", role = \"ctb\"), person(\"Aaron\", \"Wolen\", role = \"ctb\"), person(\"Ashley\", \"Manton\", role = \"ctb\"), person(\"Atsushi\", \"Yasumoto\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8335-495X\")), person(\"Ben\", \"Baumer\", role = \"ctb\"), person(\"Brian\", \"Diggs\", role = \"ctb\"), person(\"Brian\", \"Zhang\", role = \"ctb\"), person(\"Bulat\", \"Yapparov\", role = \"ctb\"), person(\"Cassio\", \"Pereira\", role = \"ctb\"), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person(\"David\", \"Hall\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", role = \"ctb\"), person(\"David\", \"Robinson\", role = \"ctb\"), person(\"Doug\", \"Hemken\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", role = \"ctb\"), person(\"Elio\", \"Campitelli\", role = \"ctb\"), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Emily\", \"Riederer\", role = \"ctb\"), person(\"Fabian\", \"Hirschmann\", role = \"ctb\"), person(\"Fitch\", \"Simeon\", role = \"ctb\"), person(\"Forest\", \"Fang\", role = \"ctb\"), person(c(\"Frank\", \"E\", \"Harrell\", \"Jr\"), role = \"ctb\", comment = \"the Sweavel package at inst/misc/Sweavel.sty\"), person(\"Garrick\", \"Aden-Buie\", role = \"ctb\"), person(\"Gregoire\", \"Detrez\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Hao\", \"Zhu\", role = \"ctb\"), person(\"Heewon\", \"Jeon\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Hodges\", \"Daniel\", role = \"ctb\"), person(\"Jacob\", \"Bien\", role = \"ctb\"), person(\"Jake\", \"Burkhead\", role = \"ctb\"), person(\"James\", \"Manton\", role = \"ctb\"), person(\"Jared\", \"Lander\", role = \"ctb\"), person(\"Jason\", \"Punyon\", role = \"ctb\"), person(\"Javier\", \"Luraschi\", role = \"ctb\"), person(\"Jeff\", \"Arnold\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", role = \"ctb\"), person(\"Jeremy\", \"Ashkenas\", role = c(\"ctb\", \"cph\"), comment = \"the CSS file at inst/misc/docco-classic.css\"), person(\"Jeremy\", \"Stephens\", role = \"ctb\"), person(\"Jim\", \"Hester\", role = \"ctb\"), person(\"Joe\", \"Cheng\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\"), person(\"Johannes\", \"Ranke\", role = \"ctb\"), person(\"John\", \"Honaker\", role = \"ctb\"), person(\"John\", \"Muschelli\", role = \"ctb\"), person(\"Jonathan\", \"Keane\", role = \"ctb\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Johan\", \"Toloe\", role = \"ctb\"), person(\"Jonathan\", \"Sidi\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Julien\", \"Barnier\", role = \"ctb\"), person(\"Kaiyin\", \"Zhong\", role = \"ctb\"), person(\"Kamil\", \"Slowikowski\", role = \"ctb\"), person(\"Karl\", \"Forner\", role = \"ctb\"), person(c(\"Kevin\", \"K.\"), \"Smith\", role = \"ctb\"), person(\"Kirill\", \"Mueller\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Leonidas\", \"Zhak\", role = \"ctb\"), person(\"Lorenz\", \"Walthert\", role = \"ctb\"), person(\"Lucas\", \"Gallindo\", role = \"ctb\"), person(\"Marius\", \"Hofert\", role = \"ctb\"), person(\"Martin\", \"Modrák\", role = \"ctb\"), person(\"Michael\", \"Chirico\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"Michel\", \"Kuhlmann\", role = \"ctb\"), person(\"Miller\", \"Patrick\", role = \"ctb\"), person(\"Nacho\", \"Caballero\", role = \"ctb\"), person(\"Nick\", \"Salkowski\", role = \"ctb\"), person(\"Niels Richard\", \"Hansen\", role = \"ctb\"), person(\"Noam\", \"Ross\", role = \"ctb\"), person(\"Obada\", \"Mahdi\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = \"ctb\", comment=c(ORCID = \"0000-0002-9101-3362\")), person(\"Pedro\", \"Faria\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\"), person(\"Ramnath\", \"Vaidyanathan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Robert\", \"Krzyzanowski\", role = \"ctb\"), person(\"Rodrigo\", \"Copetti\", role = \"ctb\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Ruaridh\", \"Williamson\", role = \"ctb\"), person(\"Sagiru\", \"Mati\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1413-3974\")), person(\"Scott\", \"Kostyshak\", role = \"ctb\"), person(\"Sebastian\", \"Meyer\", role = \"ctb\"), person(\"Sietse\", \"Brouwer\", role = \"ctb\"), person(c(\"Simon\", \"de\"), \"Bernard\", role = \"ctb\"), person(\"Sylvain\", \"Rousseau\", role = \"ctb\"), person(\"Taiyun\", \"Wei\", role = \"ctb\"), person(\"Thibaut\", \"Assus\", role = \"ctb\"), person(\"Thibaut\", \"Lamadon\", role = \"ctb\"), person(\"Thomas\", \"Leeper\", role = \"ctb\"), person(\"Tim\", \"Mastny\", role = \"ctb\"), person(\"Tom\", \"Torsney-Weir\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = \"ctb\"), person(\"Viktoras\", \"Veitas\", role = \"ctb\"), person(\"Weicheng\", \"Zhu\", role = \"ctb\"), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Zachary\", \"Foster\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.", - "Depends": [ - "R (>= 3.6.0)" - ], - "Imports": [ - "evaluate (>= 0.15)", - "highr (>= 0.11)", - "methods", - "tools", - "xfun (>= 0.52)", - "yaml (>= 2.1.19)" - ], - "Suggests": [ - "bslib", - "DBI (>= 0.4-1)", - "digest", - "formatR", - "gifski", - "gridSVG", - "htmlwidgets (>= 0.7)", - "jpeg", - "JuliaCall (>= 0.11.1)", - "magick", - "litedown (>= 0.10)", - "otel", - "otelsdk", - "png", - "ragg (>= 1.5.0)", - "reticulate (>= 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The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", - "Collate": "'block.R' 'cache.R' 'citation.R' 'hooks-html.R' 'plot.R' 'utils.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks-typst.R' 'hooks.R' 'otel.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", - "Config/roxygen2/version": "8.1.0", - "NeedsCompilation": "no", - "Author": "Yihui Xie [aut, cre] (ORCID: , URL: https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (ORCID: ), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johan Larsson [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Leonidas Zhak [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (ORCID: ), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (ORCID: ), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. 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"Description": "Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft PowerPoint' documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. The package does not require any installation of Microsoft products to be able to write Microsoft files.", - "License": "MIT + file LICENSE", - "URL": "https://ardata-fr.github.io/officeverse/, https://davidgohel.github.io/officer/", - "BugReports": "https://github.com/davidgohel/officer/issues", - "Imports": [ - "cli", - "dplyr", - "graphics", - "grDevices", - "openssl", - "R6", - "ragg", - "stats", - "tidyr", - "utils", - "uuid", - "xml2 (>= 1.1.0)", - "zip (>= 2.1.0)" - ], - "Suggests": [ - "devEMF", - "doconv (>= 0.3.0)", - "gdtools", - "ggplot2", - "knitr", - "magick", - "rmarkdown", - "rsvg", - "mschart", - "testthat", - "withr" - ], - "Encoding": "UTF-8", - "Collate": "'core_properties.R' 'custom_properties.R' 'defunct.R' 'dev-utils.R' 'docx_add.R' 'docx_comments.R' 'docx_cursor.R' 'docx_embed_font.R' 'docx_part.R' 'docx_replace.R' 'docx_section.R' 'docx_settings.R' 'docx_styles.R' 'docx_utils_funs.R' 'empty_content.R' 'formatting_properties.R' 'fortify_docx.R' 'fortify_pptx.R' 'knitr_utils.R' 'officer.R' 'ooxml.R' 'ooxml_block_objects.R' 'ooxml_run_objects.R' 'openxml_content_type.R' 'openxml_document.R' 'pack_folder.R' 'ph_location.R' 'post-proc.R' 'ppt_class_dir_collection.R' 'ppt_classes.R' 'ppt_notes.R' 'ppt_ph_dedupe_layout.R' 'ppt_ph_manipulate.R' 'ppt_ph_rename_layout.R' 'ppt_ph_with_methods.R' 'pptx_informations.R' 'pptx_layout_helper.R' 'pptx_matrix.R' 'utils.R' 'pptx_slide_manip.R' 'read_docx.R' 'docx_write.R' 'read_docx_styles.R' 'read_pptx.R' 'read_xlsx.R' 'relationship.R' 'rtf.R' 'shape_properties.R' 'shorcuts.R' 'docx_append_context.R' 'utils-xml.R' 'deprecated.R' 'zzz.R'", - "Config/roxygen2/version": "8.0.0", - "NeedsCompilation": "no", - "Author": "David Gohel [aut, cre], Stefan Moog [aut], Mark Heckmann [aut] (ORCID: ), ArData [cph], Frank Hangler [ctb] (function body_replace_all_text), Liz Sander [ctb] (several documentation fixes), Anton Victorson [ctb] (fixes xml structures), Jon Calder [ctb] (update vignettes), John Harrold [ctb] (function annotate_base), John Muschelli [ctb] (google doc compatibility), Bill Denney [ctb] (ORCID: , function as.matrix.rpptx), Nikolai Beck [ctb] (set speaker notes for .pptx documents), Greg Leleu [ctb] (fields functionality in ppt), Majid Eismann [ctb], Wahiduzzaman Khan [ctb] (vectorization of remove_slide), Hongyuan Jia [ctb] (ORCID: ), Michael Stackhouse [ctb]", - "Maintainer": "David Gohel ", - "Repository": "P3M" - }, - "openssl": { - "Package": "openssl", - "Version": "2.4.2", - "Source": "Repository", - "Type": "Package", - "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", - "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Oliver\", \"Keyes\", role = \"ctb\"))", - "Description": "Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", - "License": "MIT + file LICENSE", - "URL": "https://jeroen.r-universe.dev/openssl", - "BugReports": "https://github.com/jeroen/openssl/issues", - "SystemRequirements": "OpenSSL >= 1.0.2", - "VignetteBuilder": "knitr", - "Imports": [ - "askpass" - ], - "Suggests": [ - "curl", - "testthat (>= 2.1.0)", - "digest", - "knitr", - "rmarkdown", - "jsonlite", - "jose", - "sodium" - ], - "Encoding": "UTF-8", - "Config/roxygen2/version": "8.0.0", - "NeedsCompilation": "yes", - "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Oliver Keyes [ctb]", - "Maintainer": "Jeroen Ooms ", - "Repository": "P3M" - }, - "otel": { - "Package": "otel", - "Version": "0.2.0", - "Source": "Repository", - "Title": "OpenTelemetry R API", - "Authors@R": "person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\"))", - "Description": "High-quality, ubiquitous, and portable telemetry to enable effective observability. OpenTelemetry is a collection of tools, APIs, and SDKs used to instrument, generate, collect, and export telemetry data (metrics, logs, and traces) for analysis in order to understand your software's performance and behavior. This package implements the OpenTelemetry API: . 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Time intervals: '1337000' -> '15d 11h 23m 20s'. Vague time intervals: '2674000' -> 'about a month ago'. Bytes: '1337' -> '1.34 kB'. Rounding: '99' with 3 significant digits -> '99.0' p-values: '0.00001' -> '<0.0001'. Colors: '#FF0000' -> 'red'. 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It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes. It can read the standard output and error of the processes, using non-blocking connections. 'processx' can poll a process for standard output or error, with a timeout. It can also poll several processes at once.", - "License": "MIT + file LICENSE", - "URL": "https://processx.r-lib.org, https://github.com/r-lib/processx", - "BugReports": "https://github.com/r-lib/processx/issues", - "Depends": [ - "R (>= 3.4.0)" - ], - "Imports": [ - "ps (>= 1.9.3)", - "R6", - "utils" - ], - "Suggests": [ - "callr (>= 3.7.3)", - "cli (>= 3.3.0)", - "codetools", - "covr", - "curl", - "debugme", - "parallel", - "rlang (>= 1.0.2)", - "testthat (>= 3.0.0)", - "webfakes", - "withr" - ], - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2025-04-25", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.3", - "NeedsCompilation": "yes", - "Author": "Gábor Csárdi [aut, cre, cph] (ORCID: ), Winston Chang [aut], Posit Software, PBC [cph, fnd] (ROR: ), Ascent Digital Services [cph, fnd]", - "Maintainer": "Gábor Csárdi ", - "Repository": "P3M" - }, - "progress": { - "Package": "progress", - "Version": "1.2.3", - "Source": "Repository", - "Title": "Terminal Progress Bars", - "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Rich\", \"FitzJohn\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Configurable Progress bars, they may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. The package also provides a 'C++' 'API', that works with or without 'Rcpp'.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/r-lib/progress#readme, http://r-lib.github.io/progress/", - "BugReports": "https://github.com/r-lib/progress/issues", - "Depends": [ - "R (>= 3.6)" - ], - "Imports": [ - "crayon", - "hms", - "prettyunits", - "R6" - ], - "Suggests": [ - "Rcpp", - "testthat (>= 3.0.0)", - "withr" - ], - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "NeedsCompilation": "no", - "Author": "Gábor Csárdi [aut, cre], Rich FitzJohn [aut], Posit Software, PBC [cph, fnd]", - "Maintainer": "Gábor Csárdi ", - "Repository": "P3M" - }, - "promises": { - "Package": "promises", - "Version": "1.5.0", - "Source": "Repository", - "Type": "Package", - "Title": "Abstractions for Promise-Based Asynchronous Programming", - "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Charlie\", \"Gao\", , \"charlie.gao@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-0750-061X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", - "Description": "Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.", - "License": "MIT + file LICENSE", - "URL": "https://rstudio.github.io/promises/, https://github.com/rstudio/promises", - "BugReports": "https://github.com/rstudio/promises/issues", - "Depends": [ - "R (>= 4.1.0)" - ], - "Imports": [ - "fastmap (>= 1.1.0)", - "later", - "lifecycle", - "magrittr (>= 1.5)", - "otel (>= 0.2.0)", - "R6", - "rlang" - ], - "Suggests": [ - "future (>= 1.21.0)", - "knitr", - "mirai", - "otelsdk (>= 0.2.0)", - "purrr", - "Rcpp", - "rmarkdown", - "spelling", - "testthat (>= 3.0.0)", - "vembedr" - ], - "VignetteBuilder": "knitr", - "Config/Needs/website": "rsconnect, tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/usethis/last-upkeep": "2025-05-27", - "Encoding": "UTF-8", - "Language": "en-US", - "RoxygenNote": "7.3.3", - "NeedsCompilation": "no", - "Author": "Joe Cheng [aut], Barret Schloerke [aut, cre] (ORCID: ), Winston Chang [aut] (ORCID: ), Charlie Gao [aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", - 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"NeedsCompilation": "no", - "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] (ORCID: ), Christophe Dervieux [aut] (ORCID: ), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (ORCID: ), Andrew Dunning [ctb] (ORCID: ), Atsushi Yasumoto [ctb, cph] (ORCID: , cph: Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (ORCID: ), Devon Ryan [ctb] (ORCID: ), Frederik Aust [ctb] (ORCID: ), Jeff Allen [ctb], JooYoung Seo [ctb] (ORCID: ), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], Posit Software, PBC [cph, fnd], jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. 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With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. 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This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package 'cssselect' ().", - "NeedsCompilation": "no", - "Author": "Simon Potter [aut, trl, cre], Simon Sapin [aut], Ian Bicking [aut]", - "Maintainer": "Simon Potter ", - "Repository": "P3M" - }, - "shiny": { - "Package": "shiny", - "Version": "1.14.0", - "Source": "Repository", - "Type": "Package", - "Title": "Web Application Framework for R", - "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Garrick\", \"Aden-Buie\", , \"garrick@adenbuie.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Yihui\", \"Xie\", , \"yihui@posit.co\", role = \"aut\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Jonathan\", \"McPherson\", , \"jonathan@posit.co\", role = \"aut\"), person(\"Alan\", \"Dipert\", role = \"aut\"), person(\"Barbara\", \"Borges\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(, \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(, \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(, \"jQuery UI contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Prem Nawaz\", \"Khan\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), person(\"Victor\", \"Tsaran\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), person(\"Dennis\", \"Lembree\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), person(\"Srinivasu\", \"Chakravarthula\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), person(\"Cathy\", \"O'Connor\", role = \"ctb\", comment = \"Bootstrap accessibility plugin\"), person(, \"PayPal, Inc\", role = \"cph\", comment = \"Bootstrap accessibility plugin\"), person(\"Stefan\", \"Petre\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap-datepicker library\"), person(\"Andrew\", \"Rowls\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap-datepicker library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Salmen\", \"Bejaoui\", role = c(\"ctb\", \"cph\"), comment = \"selectize-plugin-a11y library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\"), person(, \"SpryMedia Limited\", role = c(\"ctb\", \"cph\"), comment = \"DataTables library\"), person(\"Ivan\", \"Sagalaev\", role = c(\"ctb\", \"cph\"), comment = \"highlight.js library\"), person(\"R Core Team\", role = c(\"ctb\", \"cph\"), comment = \"tar implementation from R\") )", - "Description": "Makes it incredibly easy to build interactive web applications with R. 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authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Prem Nawaz Khan [ctb] (Bootstrap accessibility plugin), Victor Tsaran [ctb] (Bootstrap accessibility plugin), Dennis Lembree [ctb] (Bootstrap accessibility plugin), Srinivasu Chakravarthula [ctb] (Bootstrap accessibility plugin), Cathy O'Connor [ctb] (Bootstrap accessibility plugin), PayPal, Inc [cph] (Bootstrap accessibility plugin), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Brian Reavis [ctb, cph] (selectize.js library), Salmen Bejaoui [ctb, cph] (selectize-plugin-a11y library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)", - "Maintainer": "Carson Sievert ", - "Repository": "P3M" - }, - "shinyjs": { - "Package": "shinyjs", - "Version": "2.1.1", - "Source": "Repository", - "Title": "Easily Improve the User Experience of Your Shiny Apps in Seconds", - "Authors@R": "person(\"Dean\", \"Attali\", email = \"daattali@gmail.com\", role = c(\"aut\", \"cre\"), comment= c(ORCID=\"0000-0002-5645-3493\"))", - "Description": "Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. 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Warnes [ctb], Zhian N. Kamvar [ctb]", - "Maintainer": "Hadley Wickham ", - "Repository": "P3M" - }, - "zip": { - "Package": "zip", - "Version": "3.0.2", - "Source": "Repository", - "Title": "Cross-Platform 'zip' Compression", - "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Arm Limited\", role = c(\"ctb\", \"cph\"), comment = \"bundled Mbed TLS crypto subset in src/mbedtls/ (Apache-2.0)\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", - "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", - "License": "MIT + file LICENSE", - "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", - "BugReports": "https://github.com/r-lib/zip/issues", - "LinkingTo": [ - "cli" - ], - "Suggests": [ - "callr", - "cli", - "curl", - "pillar", - "processx", - "R6", - "testthat", - "webfakes", - "withr" - ], - "Config/Needs/website": "tidyverse/tidytemplate", - "Config/testthat/edition": "3", - "Config/testthat/parallel": "true", - "Config/testthat/start-first": "large-files, http", - "Config/usethis/last-upkeep": "2025-05-07", - "Encoding": "UTF-8", - "Config/roxygen2/version": "8.0.0", - "NeedsCompilation": "yes", - "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Arm Limited [ctb, cph] (bundled Mbed TLS crypto subset in src/mbedtls/ (Apache-2.0)), Posit Software, PBC [cph, fnd] (ROR: )", - "Maintainer": "Gábor Csárdi ", - "Repository": "P3M" - } - } -} diff --git a/tests/renv/.gitignore b/tests/renv/.gitignore deleted file mode 100644 index 0ec0cbba2d7..00000000000 --- a/tests/renv/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -library/ -local/ -cellar/ -lock/ -python/ -sandbox/ -staging/ diff --git a/tests/renv/activate.R b/tests/renv/activate.R deleted file mode 100644 index b9191f310a3..00000000000 --- a/tests/renv/activate.R +++ /dev/null @@ -1,1438 +0,0 @@ - -local({ - - # the requested version of renv - version <- "1.2.4" - attr(version, "md5") <- "d5a3bd382107712f897630627794f81a" - attr(version, "sha") <- NULL - - # the project directory - project <- Sys.getenv("RENV_PROJECT") - if (!nzchar(project)) - 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 - # 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 - ansify <- function(text) { - if (renv_ansify_enabled()) - renv_ansify_enhanced(text) - else - renv_ansify_default(text) - } - - renv_ansify_enabled <- function() { - - override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) - if (!is.na(override)) - return(as.logical(override)) - - pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) - if (identical(pane, "build")) - return(FALSE) - - testthat <- Sys.getenv("TESTTHAT", unset = "false") - if (tolower(testthat) %in% "true") - return(FALSE) - - iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") - if (tolower(iderun) %in% "false") - return(FALSE) - - TRUE - - } - - renv_ansify_default <- function(text) { - text - } - - renv_ansify_enhanced <- function(text) { - - # R help links - pattern <- "`\\?(renv::(?:[^`])+)`" - replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`" - text <- gsub(pattern, replacement, text, perl = TRUE) - - # runnable code - pattern <- "`(renv::(?:[^`])+)`" - replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`" - text <- gsub(pattern, replacement, text, perl = TRUE) - - # return ansified text - text - - } - - renv_ansify_init <- function() { - - envir <- renv_envir_self() - if (renv_ansify_enabled()) - assign("ansify", renv_ansify_enhanced, envir = envir) - else - assign("ansify", renv_ansify_default, envir = envir) - - } - - `%||%` <- 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()) - - # also check for config environment variables that should suppress messages - # https://github.com/rstudio/renv/issues/2214 - enabled <- Sys.getenv("RENV_CONFIG_STARTUP_QUIET", unset = NA) - if (!is.na(enabled) && tolower(enabled) %in% c("true", "1")) - return(invisible()) - - enabled <- Sys.getenv("RENV_CONFIG_SYNCHRONIZED_CHECK", unset = NA) - if (!is.na(enabled) && tolower(enabled) %in% c("false", "0")) - 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) - - } - - heredoc <- function(text, leave = 0) { - - # remove leading, trailing whitespace - trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) - - # split into lines - lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] - - # compute common indent - indent <- regexpr("[^[:space:]]", lines) - common <- min(setdiff(indent, -1L)) - leave - text <- paste(substring(lines, common), collapse = "\n") - - # substitute in ANSI links for executable renv code - ansify(text) - - } - - bootstrap <- function(version, library) { - - friendly <- renv_bootstrap_version_friendly(version) - section <- header(sprintf("Bootstrapping renv %s", friendly)) - catf(section) - - # ensure the target library path exists; required for file.copy(..., recursive = TRUE) - dir.create(library, showWarnings = FALSE, recursive = TRUE) - - # try to install renv from cache - md5 <- attr(version, "md5", exact = TRUE) - if (length(md5)) { - pkgpath <- renv_bootstrap_find(version) - if (length(pkgpath) && file.exists(pkgpath)) { - ok <- file.copy(pkgpath, library, recursive = TRUE) - if (isTRUE(ok)) - return(invisible()) - } - } - - # 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)) { - - # split on ';' if present - parts <- strsplit(repos, ";", fixed = TRUE)[[1L]] - - # split into named repositories if present - idx <- regexpr("=", parts, fixed = TRUE) - keys <- substring(parts, 1L, idx - 1L) - vals <- substring(parts, idx + 1L) - names(vals) <- keys - - # if we have a single unnamed repository, call it CRAN - if (length(vals) == 1L && identical(keys, "")) - names(vals) <- "CRAN" - - return(vals) - - } - - # 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$Repositories - if (length(repos) == 0) - return(NULL) - - keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) - vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) - names(vals) <- keys - - return(vals) - - } - - renv_bootstrap_download <- function(version) { - - sha <- attr(version, "sha", exact = TRUE) - - methods <- if (!is.null(sha)) { - - # attempting to bootstrap a development version of renv - c( - function() renv_bootstrap_download_tarball(sha), - function() renv_bootstrap_download_github(sha) - ) - - } else { - - # attempting to bootstrap a release version of renv - c( - function() renv_bootstrap_download_tarball(version), - function() renv_bootstrap_download_cran_latest(version), - function() renv_bootstrap_download_cran_archive(version) - ) - - } - - for (method in methods) { - path <- tryCatch(method(), error = identity) - if (is.character(path) && file.exists(path)) - return(path) - } - - stop("All download methods failed") - - } - - renv_bootstrap_download_impl <- function(url, destfile) { - - mode <- "wb" - - # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 - fixup <- - Sys.info()[["sysname"]] == "Windows" && - substring(url, 1L, 5L) == "file:" - - if (fixup) - mode <- "w+b" - - args <- list( - url = url, - destfile = destfile, - mode = mode, - quiet = TRUE - ) - - if ("headers" %in% names(formals(utils::download.file))) { - headers <- renv_bootstrap_download_custom_headers(url) - if (length(headers) && is.character(headers)) - args$headers <- headers - } - - 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$pkgType, "source") && - !identical(getOption("pkgType"), "source") && - Sys.info()[["sysname"]] %in% c("Darwin", "Windows") - - types <- c(if (binary) "binary", "source") - - # iterate over types + repositories - for (type in types) { - for (repos in renv_bootstrap_repos()) { - - # build arguments for utils::available.packages() call - args <- list(type = type, repos = repos) - - # add custom headers if available -- note that - # utils::available.packages() will pass this to download.file() - if ("headers" %in% names(formals(utils::download.file))) { - headers <- renv_bootstrap_download_custom_headers(repos) - if (length(headers) && is.character(headers)) - args$headers <- headers - } - - # retrieve package database - db <- tryCatch( - as.data.frame( - do.call(utils::available.packages, args), - 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_find <- function(version) { - - path <- renv_bootstrap_find_cache(version) - if (length(path) && file.exists(path)) { - catf("- Using renv %s from global package cache", version) - return(path) - } - - } - - renv_bootstrap_find_cache <- function(version) { - - md5 <- attr(version, "md5", exact = TRUE) - if (is.null(md5)) - return() - - # infer path to renv cache - cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "") - if (!nzchar(cache)) { - root <- Sys.getenv("RENV_PATHS_ROOT", unset = NA) - if (!is.na(root)) - cache <- file.path(root, "cache") - } - - if (!nzchar(cache)) { - tools <- asNamespace("tools") - if (is.function(tools$R_user_dir)) { - root <- tools$R_user_dir("renv", "cache") - cache <- file.path(root, "cache") - } - } - - # start completing path to cache - file.path( - cache, - renv_bootstrap_cache_version(), - renv_bootstrap_platform_prefix(), - "renv", - version, - md5, - "renv" - ) - - } - - 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_github_token <- function() { - for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { - envval <- Sys.getenv(envvar, unset = NA) - if (!is.na(envval)) - return(envval) - } - } - - renv_bootstrap_download_github <- function(version) { - - enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") - if (!identical(enabled, "TRUE")) - return(FALSE) - - # prepare download options - token <- renv_bootstrap_github_token() - if (is.null(token)) - token <- "" - - if (nzchar(Sys.which("curl")) && nzchar(token)) { - fmt <- "--location --fail --header \"Authorization: token %s\"" - extra <- sprintf(fmt, token) - 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(token)) { - fmt <- "--header=\"Authorization: token %s\"" - extra <- sprintf(fmt, token) - 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_default <- function() { - - # read version component - version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") - - # expand placeholders - placeholders <- list( - list("%v", format(getRversion()[1, 1:2])), - list("%V", format(getRversion()[1, 1:3])) - ) - - for (placeholder in placeholders) - version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) - - # 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) - version <- paste(version, R.version[["svn rev"]], sep = "-r") - - version - - } - - renv_bootstrap_platform_prefix <- function() { - - # construct version prefix - version <- renv_bootstrap_platform_prefix_default() - - # build list of path components - components <- c(version, 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 (is.na(auto) && getRversion() >= "4.4.0") - auto <- "TRUE" - - 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 - dev <- identical(description[["RemoteType"]], "github") - remote <- if (dev) - 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 = if (dev) description[["RemoteSha"]] - ) - - fmt <- heredoc(" - 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. - ") - catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) - - FALSE - - } - - renv_bootstrap_validate_version_dev <- function(version, description) { - - expected <- description[["RemoteSha"]] - if (!is.character(expected)) - return(FALSE) - - pattern <- sprintf("^\\Q%s\\E", version) - grepl(pattern, expected, perl = TRUE) - - } - - renv_bootstrap_validate_version_release <- function(version, description) { - expected <- description[["Version"]] - is.character(expected) && identical(c(expected), c(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(project, libpath, version) - } - - renv_bootstrap_run <- function(project, libpath, version) { - tryCatch( - renv_bootstrap_run_impl(project, libpath, version), - error = function(e) { - msg <- paste( - "failed to bootstrap renv: the project will not be loaded.", - paste("Reason:", conditionMessage(e)), - "Use `renv::activate()` to re-initialize the project.", - sep = "\n" - ) - warning(msg, call. = FALSE) - } - ) - } - - renv_bootstrap_run_impl <- function(project, libpath, version) { - - # 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 = project)) - } - - # 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_cache_version <- function() { - # NOTE: users should normally not override the cache version; - # this is provided just to make testing easier - Sys.getenv("RENV_CACHE_VERSION", unset = "v5") - } - - renv_bootstrap_cache_version_previous <- function() { - version <- renv_bootstrap_cache_version() - number <- as.integer(substring(version, 2L)) - paste("v", number - 1L, sep = "") - } - - 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_patterns <- function() { - - list( - - # objects - list("{", "\t\n\tobject(\t\n\t", TRUE), - list("}", "\t\n\t)\t\n\t", TRUE), - - # arrays - list("[", "\t\n\tarray(\t\n\t", TRUE), - list("]", "\n\t\n)\n\t\n", TRUE), - - # maps - list(":", "\t\n\t=\t\n\t", TRUE), - - # newlines - list("\\u000a", "\n", FALSE) - - ) - - } - - renv_json_read_envir <- function() { - - envir <- new.env(parent = emptyenv()) - - envir[["+"]] <- `+` - envir[["-"]] <- `-` - - envir[["object"]] <- function(...) { - result <- list(...) - names(result) <- as.character(names(result)) - result - } - - envir[["array"]] <- list - - envir[["true"]] <- TRUE - envir[["false"]] <- FALSE - envir[["null"]] <- NULL - - envir - - } - - renv_json_read_remap <- function(object, patterns) { - - # repair names if necessary - if (!is.null(names(object))) { - - nms <- names(object) - for (pattern in patterns) - nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) - names(object) <- nms - - } - - # repair strings if necessary - if (is.character(object)) { - for (pattern in patterns) - object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) - } - - # recurse for other objects - if (is.recursive(object)) - for (i in seq_along(object)) - object[i] <- list(renv_json_read_remap(object[[i]], patterns)) - - # return remapped object - object - - } - - renv_json_read_default <- function(file = NULL, text = NULL) { - - # read json text - text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") - - # convert into something the R parser will understand - patterns <- renv_json_read_patterns() - transformed <- text - for (pattern in patterns) - transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) - - # parse it - rfile <- tempfile("renv-json-", fileext = ".R") - on.exit(unlink(rfile), add = TRUE) - writeLines(transformed, con = rfile) - json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] - - # evaluate in safe environment - result <- eval(json, envir = renv_json_read_envir()) - - # fix up strings if necessary -- do so only with reversible patterns - patterns <- Filter(function(pattern) pattern[[3L]], patterns) - renv_json_read_remap(result, patterns) - - } - - - # 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/tests/renv/settings.json b/tests/renv/settings.json deleted file mode 100644 index a95361c6ee5..00000000000 --- a/tests/renv/settings.json +++ /dev/null @@ -1,18 +0,0 @@ -{ - "bioconductor.version": null, - "external.libraries": [], - "ignored.packages": [], - "package.dependency.fields": ["Imports", "Depends", "LinkingTo"], - "ppm.enabled": true, - "ppm.ignored.urls": [ - "https://yihui.r-universe.dev", - "https://rstudio.r-universe.dev" - ], - "r.version": "4.6.1", - "snapshot.type": "explicit", - "use.cache": true, - "vcs.ignore.cellar": true, - "vcs.ignore.library": true, - "vcs.ignore.local": true, - "vcs.manage.ignores": true -} diff --git a/tests/run-tests.ps1 b/tests/run-tests.ps1 index 73cb9fba107..b4f798eee82 100644 --- a/tests/run-tests.ps1 +++ b/tests/run-tests.ps1 @@ -243,6 +243,21 @@ If ($AGENT_MODE) { } $DENO_ARGS += $TESTS_TO_RUN +# Point Quarto at the R of the rig project in tests/ (rproj.toml): the +# .rvenv wrapper sets the locked R version and package library itself, so +# every R process a test starts gets them, whatever its working directory. +$QUARTO_RVENV_BIN = Join-Path $QUARTO_ROOT "tests" ".rvenv" "bin" +If (Test-Path $QUARTO_RVENV_BIN) { + $OLD_QUARTO_R = $Env:QUARTO_R + $Env:QUARTO_R = $QUARTO_RVENV_BIN + $quarto_r_set = $true + if ($VERBOSE_MODE) { + Write-Host "> Using R from " -NoNewline; Write-Host "$($Env:QUARTO_R)" -ForegroundColor Blue; + } +} elseif ($VERBOSE_MODE) { + Write-Host "> No rig project environment at $QUARTO_RVENV_BIN, using R from QUARTO_R, R_HOME or PATH" +} + # Activate python virtualenv # set QUARTO_TESTS_FORCE_NO_VENV env var to not activate the virtualenv located in the project # QUARTO_TESTS_FORCE_NO_PIPENV is there for backward compatibility @@ -278,6 +293,11 @@ $DENO_EXIT_CODE = $LASTEXITCODE # Add Coverage handling +If ($quarto_r_set) { + $Env:QUARTO_R = $OLD_QUARTO_R + Remove-Variable quarto_r_set, OLD_QUARTO_R +} + If($quarto_venv_activated) { if ($VERBOSE_MODE) { Write-Host "> Exiting virtualenv activated for tests" diff --git a/tests/run-tests.sh b/tests/run-tests.sh index efd05e5d682..c1a706a2f91 100755 --- a/tests/run-tests.sh +++ b/tests/run-tests.sh @@ -124,6 +124,20 @@ then source configure-test-env.sh fi +# Point Quarto at the R of the rig project in tests/ (rproj.toml): the +# .rvenv wrapper sets the locked R version and package library itself, so +# every R process a test starts gets them, whatever its working directory. +QUARTO_RVENV_BIN="${QUARTO_ROOT}/tests/.rvenv/bin" +if [[ -d "$QUARTO_RVENV_BIN" ]] +then + export QUARTO_R="$QUARTO_RVENV_BIN" + if [[ "$VERBOSE_MODE" == "true" ]]; then + echo "> Using R from ${QUARTO_R}" + fi +elif [[ "$VERBOSE_MODE" == "true" ]]; then + echo "> No rig project environment at ${QUARTO_RVENV_BIN}, using R from QUARTO_R, R_HOME or PATH" +fi + # Activating python virtualenv # set QUARTO_TESTS_FORCE_NO_VENV env var to not activate the virtualenv located in the project # QUARTO_TESTS_FORCE_NO_PIPENV is there for backward compatibility diff --git a/tests/smoke/embed/render-embed-website-rerender.test.ts b/tests/smoke/embed/render-embed-website-rerender.test.ts index aa7b8ac431f..5fc97486d65 100644 --- a/tests/smoke/embed/render-embed-website-rerender.test.ts +++ b/tests/smoke/embed/render-embed-website-rerender.test.ts @@ -7,7 +7,7 @@ import { join, resolve } from "../../../src/deno_ral/path.ts"; import { existsSync, safeRemoveSync } from "../../../src/deno_ral/fs.ts"; import { Element } from "../../../src/core/deno-dom.ts"; -import { docs, writeTestsRenvProfile } from "../../utils.ts"; +import { docs } from "../../utils.ts"; import { ensureHtmlSelectorSatisfies, fileExists, @@ -33,7 +33,6 @@ const removeGenerated = () => { "source_files", "source.embed.ipynb", "source.embed-preview.html", - ".Rprofile", ] ) { safeRemoveSync(join(projectDir, name), { recursive: true }); @@ -48,8 +47,6 @@ test({ cwd: () => projectDir, setup: () => { removeGenerated(); - // knitr runs from the project dir, outside tests/ - writeTestsRenvProfile(projectDir); return Promise.resolve(); }, teardown: () => { diff --git a/tests/unit/preview-subdir-knitr-cwd.test.ts b/tests/unit/preview-subdir-knitr-cwd.test.ts index c8763d19b71..cddf7387bf8 100644 --- a/tests/unit/preview-subdir-knitr-cwd.test.ts +++ b/tests/unit/preview-subdir-knitr-cwd.test.ts @@ -30,9 +30,9 @@ import { unitTest } from "../test.ts"; import { assert } from "testing/asserts"; import { dirname, isAbsolute, join } from "../../src/deno_ral/path.ts"; -import { writeTestsRenvProfile } from "../utils.ts"; import { existsSync } from "../../src/deno_ral/fs.ts"; import { which } from "../../src/core/path.ts"; +import { getenv } from "../../src/core/env.ts"; import { projectContext } from "../../src/project/project-context.ts"; import { singleFileProjectContext } from "../../src/project/types/single-file/single-file.ts"; import { notebookContext } from "../../src/render/notebook/notebook-context.ts"; @@ -141,7 +141,11 @@ unitTest( // the fixture tree as a side effect only when Rscript is present, so a // skipped run leaves nothing on disk (teardown never runs otherwise). prereq: async () => { - if ((await which("Rscript")) === undefined) return false; + // R is available through QUARTO_R (rvenv wrapper) or PATH; a guard only, never an early success + const quartoR = getenv("QUARTO_R", ""); + const rAvailable = (quartoR && existsSync(quartoR)) || + (await which("Rscript")) !== undefined; + if (!rAvailable) return false; e2eBase = Deno.makeTempDirSync({ prefix: "quarto_test_14683_" }); e2eProjDir = join(e2eBase, "testsite"); e2eLabsDir = join(e2eProjDir, "labs"); @@ -153,11 +157,6 @@ unitTest( // the original cwd afterward. cwd: () => e2eLabsDir, setup: () => { - // Re-activate renv against the real tests/ project, regardless of - // this fixture's cwd — see llm-docs/testing-patterns.md → "R Tests - // That Change Working Directory" for why this is needed. - writeTestsRenvProfile(e2eProjDir); - Deno.writeTextFileSync( join(e2eProjDir, "_quarto.yml"), 'project:\n type: website\n\nwebsite:\n title: "testsite"\n', diff --git a/tests/utils.ts b/tests/utils.ts index 18a48728988..7b139c9b62c 100644 --- a/tests/utils.ts +++ b/tests/utils.ts @@ -5,7 +5,7 @@ * */ -import { basename, dirname, extname, fromFileUrl, join, relative } from "../src/deno_ral/path.ts"; +import { basename, dirname, extname, join, relative } from "../src/deno_ral/path.ts"; import { parseFormatString } from "../src/core/pandoc/pandoc-formats.ts"; import { kMetadataFormat, kOutputExt, kOutputFile } from "../src/config/constants.ts"; import { pathWithForwardSlashes, safeExistsSync } from "../src/core/path.ts"; @@ -258,19 +258,6 @@ export function docs(path: string): string { return join("docs", path); } -// Write a `.Rprofile` into `dir` that activates the tests/ renv project. -// R reads `.Rprofile` from the exact cwd only, so an R subprocess started -// outside tests/ (a test using `TestContext.cwd`) would not see the renv -// library holding knitr/rmarkdown on CI. -export function writeTestsRenvProfile(dir: string) { - const testsDir = pathWithForwardSlashes(dirname(fromFileUrl(import.meta.url))); - Deno.writeTextFileSync( - join(dir, ".Rprofile"), - `Sys.setenv(RENV_PROJECT = "${testsDir}")\n` + - `source("${testsDir}/renv/activate.R")\n`, - ); -} - export function fileLoader(...path: string[]) { return (file: string, to: string) => { const input = docs(join(...path, file)); From b331d203b3ca21459a5aacb9371fed8fd43dc934 Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 14:48:27 +0100 Subject: [PATCH 3/9] Set up the R test environment with rig in CI The smoke-test workflow installs a pinned rig and runs rig proj sync --locked --no-install-r, so a stale lock fails the job and the R from setup-r is used. The renv steps, including the renv cache save and the renv::status() check, are gone; every locked package is a P3M binary, so there is no cache for now. Dev rmarkdown/knitr, extra-r-packages and sessioninfo are installed into the project library afterwards, then checked through the project's Rscript wrapper so the check sees what the tests load. extra-r-packages now goes to rig pkg install; renv's pkg@1.2.3 is rewritten to pkg@=1.2.3 because rig reads a bare version as a minimum. --- .github/actions/setup-rig/action.yml | 40 ++++++ .github/workflows/test-ff-matrix.yml | 4 +- .github/workflows/test-smokes-parallel.yml | 2 +- .github/workflows/test-smokes.yml | 145 ++++++++++----------- 4 files changed, 111 insertions(+), 80 deletions(-) create mode 100644 .github/actions/setup-rig/action.yml diff --git a/.github/actions/setup-rig/action.yml b/.github/actions/setup-rig/action.yml new file mode 100644 index 00000000000..952e3887563 --- /dev/null +++ b/.github/actions/setup-rig/action.yml @@ -0,0 +1,40 @@ +name: "Set up rig" +description: "Installs a pinned rig release and adds it to PATH. rig proj is experimental, so callers get one pinned version rather than latest." +inputs: + version: + description: "rig version to install, without the leading v" + required: false + default: "0.11.1" + +runs: + using: "composite" + steps: + - name: Install rig (Windows) + if: runner.os == 'Windows' + shell: pwsh + env: + RIG_VERSION: ${{ inputs.version }} + run: | + $zip = Join-Path $env:RUNNER_TEMP "rig.zip" + $dest = Join-Path $env:RUNNER_TEMP "rig" + Invoke-WebRequest -Uri "https://github.com/r-lib/rig/releases/download/v$($env:RIG_VERSION)/rig-windows-x86_64-$($env:RIG_VERSION).zip" -OutFile $zip + Expand-Archive -Path $zip -DestinationPath $dest -Force + Join-Path $dest "bin" | Out-File -FilePath $env:GITHUB_PATH -Append -Encoding utf8 + & (Join-Path $dest "bin/rig.exe") --version + + - name: Install rig + if: runner.os != 'Windows' + shell: bash + env: + RIG_VERSION: ${{ inputs.version }} + run: | + case "$RUNNER_OS-$RUNNER_ARCH" in + Linux-X64) asset="rig-linux-x86_64-${RIG_VERSION}.tar.gz" ;; + macOS-ARM64) asset="rig-macos-arm64-${RIG_VERSION}.tar.gz" ;; + *) echo "::error::No rig build configured for $RUNNER_OS-$RUNNER_ARCH"; exit 1 ;; + esac + dest="$RUNNER_TEMP/rig" + mkdir -p "$dest" + curl -fsSL "https://github.com/r-lib/rig/releases/download/v${RIG_VERSION}/${asset}" | tar -xz -C "$dest" + echo "$dest/bin" >> "$GITHUB_PATH" + "$dest/bin/rig" --version diff --git a/.github/workflows/test-ff-matrix.yml b/.github/workflows/test-ff-matrix.yml index 2fa09a3cacc..5361b454189 100644 --- a/.github/workflows/test-ff-matrix.yml +++ b/.github/workflows/test-ff-matrix.yml @@ -4,7 +4,7 @@ on: workflow_call: inputs: extra-r-packages: - description: "Comma-separated R packages to pass to renv::install" + description: "Comma-separated R packages to pass to rig pkg install (see test-smokes.yml)" required: false type: string default: "" @@ -46,7 +46,7 @@ on: workflow_dispatch: inputs: extra-r-packages: - description: "extra R package to install for the runs (like a dev version of one of the deps) - comma separated, passed to renv::install" + description: "extra R packages installed on top of tests/rproj.lock (like a dev version of one of the deps) - comma separated, passed to rig pkg install: pkg, owner/repo[@ref], gitlab::group/project, url::https://...; pkg@1.2.3 means exactly 1.2.3" required: false type: string default: "" diff --git a/.github/workflows/test-smokes-parallel.yml b/.github/workflows/test-smokes-parallel.yml index 168433b3eb4..e42e2ccd9d5 100644 --- a/.github/workflows/test-smokes-parallel.yml +++ b/.github/workflows/test-smokes-parallel.yml @@ -10,7 +10,7 @@ on: default: 10 type: number extra-r-packages: - description: "extra R package to install for the tests runs (like a dev version of one of the deps) - comma separated, passed to renv::install" + description: "extra R packages installed on top of tests/rproj.lock (like a dev version of one of the deps) - comma separated, passed to rig pkg install: pkg, owner/repo[@ref], gitlab::group/project, url::https://...; pkg@1.2.3 means exactly 1.2.3" required: false type: string default: "" diff --git a/.github/workflows/test-smokes.yml b/.github/workflows/test-smokes.yml index faccfcc9ce9..d6368541b47 100644 --- a/.github/workflows/test-smokes.yml +++ b/.github/workflows/test-smokes.yml @@ -15,7 +15,7 @@ on: type: boolean default: false extra-r-packages: - description: "extra R package to install for the runs (like a dev version of one of the deps) - comma separated, passed to renv::install" + description: "extra R packages installed on top of tests/rproj.lock (like a dev version of one of the deps) - comma separated, passed to rig pkg install: pkg, owner/repo[@ref], gitlab::group/project, url::https://...; pkg@1.2.3 means exactly 1.2.3" required: false type: string default: "" @@ -67,7 +67,7 @@ on: type: boolean default: false extra-r-packages: - description: "extra R package to install for the runs (like a dev version of one of the deps) - comma separated, passed to renv::install" + description: "extra R packages installed on top of tests/rproj.lock (like a dev version of one of the deps) - comma separated, passed to rig pkg install: pkg, owner/repo[@ref], gitlab::group/project, url::https://...; pkg@1.2.3 means exactly 1.2.3" required: false type: string default: "" @@ -110,6 +110,16 @@ jobs: # Empty keeps the standard checkout behavior. ref: ${{ inputs.ref }} + - name: Check the ref supports the rig test environment + shell: bash + run: | + for f in tests/rproj.lock .github/actions/setup-rig/action.yml; do + if [ ! -f "$f" ]; then + echo "::error::This checkout has no $f. The R test environment needs a ref that uses the rig project (releases before it was introduced are not supported)." + exit 1 + fi + done + # macOS runners boot with an unresolvable `.local` hostname, so any process # resolving its own hostname stalls ~35s (actions/runner-images#14568). - name: Set a resolvable hostname (macOS) @@ -199,6 +209,9 @@ jobs: # required to avoid rtools bin in path windows-path-include-rtools: false + - name: Set up rig + uses: ./.github/actions/setup-rig + - name: Install node (for Playwright, MECA) uses: actions/setup-node@v6 with: @@ -292,29 +305,6 @@ jobs: if: ${{ runner.os != 'Windows' }} run: npm install -g meca --loglevel=error --no-audit - - name: Set RENV_PATHS_ROOT - shell: bash - run: | - echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV - - - name: Get R and OS version - id: get-version - run: | - cat("os-version=", sessionInfo()$running, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) - cat("r-version=", R.Version()$version.string, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) - shell: Rscript {0} - - - name: Restore Renv package cache - id: cache-renv-packages-restore - uses: actions/cache/restore@v5 - with: - path: | - ${{ env.RENV_PATHS_ROOT }} - renv/library - key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-renv-2-${{ hashFiles('tests/renv.lock') }} - restore-keys: | - ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-renv-2- - - name: Install missing system deps if: runner.os == 'Linux' run: | @@ -340,56 +330,68 @@ jobs: brew install --cask xquartz brew install poppler librsvg - - name: Restore R packages - id: restore-r-packages + - name: Sync R packages from rproj.lock working-directory: tests + shell: bash run: | - cat("::group::Installing renv if needed\n") - if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv') - cat("::endgroup::\n") - cat("::group::Restoring R packages from renv.lock\n") - renv::restore() - cat("::endgroup::\n") - cat("::group::Verifying R packages are synchronized after restore\n") - status <- renv::status() - if (!isTRUE(status$synchronized)) { - cat("::error::R packages are not synchronized after restore - some packages may have failed to install\n") - quit(status = 1) - } - cat("::endgroup::\n") - cat("::group::Installing dev versions of knitr and rmarkdown\n") - # Install dev versions for our testing - # Use r-universe to avoid github api calls - try(install.packages('rmarkdown', repos = c('https://rstudio.r-universe.dev', getOption('repos')))) - try(install.packages('knitr', repos = c('https://yihui.r-universe.dev', getOption('repos')))) - cat("::endgroup::\n") - # A failed dev install keeps the renv-restored version; flag it instead of failing setup - for (pkg in c('rmarkdown', 'knitr')) { + # Refs that predate the rig project are rejected by the preflight step after checkout. + echo "::group::rig proj sync" + rig proj sync --locked --no-install-r + echo "::endgroup::" + + - name: Install dev and extra R packages + working-directory: tests + shell: bash + env: + EXTRA_R_PACKAGES: ${{ inputs.extra-r-packages }} + run: | + # Installs on top of the lock must target the project library and the + # exact R the sync used; rig's default is the default R's user library. + r_version=$(sed -n 's/^r-version = //p' .rvenv/rvenv.cfg | tr -d '\r') + r_lib="$(cd .rvenv/lib && { pwd -W 2>/dev/null || pwd; })" + overlay() { rig pkg install --r-version "$r_version" --library "$r_lib" "$@"; } + + echo "::group::Installing dev versions of knitr and rmarkdown" + # Use r-universe to avoid GitHub API calls. A failed dev install keeps + # the locked version; the check below flags it instead of failing setup. + overlay --with-repos https://rstudio.r-universe.dev rmarkdown || true + overlay --with-repos https://yihui.r-universe.dev knitr || true + echo "::endgroup::" + + if [ -n "$EXTRA_R_PACKAGES" ]; then + echo "::notice::Running with the following extra R packages: $EXTRA_R_PACKAGES" + echo "::group::Installing extra R packages" + specs=() + IFS=',' read -ra items <<< "$EXTRA_R_PACKAGES" + for item in "${items[@]}"; do + item="${item#"${item%%[![:space:]]*}"}" + item="${item%"${item##*[![:space:]]}"}" + # renv's pkg@1.2.3 is an exact version; rig reads it as a minimum. + if [[ "$item" =~ ^[A-Za-z][A-Za-z0-9.]*@[0-9] ]]; then item="${item/@/@=}"; fi + specs+=("$item") + done + overlay "${specs[@]}" + echo "::endgroup::" + fi + + echo "::group::Installing sessioninfo" + overlay sessioninfo + echo "::endgroup::" + + # Run through the wrapper so the check sees the library the tests load. + cat > .rvenv/ci-r-check.R <<'EOF' + for (pkg in c("rmarkdown", "knitr")) { repo <- packageDescription(pkg)$Repository - if (is.null(repo) || !grepl('r-universe.dev', repo, fixed = TRUE)) { + if (is.null(repo) || !grepl("r-universe.dev", repo, fixed = TRUE)) { cat(sprintf("::notice::Dev version of %s not installed; tests use %s from %s\n", - pkg, packageVersion(pkg), if (is.null(repo)) "unknown source" else repo)) + pkg, format(packageVersion(pkg)), if (is.null(repo)) "unknown source" else repo)) } } - if ('${{ inputs.extra-r-packages }}' != '') { - cat(sprintf("::notice::Running with the following extra R packages for renv: %s\n", "${{ inputs.extra-r-packages }}")) - cat("::group::Installing extra R packages\n") - renv::install(strsplit("${{ inputs.extra-r-packages }}", split = ",")[[1]]) - cat("::endgroup::\n") - } - shell: Rscript {0} - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - - name: Show R session information - working-directory: tests - run: | - # Session info cat("::group::Session info\n") - renv::install("sessioninfo") sessioninfo::session_info(pkgs = "installed", include_base = TRUE) cat("::endgroup::\n") - shell: Rscript {0} + EOF + .rvenv/bin/Rscript .rvenv/ci-r-check.R - name: Install uv for Python uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1 @@ -719,17 +721,6 @@ jobs: key: ${{ steps.cache-typst.outputs.cache-primary-key }} path: ${{ steps.cache-typst.outputs.cache-path }} - - name: Save Renv package cache - # don't save cache if we have extra R packages, or if the cache restore or - # renv::restore did not complete (partial library, see Typst cache above) - if: ${{ !cancelled() && steps.restore-r-packages.outcome == 'success' && steps.cache-renv-packages-restore.outputs.cache-hit != 'true' && inputs.extra-r-packages == '' }} - uses: actions/cache/save@v5 - with: - path: | - ${{ env.RENV_PATHS_ROOT }} - renv/library - key: ${{ steps.cache-renv-packages-restore.outputs.cache-primary-key }} - - uses: actions/upload-artifact@v7 # Include the OS because sibling jobs share the workflow run. if: ${{ !cancelled() && runner.os != 'Windows' && hashFiles('tests/integration/playwright/playwright-report/**/*') != '' }} From d56cb9a10c26f37568985e2e8dcadfb9d1d063ce Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 14:53:23 +0100 Subject: [PATCH 4/9] Document the rig project test environment README, the testing rules and the test-pattern notes described renv: how to add a dependency, and the per-fixture .Rprofile that R tests outside tests/ needed. With QUARTO_R pointing at the project's Rscript wrapper that workaround and its rule are gone. --- .claude/rules/testing/overview.md | 2 +- .claude/rules/testing/unit-test-with-r.md | 18 ---------- dev-docs/configuring-test-deps.md | 9 ++--- llm-docs/testing-patterns.md | 27 +++++--------- tests/README.md | 44 ++++++++++++----------- 5 files changed, 36 insertions(+), 64 deletions(-) delete mode 100644 .claude/rules/testing/unit-test-with-r.md diff --git a/.claude/rules/testing/overview.md b/.claude/rules/testing/overview.md index 8fae09dc038..c8f9e075680 100644 --- a/.claude/rules/testing/overview.md +++ b/.claude/rules/testing/overview.md @@ -53,7 +53,7 @@ Run configuration script to set up: ``` Managed via: -- **R**: renv (`renv.lock`) +- **R**: rig project (`rproj.toml`, `rproj.lock`); `run-tests` sets `QUARTO_R` to `tests/.rvenv/bin` - **Python**: uv (`pyproject.toml`, `uv.lock`) - **Julia**: Pkg.jl (`Project.toml`, `Manifest.toml`) diff --git a/.claude/rules/testing/unit-test-with-r.md b/.claude/rules/testing/unit-test-with-r.md deleted file mode 100644 index 65207716172..00000000000 --- a/.claude/rules/testing/unit-test-with-r.md +++ /dev/null @@ -1,18 +0,0 @@ ---- -paths: - - "tests/unit/preview-subdir-knitr-cwd.test.ts" - - "tests/smoke/embed/render-embed-website-rerender.test.ts" ---- - -# R tests that change working directory - -These tests run a knitr subprocess with cwd set to a scratch or fixture -directory (required to reproduce the bug). R's `.Rprofile` lookup is -cwd-exact, so it won't pick up `tests/renv` activation there — on CI the R -subprocess fails with `there is no package called 'rmarkdown'`. `setup()` -calls `writeTestsRenvProfile(dir)` (`tests/utils.ts`), which writes a -`.Rprofile` into the fixture dir to re-activate renv against the real -`tests/` project. Any new test whose knitr cwd is outside `tests/` needs the -same call. - -**Details:** `llm-docs/testing-patterns.md` → "R Tests That Change Working Directory" diff --git a/dev-docs/configuring-test-deps.md b/dev-docs/configuring-test-deps.md index 24aa78ccdd5..f67533eed9d 100644 --- a/dev-docs/configuring-test-deps.md +++ b/dev-docs/configuring-test-deps.md @@ -62,9 +62,7 @@ ## R -- Add the dependencies in `DESCRIPTION` file -- Run `renv::install()` to install the dependencies -- Run `renv::snapshot()` to lock the versions in `renv.lock` +- Run `rig proj add ` from `tests/`: it adds the dependency to `rproj.toml`, locks it in `rproj.lock` and installs it ## Julia @@ -82,6 +80,5 @@ # Updating test dependencies -- When `main` updates the test environment (`tests/renv.lock`, `tests/uv.lock`, `tests/Manifest.toml`, or the R / Python / Julia versions in `.github/workflows/test-smokes.yml`), backport the update to the current stable branch (e.g. `v1.10`) while it still receives patch releases, as its own PR (see `checklist-backport-a-pr.md`). - - Patch releases are then tested against the same current R, Python, Julia and package versions users install. - - CI caches are shared: the R cache key is built from the OS, the R version and the `tests/renv.lock` hash, and any branch can read caches saved on `main`. A stable branch with identical lock files gets cache hits; a diverged one does a slow cold restore on each PR. +- When `main` updates the test environment (`tests/rproj.lock`, `tests/uv.lock`, `tests/Manifest.toml`, or the R / Python / Julia versions in `.github/workflows/test-smokes.yml`), backport the update to the current stable branch (e.g. `v1.10`) while it still receives patch releases, as its own PR (see `checklist-backport-a-pr.md`). + - Patch releases are then tested against the same current R, Python, Julia and package versions users install. \ No newline at end of file diff --git a/llm-docs/testing-patterns.md b/llm-docs/testing-patterns.md index 46ef5dfb48a..1cd5ed241f7 100644 --- a/llm-docs/testing-patterns.md +++ b/llm-docs/testing-patterns.md @@ -220,7 +220,7 @@ unitTest("runs from workingDir", async () => { **Key points:** -- A test that runs R/knitr from the new cwd also needs the renv activation described in "R Tests That Change Working Directory" below. +- A test that runs R/knitr from the new cwd needs no extra setup: see "R Tests That Change Working Directory" below. - The harness calls `cwd()` **before** `setup()`, so the directory must already exist when `cwd()` runs — create it at module scope, not in `setup`. - `teardown` runs **before** the harness restores the cwd, so on Windows the temp dir may still be the cwd and resist removal. Wrap the removal in try/catch (best-effort) — see `tests/smoke/use/template.test.ts` and `tests/unit/dotenv-config.test.ts`. @@ -378,7 +378,7 @@ See `tests/smoke/use/template.test.ts` for extension template patterns. - **Julia**: `tests/Project.toml` + `tests/Manifest.toml` - **Python**: `tests/.venv/` (managed by uv/pyproject.toml) -- **R**: `tests/renv/` + `tests/renv.lock` +- **R**: `tests/rproj.toml` + `tests/rproj.lock` (rig project; library in `tests/.rvenv/`) The `configure-test-env` scripts ONLY manage these main environments. CI builds depend on this structure. @@ -415,9 +415,9 @@ julia --project=. -e 'using Pkg; Pkg.add("PackageName")' cd tests uv add packagename -# R: Edit tests/DESCRIPTION, then +# R: from tests/ (updates rproj.toml and rproj.lock, installs into tests/.rvenv/lib) cd tests -Rscript -e "renv::install(); renv::snapshot()" +rig proj add packagename ``` **Note:** While Quarto supports local Project.toml files in document directories for production use, the quarto-cli test infrastructure specifically does NOT support this pattern. @@ -425,21 +425,10 @@ All test dependencies must be in the main `tests/` environment. ### R Tests That Change Working Directory -R resolves `.Rprofile` from the **exact** process cwd (no parent-directory search). -On CI, rmarkdown/knitr live only in `tests/renv`'s project library, activated when cwd is `tests/` (via `tests/.Rprofile` sourcing `renv/activate.R`). -Most knitr tests never leave `tests/` — they pass paths relative to the current cwd instead of changing directories — so activation happens automatically. - -A test that changes cwd through `TestContext.cwd()` loses that activation. The R subprocess starts outside `tests/`, and package loads may fail with `there is no package called 'rmarkdown'`. -A developer machine with rmarkdown on the default `.libPaths()` may mask this CI failure. - -**Fix:** call `writeTestsRenvProfile(dir)` (`tests/utils.ts`) in `setup()` to write a `.Rprofile` in the fixture cwd that points renv to the test project. It writes: - -```r -Sys.setenv(RENV_PROJECT = "") -source("/renv/activate.R") -``` - -`renv/activate.R` uses `RENV_PROJECT` as the project root instead of the current directory. +`run-tests.ps1|.sh` set `QUARTO_R` to `tests/.rvenv/bin`, the wrapper scripts `rig proj sync` writes. +Quarto resolves `Rscript` from `QUARTO_R` first (`rBinaryPath()` in `src/core/resources.ts`), and the wrapper sets the R version and the project library itself. +An R subprocess therefore finds rmarkdown and knitr whatever its cwd, and a test whose knitr cwd is outside `tests/` (through `TestContext.cwd()`) needs no R setup. +Running tests without `run-tests` (e.g. `deno test` directly) does not set `QUARTO_R`; set it to `tests/.rvenv/bin` yourself. ## Best Practices diff --git a/tests/README.md b/tests/README.md index f0cbe46bace..e8008ba43d8 100644 --- a/tests/README.md +++ b/tests/README.md @@ -24,8 +24,8 @@ The test infrastructure is in `test.ts`, `test-deps.ts`, `quarto-cmd.ts`, `verif Here are what is expected in the environment for the tests : -- R should be installed and on `PATH`. [**rig**](https://github.com/r-lib/rig) can manage R versions. - For example, run `rig install 4.4.2` and `rig default 4.4.2`. +- [**rig**](https://github.com/r-lib/rig) 0.11.1 or later should be installed and on `PATH`. + It installs the R version the test environment is locked to, and its packages (see [R](#r) below). - On Windows, Rtools should be too (for source package installation) - Python should be installed and in PATH - [**pyenv**](https://github.com/pyenv/pyenv) is a good option to manage Python versions. - On Windows, use [`pyenv-win`](https://pyenv-win.github.io/pyenv-win/), install Python from , or use `winget`. @@ -36,6 +36,7 @@ Running tests require to have a local environment setup with Quarto development, The `tests/` folder contains `configure-test-env.sh` and `configure-test-env.ps1`. These scripts check the required tools and synchronize test dependencies. +For R, this is `rig proj sync` plus the development versions of rmarkdown and knitr, so rig must be on `PATH` (the scripts print an install hint if it is not). Run the appropriate script at least once. It also runs before tests by default. Set `QUARTO_TESTS_NO_CONFIG` to skip this step when running tests. @@ -82,26 +83,21 @@ Dependencies are managed using the following tools: #### R -We use [**renv**](https://rstudio.github.io/renv/). -The `renv.lock` file and `renv/` folder define the R environment. +We use a [**rig** project](https://rig.r-lib.org/proj-guide.html) (`rig proj`, experimental in rig). +`rproj.toml` declares the R packages and the R version, and `rproj.lock` pins the resolved versions for Windows, macOS and Linux. +`configure-test-env` runs `rig proj sync`, which installs the locked R version if it is missing and the packages into `tests/.rvenv/lib`, then installs the development versions of rmarkdown and knitr from r-universe on top. +Running `rig proj sync` again restores the locked versions, so run `configure-test-env` rather than a bare sync to keep the development versions. -Updating `renv.lock` is done using `renv::snapshot()`. -Do not modify the file manually. +`run-tests` sets `QUARTO_R` to `tests/.rvenv/bin`. +The `Rscript` wrapper there sets the R version and the project library itself, so every R process a test starts uses them, whatever its working directory. +To run R by hand with the test environment, use `tests/.rvenv/bin/Rscript`, or set `QUARTO_R` the same way when running `quarto` yourself. +A plain `Rscript` started in `tests/` with another R version warns that the project needs R 4.6 and does not load the project packages. -The test project uses [explicit dependency discovery](https://rstudio.github.io/renv/reference/dependencies.html?q=dependen#explicit-dependencies) through a `DESCRIPTION` file. -This avoids scanning every file under `tests/` for R dependencies. To add an R package dependency: -- Add package(s) to `DESCRIPTION` in `tests/` -- `renv::install()` the package into the project library +- Run `rig proj add ` from `tests/`, which updates `rproj.toml` and `rproj.lock` and installs the package - Finish to work on your test -- `renv::snapshot()` to record the new dependency in the `renv.lock` -- Commit the new `DESCRIPTION` and `renv.lock` - -See [documentation](https://rstudio.github.io/renv/) if you need to tweak the R environment. - -After a dependency update, you can run `configure-test-env.sh` or `configure-test-env.ps1` to update the environment, or manually run `renv::restore()` to recreate the environment with new versions. -Be sure to update your R version if needed. +- Commit `rproj.toml` and `rproj.lock` #### Python @@ -151,7 +147,7 @@ Julia will use that environment instead of the main `tests/` environment. The `configure-test-env` scripts only manage the main environment, so tests with local environments will fail in CI even if they work locally. **Note:** This applies to ALL engines (Julia, Python, R). -Python and R will also use local `.venv/` or `renv.lock` if present. +Python and R will also use local `.venv/` or `rproj.toml`/`.rvenv` if present. The quarto-cli test infrastructure uses a single managed environment per language at `tests/`, and CI only configures these main environments. See [documentation](https://pkgdocs.julialang.org/v1/managing-packages/) on how to add, remove, update if you need to tweak the Julia environment. @@ -301,7 +297,11 @@ When `run-tests.sh` receives a supported document path, it invokes that script a $ ./run-tests.sh smoke/smoke-all.test.ts -- docs/smoke-all/2023/01/04/issue-3847.qmd > Checking and configuring environment for tests >>>> Configuring R environment -* The library is already synchronized with the lockfile. + > Syncing R packages from rproj.lock +Deployment complete, installed 9 packages + > Installing dev knitr and rmarkdown +Installed 7 packages (/home/cderv/project/quarto-cli/tests/.rvenv/lib) +Installed 3 packages (/home/cderv/project/quarto-cli/tests/.rvenv/lib) >>>> Configuring Python environment Setting up python environnement with pipenv Installing dependencies from Pipfile.lock (0ded54)... @@ -352,7 +352,11 @@ ok | 1 passed | 0 failed (1s) > Setting all the paths required... > Checking and configuring environment for tests >>>> Configuring R environment -* The library is already synchronized with the lockfile. + > Syncing R packages from rproj.lock +Deployment complete, installed 9 packages + > Installing dev knitr and rmarkdown +Installed 7 packages (C:/Users/cderv/project/quarto-cli/tests/.rvenv/lib) +Installed 3 packages (C:/Users/cderv/project/quarto-cli/tests/.rvenv/lib) >>>> Configuring python environment Setting up python environnement with pipenv Installing dependencies from Pipfile.lock (0ded54)... From 3f1336e84201a159b171d8b86ef6b3223ab4d853 Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 15:06:20 +0100 Subject: [PATCH 5/9] Say QUARTO_R must be absolute when set by hand rBinaryPath() checks QUARTO_R against the current working directory on every call and does not cache it, so a relative tests/.rvenv/bin stops resolving once a test changes cwd and Quarto falls back to the R on PATH. run-tests already exports an absolute path; the docs telling contributors to set it themselves now say so too. --- llm-docs/testing-patterns.md | 2 +- tests/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/llm-docs/testing-patterns.md b/llm-docs/testing-patterns.md index 1cd5ed241f7..53bd5cbd5ef 100644 --- a/llm-docs/testing-patterns.md +++ b/llm-docs/testing-patterns.md @@ -428,7 +428,7 @@ All test dependencies must be in the main `tests/` environment. `run-tests.ps1|.sh` set `QUARTO_R` to `tests/.rvenv/bin`, the wrapper scripts `rig proj sync` writes. Quarto resolves `Rscript` from `QUARTO_R` first (`rBinaryPath()` in `src/core/resources.ts`), and the wrapper sets the R version and the project library itself. An R subprocess therefore finds rmarkdown and knitr whatever its cwd, and a test whose knitr cwd is outside `tests/` (through `TestContext.cwd()`) needs no R setup. -Running tests without `run-tests` (e.g. `deno test` directly) does not set `QUARTO_R`; set it to `tests/.rvenv/bin` yourself. +Running tests without `run-tests` (e.g. `deno test` directly) does not set `QUARTO_R`; set it to the absolute path of `tests/.rvenv/bin` yourself (a relative value stops resolving once a test changes cwd). ## Best Practices diff --git a/tests/README.md b/tests/README.md index e8008ba43d8..6b75cdbca21 100644 --- a/tests/README.md +++ b/tests/README.md @@ -90,7 +90,7 @@ Running `rig proj sync` again restores the locked versions, so run `configure-te `run-tests` sets `QUARTO_R` to `tests/.rvenv/bin`. The `Rscript` wrapper there sets the R version and the project library itself, so every R process a test starts uses them, whatever its working directory. -To run R by hand with the test environment, use `tests/.rvenv/bin/Rscript`, or set `QUARTO_R` the same way when running `quarto` yourself. +To run R by hand with the test environment, use `tests/.rvenv/bin/Rscript`, or set `QUARTO_R` to the absolute path of `tests/.rvenv/bin` when running `quarto` yourself. A plain `Rscript` started in `tests/` with another R version warns that the project needs R 4.6 and does not load the project packages. To add an R package dependency: From 4764d9dd09f75cffa2bf76a032bb4e739e28614b Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 15:08:15 +0100 Subject: [PATCH 6/9] Point the VS Code test debug config at the rig project R run-tests sets QUARTO_R to tests/.rvenv/bin, but the "Run Quarto test" launch config starts deno test directly. Without QUARTO_R, tests that run knitr from a cwd outside tests/ get the R on PATH and no project library when debugged, now that no per-fixture .Rprofile activates one. --- .vscode/launch.json | 1 + 1 file changed, 1 insertion(+) diff --git a/.vscode/launch.json b/.vscode/launch.json index fdd6e922d69..f108171d6b4 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -55,6 +55,7 @@ "QUARTO_ROOT": "${workspaceFolder}", "QUARTO_BIN_PATH": "${workspaceFolder}/package/dist/bin", "QUARTO_SHARE_PATH": "${workspaceFolder}/src/resources", + "QUARTO_R": "${workspaceFolder}/tests/.rvenv/bin", "QUARTO_DEBUG": "true" }, "attachSimplePort": 9229, From fe43d3a714599f8acf5333d7303236babea9165f Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 15:09:59 +0100 Subject: [PATCH 7/9] Tighten the rig test environment docs The lock targets Windows x86_64, macOS arm64 and Linux x86_64 only; other platforms resolve to source packages. Release mode on a tag from before the rig project now fails in each smoke leg, so D10 names that requirement too. Also restore the trailing newline in configuring-test-deps.md. --- dev-docs/configuring-test-deps.md | 2 +- llm-docs/built-version-testing-architecture.md | 3 ++- tests/README.md | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/dev-docs/configuring-test-deps.md b/dev-docs/configuring-test-deps.md index f67533eed9d..285a3923aef 100644 --- a/dev-docs/configuring-test-deps.md +++ b/dev-docs/configuring-test-deps.md @@ -81,4 +81,4 @@ # Updating test dependencies - When `main` updates the test environment (`tests/rproj.lock`, `tests/uv.lock`, `tests/Manifest.toml`, or the R / Python / Julia versions in `.github/workflows/test-smokes.yml`), backport the update to the current stable branch (e.g. `v1.10`) while it still receives patch releases, as its own PR (see `checklist-backport-a-pr.md`). - - Patch releases are then tested against the same current R, Python, Julia and package versions users install. \ No newline at end of file + - Patch releases are then tested against the same current R, Python, Julia and package versions users install. diff --git a/llm-docs/built-version-testing-architecture.md b/llm-docs/built-version-testing-architecture.md index f680db7c0f9..302e21eb4ae 100644 --- a/llm-docs/built-version-testing-architecture.md +++ b/llm-docs/built-version-testing-architecture.md @@ -164,7 +164,7 @@ In practice: - For signed Windows artifacts from a branch, dispatch `create-release` with `publish-release=false` and `smoke-artifacts-only=true`. The resulting workflow run starts the available test legs automatically (D7). - Dispatch `nightly` with a `run-id` to retest an earlier `create-release` run. - Dispatch `release` for post-publish verification, such as the optional prerelease checklist step. - It works only for releases cut after the harness support merged (D10). + It works only for releases cut after the harness support and the rig test environment merged (D10). ## Built-mode test legs (scheduler layout) @@ -298,6 +298,7 @@ All built legs currently run after every completed `create-release` run, unless ### D10. Release mode only works for post-harness tags Release mode checks out the tag, so the harness at that tag must already contain `tests/quarto-cmd.ts` — a preflight fails clearly for older releases. +The smoke legs also need the rig test environment (`tests/rproj.lock`): on a tag from before it, each leg fails at its "Check the ref supports the rig test environment" step. Testing an older binary with the current harness would require decoupling the harness from the target ref. Nightly and release legs use the harness from the target ref. Refs that contain `tests/quarto-cmd.ts` but predate the `quartoSpawnEnvOptions()` fix in `playwright-tests.test.ts` (#14706) run Playwright with dev-tree resources. diff --git a/tests/README.md b/tests/README.md index 6b75cdbca21..0d40822bb57 100644 --- a/tests/README.md +++ b/tests/README.md @@ -84,7 +84,7 @@ Dependencies are managed using the following tools: #### R We use a [**rig** project](https://rig.r-lib.org/proj-guide.html) (`rig proj`, experimental in rig). -`rproj.toml` declares the R packages and the R version, and `rproj.lock` pins the resolved versions for Windows, macOS and Linux. +`rproj.toml` declares the R packages and the R version, and `rproj.lock` pins the resolved versions for Windows x86_64, macOS arm64 and Linux x86_64 (other platforms fall back to source packages). `configure-test-env` runs `rig proj sync`, which installs the locked R version if it is missing and the packages into `tests/.rvenv/lib`, then installs the development versions of rmarkdown and knitr from r-universe on top. Running `rig proj sync` again restores the locked versions, so run `configure-test-env` rather than a bare sync to keep the development versions. From e7966db099f856edc16eaef445490ed55dd39638 Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 15:14:04 +0100 Subject: [PATCH 8/9] Let rig install R for the smoke tests in CI setup-r installs R on Windows into C:\R, but rig only looks for R under C:\Program Files\R, so with --no-install-r the sync bound to the runner image's own R rather than the pinned 4.6.1, and would fail once the image moves to the next R minor. Dropping setup-r and letting rig proj sync install the R version the lock needs gives every OS the same R source as a contributor's machine: the latest 4.6.x, which the lock was solved for, instead of a separately pinned patch release. --- .github/workflows/test-smokes.yml | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/.github/workflows/test-smokes.yml b/.github/workflows/test-smokes.yml index d6368541b47..fe66d75a940 100644 --- a/.github/workflows/test-smokes.yml +++ b/.github/workflows/test-smokes.yml @@ -138,7 +138,7 @@ jobs: shell: bash # Drops a slow azure.archive.ubuntu.com from the apt mirror list so the job uses - # archive.ubuntu.com (actions/runner-images#14823): sampled here before setup-r, + # archive.ubuntu.com (actions/runner-images#14823): sampled here before rig installs R, # and after a failed attempt in later apt steps run via $APT_WITH_FALLBACK. # Inline, not a local action, because release mode checks out older tags. - name: Configure apt mirror fallback @@ -201,14 +201,6 @@ jobs: fi exit 0 - - name: Set up R - uses: r-lib/actions/setup-r@v2 - with: - r-version: "4.6.1" - use-public-rspm: true - # required to avoid rtools bin in path - windows-path-include-rtools: false - - name: Set up rig uses: ./.github/actions/setup-rig @@ -335,8 +327,9 @@ jobs: shell: bash run: | # Refs that predate the rig project are rejected by the preflight step after checkout. + # rig installs the R version the lock needs if the runner does not have it. echo "::group::rig proj sync" - rig proj sync --locked --no-install-r + rig proj sync --locked echo "::endgroup::" - name: Install dev and extra R packages From df09b47ce3457a4e6551cd1b6fbd9dfbc54d79a0 Mon Sep 17 00:00:00 2001 From: Christophe Dervieux Date: Thu, 5 Nov 2026 17:07:47 +0100 Subject: [PATCH 9/9] Install R in its own step before rig proj sync On Linux, when rig proj sync has to install R it re-runs the whole sync under sudo, not only the R install. The project library in tests/.rvenv/lib then ends up owned by root, and every later rig pkg install as the runner user fails (rig reports only "0 succeeded, 1 failed", without the permission error). This broke all Linux smoke jobs at the dev/extra R packages step. Installing R with rig add first keeps sudo to the R install, and the sync goes back to --no-install-r, which rig's help suggests for CI. The version comes from rproj.lock, so it stays the latest patch of the minor the lock was solved for. Admin mode is kept over user mode, which rig documents as less tested on Linux. --- .github/workflows/test-smokes.yml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-smokes.yml b/.github/workflows/test-smokes.yml index fe66d75a940..ff301578045 100644 --- a/.github/workflows/test-smokes.yml +++ b/.github/workflows/test-smokes.yml @@ -322,14 +322,22 @@ jobs: brew install --cask xquartz brew install poppler librsvg + - name: Install R from rproj.lock + working-directory: tests + shell: bash + run: | + # A separate step because on Linux rig proj sync re-runs itself under sudo + # to install R, which leaves the project library owned by root. + r_version=$(sed -n 's/^r_version = "\(.*\)"/\1/p' rproj.lock | head -n 1 | tr -d '\r') + rig add "$r_version" + - name: Sync R packages from rproj.lock working-directory: tests shell: bash run: | # Refs that predate the rig project are rejected by the preflight step after checkout. - # rig installs the R version the lock needs if the runner does not have it. echo "::group::rig proj sync" - rig proj sync --locked + rig proj sync --locked --no-install-r echo "::endgroup::" - name: Install dev and extra R packages