From 3d2d312ee013043f7f88d950fb9f0efba62e92a7 Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Fri, 30 Jun 2023 12:54:43 +0000 Subject: [PATCH 01/22] renv update from pharmaverse/admiralci --- .Rprofile | 15 +- .github/workflows/common.yml | 18 +- renv.lock | 1302 +++++++++++++++++----------------- renv/.gitignore | 1 + renv/activate.R | 46 +- renv/settings.dcf | 6 +- 6 files changed, 702 insertions(+), 686 deletions(-) diff --git a/.Rprofile b/.Rprofile index 3ac58f50..63eee448 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,5 +1,16 @@ -if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) { - source("renv/activate.R") +# Set renv profile base on R version. +renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") +if (file.exists("./renv/profile")) { + message("Using renv profile from `renv/profile` file.") +} else if (renv_profile %in% c("4.1", "4.2", "4.3")) { + message("Set renv profile to `", renv_profile, "`") + Sys.setenv("RENV_PROFILE" = renv_profile) } else { + message("This repository do not contains the renv profile for your R version.") +} + +if ((Sys.getenv("GITHUB_ACTIONS") != "") || (Sys.getenv("DOCKER_CONTAINER_CONTEXT") != "")) { options(repos = c(CRAN = "https://cran.rstudio.com")) + Sys.setenv(RENV_AUTOLOADER_ENABLED=FALSE) } +source("renv/activate.R") diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index ed767000..1962f5c6 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -45,25 +45,25 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/style.yml@main if: github.event_name == 'pull_request' with: - r-version: $R_VERSION + r-version: "4.1" spellcheck: name: Spelling uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main if: github.event_name == 'pull_request' with: - r-version: $R_VERSION + r-version: "4.1" readme: name: Render README uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main if: github.event_name == 'push' with: - r-version: $R_VERSION + r-version: "4.1" validation: name: Validation uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main if: github.event_name == 'release' with: - r-version: $R_VERSION + r-version: "4.1" check: name: Check uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main @@ -73,7 +73,7 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main if: github.event_name == 'push' with: - r-version: $R_VERSION + r-version: "4.1" # Whether to skip multiversion docs # Note that if you have multiple versions of docs, # your URL links are likely to break due to path changes @@ -83,7 +83,7 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main if: github.event_name == 'pull_request' with: - r-version: $R_VERSION + r-version: "4.1" links: name: Links uses: pharmaverse/admiralci/.github/workflows/links.yml@main @@ -95,7 +95,7 @@ jobs: if: > github.event_name == 'push' || github.event_name == 'pull_request' with: - r-version: $R_VERSION + r-version: "4.1" # Whether to skip code coverage badge creation # Setting to 'false' will require you to create # an orphan branch called 'badges' in your repository @@ -106,10 +106,10 @@ jobs: if: > github.event_name == 'push' || github.event_name == 'pull_request' with: - r-version: $R_VERSION + r-version: "4.1" man-pages: name: Man Pages uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main if: github.event_name == 'pull_request' with: - r-version: $R_VERSION + r-version: "4.1" diff --git a/renv.lock b/renv.lock index b6e48a22..66174483 100644 --- a/renv.lock +++ b/renv.lock @@ -1,390 +1,349 @@ { "R": { - "Version": "4.0.5", + "Version": "4.1.3", "Repositories": [ { "Name": "CRAN", "URL": "https://cloud.r-project.org" }, { - "Name": "MRAN", - "URL": "https://cran.microsoft.com/snapshot/2021-03-31" + "Name": "RSPM", + "URL": "https://packagemanager.posit.co/cran/2022-03-10" } ] }, "Packages": { - "BH": { - "Package": "BH", - "Version": "1.75.0-0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "e4c04affc2cac20c8fec18385cd14691", - "Requirements": [] - }, "DT": { "Package": "DT", - "Version": "0.17", + "Version": "0.21", "Source": "Repository", - "Repository": "CRAN", - "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0", + "Repository": "RSPM", "Requirements": [ "crosstalk", "htmltools", "htmlwidgets", + "jquerylib", "jsonlite", "magrittr", "promises" - ] - }, - "KernSmooth": { - "Package": "KernSmooth", - "Version": "2.23-18", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9e703ad8bf0e99f3691f05da32dfe68b", - "Requirements": [] - }, - "MASS": { - "Package": "MASS", - "Version": "7.3-53.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "4ef21dd0348b9abb7f8bd1d77e4cd0c3", - "Requirements": [] - 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"Repository": "CRAN", - "Hash": "e8a22846fff485f0be3770c2da758713", + "Repository": "RSPM", "Requirements": [ "sys" - ] - }, - "assertthat": { - "Package": "assertthat", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "50c838a310445e954bc13f26f26a6ecf", - "Requirements": [] + ], + "Hash": "e8a22846fff485f0be3770c2da758713" }, "backports": { "Package": "backports", - "Version": "1.2.1", + "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "644043219fc24e190c2f620c1a380a69", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "c39fbec8a30d23e721980b8afb31984c" }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "543776ae6848fde2f48ff3816d0628bc", - "Requirements": [] - }, - "boot": { - "Package": "boot", - "Version": "1.3-27", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "d9778c960792721e8433daaf3db8f16a", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "543776ae6848fde2f48ff3816d0628bc" }, "brew": { "Package": "brew", - 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"Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", "Requirements": [ + "R", "R6", "cli", - "rprojroot" - ] + "rprojroot", + "utils" + ], + "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21" }, "devtools": { "Package": "devtools", - "Version": "2.3.2", + "Version": "2.4.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "415656f50722f5b6e6bcf80855ce11b9", + "Repository": "RSPM", "Requirements": [ - "DT", + "R", "callr", "cli", - "covr", "desc", "ellipsis", + "fs", "httr", - "jsonlite", + "lifecycle", "memoise", "pkgbuild", "pkgload", @@ -395,46 +354,59 @@ "rstudioapi", "rversions", "sessioninfo", + "stats", "testthat", + "tools", "usethis", + "utils", "withr" - ] + ], + "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5" }, "diffdf": { "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "9ddedef46959baad2080047a1b0117fe", + "Repository": "RSPM", "Requirements": [ + "R", "tibble" - ] + ], + "Hash": "9ddedef46959baad2080047a1b0117fe" }, "diffobj": { "Package": "diffobj", - 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}, - "spatial": { - "Package": "spatial", - "Version": "7.3-13", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8d0918547149f72e78ae942ccd1fdbc7", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "947e4e02a79effa5d512473e10f41797" }, "spelling": { "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b8c899a5c83f0d897286550481c91798", + "Repository": "RSPM", "Requirements": [ "commonmark", "hunspell", "knitr", "xml2" - ] + ], + "Hash": "b8c899a5c83f0d897286550481c91798" }, "staged.dependencies": { "Package": "staged.dependencies", - "Version": "0.2.7", + "Version": "0.2.8", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteRepo": "staged.dependencies", "RemoteUsername": "openpharma", - "RemoteRef": "HEAD", - "RemoteSha": "669f45a95d8772899551ad51fc3b38a3b5a1056a", - "Hash": "348648f944ce5dbcbdc2b120c9ba3a3c", + "RemoteRepo": "staged.dependencies", + "RemoteRef": "main", + "RemoteSha": "ce7c112ba3d75cf48e4dd6310b3140ab0ec3b486", "Requirements": [ "desc", "devtools", @@ -1321,91 +1275,92 @@ "glue", "httr", "jsonlite", + "methods", "rcmdcheck", "remotes", "rlang", + "stats", "tidyr", + "utils", "withr", "yaml" - ] + ], + "Hash": "89f2e1d1009601f58f64b7092abcc0d7" }, "stringi": { "Package": "stringi", - "Version": "1.5.3", + "Version": "1.7.6", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a063ebea753c92910a4cca7b18bc1f05", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "stats", + "tools", + "utils" + ], + "Hash": "bba431031d30789535745a9627ac9271" }, "stringr": { "Package": "stringr", "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0759e6b6c0957edb1311028a49a35e76", + "Repository": "RSPM", "Requirements": [ + "R", "glue", "magrittr", "stringi" - ] + ], + "Hash": "0759e6b6c0957edb1311028a49a35e76" }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "c855e70eb69b3dd8883660b7110e0c44", "Requirements": [ + "R", "R.cache", "cli", "magrittr", "purrr", "rlang", "rprojroot", + "tools", "vctrs", "withr" - ] - }, - "survival": { - "Package": "survival", - "Version": "3.2-10", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6b7453cd9bb32b12577c78d54eeea56a", - "Requirements": [ - "Matrix" - ] + ], + "Hash": "ed8c90822b7da46beee603f263a85fe0" }, "sys": { "Package": "sys", "Version": "3.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b227d13e29222b4574486cfcbde077fa", - "Requirements": [] + "Repository": "RSPM", + "Hash": "b227d13e29222b4574486cfcbde077fa" }, "systemfonts": { "Package": "systemfonts", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "90b28393209827327de889f49935140a", + "Repository": "RSPM", "Requirements": [ + "R", "cpp11" - ] + ], + "Hash": "90b28393209827327de889f49935140a" }, "testthat": { "Package": "testthat", - "Version": "3.0.2", + "Version": "3.1.7", "Source": "Repository", "Repository": "CRAN", - "Hash": "495e0434d9305716b6a87031570ce109", "Requirements": [ + "R", "R6", "brio", "callr", "cli", - "crayon", "desc", "digest", "ellipsis", @@ -1413,50 +1368,56 @@ "jsonlite", "lifecycle", "magrittr", + "methods", "pkgload", "praise", "processx", "ps", "rlang", + "utils", "waldo", "withr" - ] + ], + "Hash": "7eb5fd202a61d2fb78af5869b6c08998" }, "textshaping": { "Package": "textshaping", "Version": "0.3.6", "Source": "Repository", - "Repository": "CRAN", - "Hash": "1ab6223d3670fac7143202cb6a2d43d5", + "Repository": "RSPM", "Requirements": [ + "R", "cpp11", "systemfonts" - ] + ], + "Hash": "1ab6223d3670fac7143202cb6a2d43d5" }, "tibble": { "Package": "tibble", - "Version": "3.1.0", + "Version": "3.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "4d894a114dbd4ecafeda5074e7c538e6", "Requirements": [ - "ellipsis", + "R", "fansi", "lifecycle", "magrittr", + "methods", "pillar", "pkgconfig", "rlang", + "utils", "vctrs" - ] + ], + "Hash": "37695ff125982007d42a59ad10982ff2" }, "tidyr": { "Package": "tidyr", - "Version": "1.1.3", + "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "450d7dfaedde58e28586b854eeece4fa", + "Repository": "RSPM", "Requirements": [ + "R", "cpp11", "dplyr", "ellipsis", @@ -1467,40 +1428,44 @@ "rlang", "tibble", "tidyselect", + "utils", "vctrs" - ] + ], + "Hash": "d8b95b7fee945d7da6888cf7eb71a49c" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.0", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "6ea435c354e8448819627cf686f66e0a", "Requirements": [ - "ellipsis", + "R", + "cli", "glue", - "purrr", + "lifecycle", "rlang", - "vctrs" - ] + "vctrs", + "withr" + ], + "Hash": "79540e5fcd9e0435af547d885f184fd5" }, "tinytex": { "Package": "tinytex", - "Version": "0.42", + "Version": "0.37", "Source": "Repository", - "Repository": "CRAN", - "Hash": "7629c6c1540835d5248e6e7df265fa74", + "Repository": "RSPM", "Requirements": [ "xfun" - ] + ], + "Hash": "a80abeb527a977e4bef21873d29222dd" }, "usethis": { "Package": "usethis", - "Version": "2.1.6", + "Version": "2.1.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a67a22c201832b12c036cc059f1d137d", + "Repository": "RSPM", "Requirements": [ + "R", "cli", "clipr", "crayon", @@ -1517,134 +1482,143 @@ "rlang", "rprojroot", "rstudioapi", + "stats", + "utils", "whisker", "withr", "yaml" - ] + ], + "Hash": "c499f488e6dd7718accffaee5bc5a79b" }, "utf8": { "Package": "utf8", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "c9c462b759a5cc844ae25b5942654d13" }, "vctrs": { "Package": "vctrs", - "Version": "0.5.0", + "Version": "0.6.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "001fd6a5ebfff8316baf9fb2b5516dc9", "Requirements": [ + "R", "cli", "glue", "lifecycle", "rlang" - ] - }, - "visNetwork": { - "Package": "visNetwork", - "Version": "2.0.9", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "12545f2acf49d1d346d075580122d89c", - "Requirements": [ - "htmltools", - "htmlwidgets", - "jsonlite", - "magrittr" - ] + ], + "Hash": "7e877404388794361277be95d8445de8" }, "waldo": { "Package": "waldo", - "Version": "0.2.5", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "20c45f1d511a3f730b7b469f4d11e104", "Requirements": [ "cli", "diffobj", "fansi", "glue", + "methods", "rematch2", "rlang", "tibble" - ] + ], + "Hash": "035fba89d0c86e2113120f93301b98ad" }, "whisker": { "Package": "whisker", "Version": "0.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ca970b96d894e90397ed20637a0c1bbe", - "Requirements": [] + "Repository": "RSPM", + "Hash": "ca970b96d894e90397ed20637a0c1bbe" }, "withr": { "Package": "withr", "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c0e49a9760983e81e55cdd9be92e7182", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats" + ], + "Hash": "c0e49a9760983e81e55cdd9be92e7182" }, "xfun": { "Package": "xfun", "Version": "0.34", "Source": "Repository", "Repository": "CRAN", - "Hash": "9eba2411b0b1f879797141bd24df7407", - "Requirements": [] + "Requirements": [ + "stats", + "tools" + ], + "Hash": "9eba2411b0b1f879797141bd24df7407" }, "xml2": { "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "40682ed6a969ea5abfd351eb67833adc", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "methods" + ], + "Hash": "40682ed6a969ea5abfd351eb67833adc" }, "xmlparsedata": { "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "45e4bf3c46476896e821fc0a408fb4fc", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "45e4bf3c46476896e821fc0a408fb4fc" }, "xopen": { "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6c85f015dee9cc7710ddd20f86881f58", + "Repository": "RSPM", "Requirements": [ + "R", "processx" - ] + ], + "Hash": "6c85f015dee9cc7710ddd20f86881f58" }, "xtable": { "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", - "Requirements": [] + "Repository": "RSPM", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" }, "yaml": { "Package": "yaml", - "Version": "2.2.1", + "Version": "2.3.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2826c5d9efb0a88f657c7a679c7106db", - "Requirements": [] + "Repository": "RSPM", + "Hash": "458bb38374d73bf83b1bb85e353da200" }, "zip": { "Package": "zip", - "Version": "2.2.2", + "Version": "2.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88", - "Requirements": [] + "Repository": "RSPM", + "Hash": "c7eef2996ac270a18c2715c997a727c5" } } } diff --git a/renv/.gitignore b/renv/.gitignore index 6ae4167d..2649d0a0 100644 --- a/renv/.gitignore +++ b/renv/.gitignore @@ -5,3 +5,4 @@ local/ lock/ python/ staging/ +profile diff --git a/renv/activate.R b/renv/activate.R index 019b5a66..360dd528 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "0.16.0" + version <- "0.17.0" # the project directory project <- getwd() @@ -94,8 +94,11 @@ local({ return(repos) # if we're testing, re-use the test repositories - if (renv_bootstrap_tests_running()) - return(getOption("renv.tests.repos")) + if (renv_bootstrap_tests_running()) { + repos <- getOption("renv.tests.repos") + if (!is.null(repos)) + return(repos) + } # retrieve current repos repos <- getOption("repos") @@ -344,8 +347,7 @@ local({ return() # allow directories - info <- file.info(tarball, extra_cols = FALSE) - if (identical(info$isdir, TRUE)) { + if (dir.exists(tarball)) { name <- sprintf("renv_%s.tar.gz", version) tarball <- file.path(tarball, name) } @@ -659,8 +661,8 @@ local({ if (version == loadedversion) return(TRUE) - # assume four-component versions are from GitHub; three-component - # versions are from CRAN + # assume four-component versions are from GitHub; + # three-component versions are from CRAN components <- strsplit(loadedversion, "[.-]")[[1]] remote <- if (length(components) == 4L) paste("rstudio/renv", loadedversion, sep = "@") @@ -700,6 +702,12 @@ local({ # warn if the version of renv loaded does not match renv_bootstrap_validate_version(version) + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warning) + # load the project renv::load(project) @@ -842,11 +850,29 @@ local({ renv_json_read <- function(file = NULL, text = NULL) { + jlerr <- NULL + # if jsonlite is loaded, use that instead - if ("jsonlite" %in% loadedNamespaces()) - renv_json_read_jsonlite(file, text) + if ("jsonlite" %in% loadedNamespaces()) { + + json <- catch(renv_json_read_jsonlite(file, text)) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- catch(renv_json_read_default(file, text)) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) else - renv_json_read_default(file, text) + stop(json) } diff --git a/renv/settings.dcf b/renv/settings.dcf index 0c5119c7..fd205f80 100644 --- a/renv/settings.dcf +++ b/renv/settings.dcf @@ -1,6 +1,10 @@ -ignored.packages: +bioconductor.version: +external.libraries: +ignored.packages: admiral, admiraldev, admiral.test, admiralci package.dependency.fields: Imports, Depends, LinkingTo r.version: snapshot.type: implicit use.cache: TRUE +vcs.ignore.cellar: TRUE vcs.ignore.library: TRUE +vcs.ignore.local: TRUE From 223b1b2290e219da08584d74f469db5e25212d70 Mon Sep 17 00:00:00 2001 From: galachad Date: Fri, 28 Jul 2023 07:40:32 +0000 Subject: [PATCH 02/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 23 +++++---- .devcontainer/4.1/devcontainer.json | 77 +++++++++++++++++++++++++++++ .devcontainer/4.2/devcontainer.json | 77 +++++++++++++++++++++++++++++ .devcontainer/devcontainer.json | 77 +++++++++++++++++++++++++++++ .devcontainer/rstudio-prefs.json | 8 +++ 5 files changed, 250 insertions(+), 12 deletions(-) create mode 100644 .devcontainer/4.1/devcontainer.json create mode 100644 .devcontainer/4.2/devcontainer.json create mode 100644 .devcontainer/devcontainer.json create mode 100644 .devcontainer/rstudio-prefs.json diff --git a/.Rprofile b/.Rprofile index 63eee448..77ae067e 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,16 +1,15 @@ # Set renv profile base on R version. -renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") -if (file.exists("./renv/profile")) { - message("Using renv profile from `renv/profile` file.") -} else if (renv_profile %in% c("4.1", "4.2", "4.3")) { - message("Set renv profile to `", renv_profile, "`") - Sys.setenv("RENV_PROFILE" = renv_profile) +if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) { + renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") + if (file.exists("./renv/profile")) { + message("Using renv profile from `renv/profile` file.") + } else if (renv_profile %in% c("4.1", "4.2", "4.3")) { + message("Set renv profile to `", renv_profile, "`") + Sys.setenv("RENV_PROFILE" = renv_profile) + } else { + message("This repository do not contains the renv profile for your R version.") + } + source("renv/activate.R") } else { - message("This repository do not contains the renv profile for your R version.") -} - -if ((Sys.getenv("GITHUB_ACTIONS") != "") || (Sys.getenv("DOCKER_CONTAINER_CONTEXT") != "")) { options(repos = c(CRAN = "https://cran.rstudio.com")) - Sys.setenv(RENV_AUTOLOADER_ENABLED=FALSE) } -source("renv/activate.R") diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json new file mode 100644 index 00000000..a0415f8b --- /dev/null +++ b/.devcontainer/4.1/devcontainer.json @@ -0,0 +1,77 @@ +{ + // https://containers.dev/implementors/json_reference/ + "name": "Admiral R-4.1 (RStudio) container", + "image": "ghcr.io/pharmaverse/admiralci-4.1:latest", + // Install Dev Container Features. More info: https://containers.dev/features + "containerEnv": { + "ROOT": "true", + "PASSWORD": "rstudio", + "DISABLE_AUTH": "true" + }, + "features": { + "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { + "version": "none", + "vscodeRSupport": "full", + "installRadian": true, + "installVscDebugger": true + }, + "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, + "ghcr.io/devcontainers/features/common-utils:2": { + "installZsh": true, + "configureZshAsDefaultShell": true, + "installOhMyZsh": true, + "username": "rstudio", + "upgradePackages": false + + }, + "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} + }, + "init": true, + "overrideCommand": false, + + "postCreateCommand": { + "renv": "R -q -e 'renv::activate(profile = \"4.1\"); renv::restore(); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = \".\", verbose = 1), verbose = 1);'", + "rstudio": "jq --arg folder \"$(pwd)/\" '. + { \"initial_working_directory\": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json" + }, + + "customizations": { + "vscode": { + "settings": { + "r.rterm.linux": "/usr/local/bin/radian", + "r.bracketedPaste": true, + "editor.bracketPairColorization.enabled": true, + "editor.guides.bracketPairs": "active" + }, + "extensions": [ + "vsls-contrib.codetour", + "GitHub.copilot", + "GitHub.copilot-chat", + // R extensions + "ikuyadeu.r", + "REditorSupport.r-lsp", + // Extra extension + "streetsidesoftware.code-spell-checker", + "eamodio.gitlens", + "cweijan.vscode-office", + "donjayamanne.githistory", + "GitHub.vscode-github-actions", + "GitHub.vscode-pull-request-github", + "GitHub.remotehub", + "alefragnani.Bookmarks", + "vscode-icons-team.vscode-icons" + ] + } + }, + + // RStudio ports + "forwardPorts": [8787], + "portsAttributes": { + "8787": { + "label": "Rstudio", + "requireLocalPort": true, + "onAutoForward": "ignore" + } + }, + // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root + "remoteUser": "rstudio" +} diff --git a/.devcontainer/4.2/devcontainer.json b/.devcontainer/4.2/devcontainer.json new file mode 100644 index 00000000..493aba1a --- /dev/null +++ b/.devcontainer/4.2/devcontainer.json @@ -0,0 +1,77 @@ +{ + // https://containers.dev/implementors/json_reference/ + "name": "Admiral R-4.2 (RStudio) container", + "image": "ghcr.io/pharmaverse/admiralci-4.2:latest", + // Install Dev Container Features. More info: https://containers.dev/features + "containerEnv": { + "ROOT": "true", + "PASSWORD": "rstudio", + "DISABLE_AUTH": "true" + }, + "features": { + "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { + "version": "none", + "vscodeRSupport": "full", + "installRadian": true, + "installVscDebugger": true + }, + "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, + "ghcr.io/devcontainers/features/common-utils:2": { + "installZsh": true, + "configureZshAsDefaultShell": true, + "installOhMyZsh": true, + "username": "rstudio", + "upgradePackages": false + + }, + "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} + }, + "init": true, + "overrideCommand": false, + + "postCreateCommand": { + "renv": "R -q -e 'renv::activate(profile = \"4.2\"); renv::restore(); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = \".\", verbose = 1), verbose = 1);'", + "rstudio": "jq --arg folder \"$(pwd)/\" '. + { \"initial_working_directory\": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json" + }, + + "customizations": { + "vscode": { + "settings": { + "r.rterm.linux": "/usr/local/bin/radian", + "r.bracketedPaste": true, + "editor.bracketPairColorization.enabled": true, + "editor.guides.bracketPairs": "active" + }, + "extensions": [ + "vsls-contrib.codetour", + "GitHub.copilot", + "GitHub.copilot-chat", + // R extensions + "ikuyadeu.r", + "REditorSupport.r-lsp", + // Extra extension + "streetsidesoftware.code-spell-checker", + "eamodio.gitlens", + "cweijan.vscode-office", + "donjayamanne.githistory", + "GitHub.vscode-github-actions", + "GitHub.vscode-pull-request-github", + "GitHub.remotehub", + "alefragnani.Bookmarks", + "vscode-icons-team.vscode-icons" + ] + } + }, + + // RStudio ports + "forwardPorts": [8787], + "portsAttributes": { + "8787": { + "label": "Rstudio", + "requireLocalPort": true, + "onAutoForward": "ignore" + } + }, + // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root + "remoteUser": "rstudio" +} diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..47a8a0f6 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,77 @@ +{ + // https://containers.dev/implementors/json_reference/ + "name": "Admiral R-4.3 (RStudio) container", + "image": "ghcr.io/pharmaverse/admiralci-4.3:latest", + // Install Dev Container Features. More info: https://containers.dev/features + "containerEnv": { + "ROOT": "true", + "PASSWORD": "rstudio", + "DISABLE_AUTH": "true", + "DOCKER_CONTAINER_CONTEXT": "" + }, + "features": { + "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { + "version": "none", + "vscodeRSupport": "full", + "installRadian": true, + "installVscDebugger": true + }, + "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, + "ghcr.io/devcontainers/features/common-utils:2": { + "installZsh": true, + "configureZshAsDefaultShell": true, + "installOhMyZsh": true, + "username": "rstudio", + "upgradePackages": false + }, + "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} + }, + "init": true, + "overrideCommand": false, + + "postCreateCommand": { + "renv": "R -q -e 'renv::activate(profile = \"4.3\"); renv::restore(); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = \".\", verbose = 1), verbose = 1);'", + "rstudio": "jq --arg folder \"$(pwd)/\" '. + { \"initial_working_directory\": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json" + }, + + "customizations": { + "vscode": { + "settings": { + "r.rterm.linux": "/usr/local/bin/radian", + "r.bracketedPaste": true, + "editor.bracketPairColorization.enabled": true, + "editor.guides.bracketPairs": "active" + }, + "extensions": [ + "vsls-contrib.codetour", + "GitHub.copilot", + "GitHub.copilot-chat", + // R extensions + "ikuyadeu.r", + "REditorSupport.r-lsp", + // Extra extension + "streetsidesoftware.code-spell-checker", + "eamodio.gitlens", + "cweijan.vscode-office", + "donjayamanne.githistory", + "GitHub.vscode-github-actions", + "GitHub.vscode-pull-request-github", + "GitHub.remotehub", + "alefragnani.Bookmarks", + "vscode-icons-team.vscode-icons" + ] + } + }, + + // RStudio ports + "forwardPorts": [8787], + "portsAttributes": { + "8787": { + "label": "Rstudio", + "requireLocalPort": true, + "onAutoForward": "ignore" + } + }, + // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root + "remoteUser": "rstudio" +} diff --git a/.devcontainer/rstudio-prefs.json b/.devcontainer/rstudio-prefs.json new file mode 100644 index 00000000..2d5cce84 --- /dev/null +++ b/.devcontainer/rstudio-prefs.json @@ -0,0 +1,8 @@ +{ + "save_workspace": "never", + "always_save_history": false, + "reuse_sessions_for_project_links": true, + "posix_terminal_shell": "bash", + "initial_working_directory": "/workspaces", + "show_hidden_files": true +} From cff50144d7ba6e3d85e72a183077ed8ed28f950f Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Wed, 2 Aug 2023 12:38:33 +0000 Subject: [PATCH 03/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/.Rprofile b/.Rprofile index 77ae067e..b596c18f 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,15 +1,17 @@ # Set renv profile base on R version. -if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) { - renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") - if (file.exists("./renv/profile")) { - message("Using renv profile from `renv/profile` file.") - } else if (renv_profile %in% c("4.1", "4.2", "4.3")) { +renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") +if (file.exists("./renv/profile")) { + message("Using renv profile from `renv/profile` file.") + if (renv_profile %in% c("4.1", "4.2", "4.3")) { message("Set renv profile to `", renv_profile, "`") Sys.setenv("RENV_PROFILE" = renv_profile) } else { - message("This repository do not contains the renv profile for your R version.") + message("This repository do not contains the renv profile for your R version.") } - source("renv/activate.R") -} else { +} + +if ((Sys.getenv("GITHUB_ACTIONS") != "") || (Sys.getenv("DOCKER_CONTAINER_CONTEXT") != "")) { options(repos = c(CRAN = "https://cran.rstudio.com")) + Sys.setenv(RENV_AUTOLOADER_ENABLED=FALSE) } +source("renv/activate.R") \ No newline at end of file From 35247936af78f7ddc9c805b2c8c59150f997384f Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Wed, 2 Aug 2023 16:16:32 +0000 Subject: [PATCH 04/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 2 +- .devcontainer/codespaces_rstudio_status.sh | 28 ++++++++++++++++++++++ 2 files changed, 29 insertions(+), 1 deletion(-) create mode 100644 .devcontainer/codespaces_rstudio_status.sh diff --git a/.Rprofile b/.Rprofile index b596c18f..16457c27 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,6 +1,6 @@ # Set renv profile base on R version. renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") -if (file.exists("./renv/profile")) { +if (file.exists("./renv/profiles")) { message("Using renv profile from `renv/profile` file.") if (renv_profile %in% c("4.1", "4.2", "4.3")) { message("Set renv profile to `", renv_profile, "`") diff --git a/.devcontainer/codespaces_rstudio_status.sh b/.devcontainer/codespaces_rstudio_status.sh new file mode 100644 index 00000000..e7d19f23 --- /dev/null +++ b/.devcontainer/codespaces_rstudio_status.sh @@ -0,0 +1,28 @@ +echo "Waiting for rstudio-server to be ready.." + +# Get rstudio url and open it +url=$(jq -r ".CODESPACE_NAME" /workspaces/.codespaces/shared/environment-variables.json) +url_rstudio="https://$url-8787.preview.app.github.dev" + +# loop over url_rstudio until getting success status +MAX_RETRIES=10 +WAIT_TIME=5 + +retries=0 + +while [ $retries -lt $MAX_RETRIES ]; do + http_status=$(curl -s -o /dev/null -w "%{http_code}" "$url_rstudio") + + # Check status code (exit successfully if code in success/redirection category) + if [ $http_status -ge 200 ]; then + echo "Rstudio server ready ! You can now go to this url : $url_rstudio" + exit 0 + else + echo "$http_status" + sleep $WAIT_TIME + ((retries++)) + fi +done + +echo "Error accessing rstudio ($url_rstudio) - Timeout reached." +exit 1 \ No newline at end of file From 78d9680b3e63c4dd10b4702cf924cda98927a08b Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Thu, 3 Aug 2023 08:27:30 +0000 Subject: [PATCH 05/22] renv / codespaces update from pharmaverse/admiralci --- .devcontainer/devcontainer.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 47a8a0f6..2929310c 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -6,8 +6,7 @@ "containerEnv": { "ROOT": "true", "PASSWORD": "rstudio", - "DISABLE_AUTH": "true", - "DOCKER_CONTAINER_CONTEXT": "" + "DISABLE_AUTH": "true" }, "features": { "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { From 9cca2d856b5e233b17c5bf1e6fe619c2a509916d Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Thu, 3 Aug 2023 09:46:43 +0000 Subject: [PATCH 06/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.Rprofile b/.Rprofile index 16457c27..c57642c3 100644 --- a/.Rprofile +++ b/.Rprofile @@ -10,8 +10,8 @@ if (file.exists("./renv/profiles")) { } } -if ((Sys.getenv("GITHUB_ACTIONS") != "") || (Sys.getenv("DOCKER_CONTAINER_CONTEXT") != "")) { +if (Sys.getenv("GITHUB_ACTIONS") != "") { options(repos = c(CRAN = "https://cran.rstudio.com")) Sys.setenv(RENV_AUTOLOADER_ENABLED=FALSE) } -source("renv/activate.R") \ No newline at end of file +source("renv/activate.R") From 1c5fcf1ca180155ce793b44fd1631bad7cc99253 Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Thu, 3 Aug 2023 09:46:53 +0000 Subject: [PATCH 07/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rprofile b/.Rprofile index c57642c3..52cae5ad 100644 --- a/.Rprofile +++ b/.Rprofile @@ -14,4 +14,4 @@ if (Sys.getenv("GITHUB_ACTIONS") != "") { options(repos = c(CRAN = "https://cran.rstudio.com")) Sys.setenv(RENV_AUTOLOADER_ENABLED=FALSE) } -source("renv/activate.R") +source("renv/activate.R") \ No newline at end of file From 3dd4a093863d00cd52e84da64ca05dee6d86f4b8 Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 3 Aug 2023 09:55:43 +0000 Subject: [PATCH 08/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 2 +- .devcontainer/codespaces_rstudio_status.sh | 28 ---------------------- 2 files changed, 1 insertion(+), 29 deletions(-) delete mode 100644 .devcontainer/codespaces_rstudio_status.sh diff --git a/.Rprofile b/.Rprofile index 52cae5ad..c57642c3 100644 --- a/.Rprofile +++ b/.Rprofile @@ -14,4 +14,4 @@ if (Sys.getenv("GITHUB_ACTIONS") != "") { options(repos = c(CRAN = "https://cran.rstudio.com")) Sys.setenv(RENV_AUTOLOADER_ENABLED=FALSE) } -source("renv/activate.R") \ No newline at end of file +source("renv/activate.R") diff --git a/.devcontainer/codespaces_rstudio_status.sh b/.devcontainer/codespaces_rstudio_status.sh deleted file mode 100644 index e7d19f23..00000000 --- a/.devcontainer/codespaces_rstudio_status.sh +++ /dev/null @@ -1,28 +0,0 @@ -echo "Waiting for rstudio-server to be ready.." - -# Get rstudio url and open it -url=$(jq -r ".CODESPACE_NAME" /workspaces/.codespaces/shared/environment-variables.json) -url_rstudio="https://$url-8787.preview.app.github.dev" - -# loop over url_rstudio until getting success status -MAX_RETRIES=10 -WAIT_TIME=5 - -retries=0 - -while [ $retries -lt $MAX_RETRIES ]; do - http_status=$(curl -s -o /dev/null -w "%{http_code}" "$url_rstudio") - - # Check status code (exit successfully if code in success/redirection category) - if [ $http_status -ge 200 ]; then - echo "Rstudio server ready ! You can now go to this url : $url_rstudio" - exit 0 - else - echo "$http_status" - sleep $WAIT_TIME - ((retries++)) - fi -done - -echo "Error accessing rstudio ($url_rstudio) - Timeout reached." -exit 1 \ No newline at end of file From baa82b519fff65a539e7252064177d5756d3eb41 Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 3 Aug 2023 11:47:27 +0000 Subject: [PATCH 09/22] renv / codespaces update from pharmaverse/admiralci --- .devcontainer/4.1/devcontainer.json | 12 +- .devcontainer/4.2/devcontainer.json | 12 +- .devcontainer/devcontainer.json | 11 +- .devcontainer/postCreateCommand.sh | 5 + renv/activate.R | 393 ++++++++++++++++++++-------- 5 files changed, 297 insertions(+), 136 deletions(-) create mode 100644 .devcontainer/postCreateCommand.sh diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json index a0415f8b..f287993d 100644 --- a/.devcontainer/4.1/devcontainer.json +++ b/.devcontainer/4.1/devcontainer.json @@ -18,21 +18,19 @@ "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, "ghcr.io/devcontainers/features/common-utils:2": { "installZsh": true, - "configureZshAsDefaultShell": true, + "configureZshAsDefaultShell": false, "installOhMyZsh": true, "username": "rstudio", "upgradePackages": false - }, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} }, "init": true, "overrideCommand": false, - "postCreateCommand": { - "renv": "R -q -e 'renv::activate(profile = \"4.1\"); renv::restore(); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = \".\", verbose = 1), verbose = 1);'", - "rstudio": "jq --arg folder \"$(pwd)/\" '. + { \"initial_working_directory\": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json" - }, + "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", + + "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", "customizations": { "vscode": { @@ -69,7 +67,7 @@ "8787": { "label": "Rstudio", "requireLocalPort": true, - "onAutoForward": "ignore" + "onAutoForward": "openBrowser" } }, // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root diff --git a/.devcontainer/4.2/devcontainer.json b/.devcontainer/4.2/devcontainer.json index 493aba1a..9878fa4b 100644 --- a/.devcontainer/4.2/devcontainer.json +++ b/.devcontainer/4.2/devcontainer.json @@ -18,21 +18,19 @@ "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, "ghcr.io/devcontainers/features/common-utils:2": { "installZsh": true, - "configureZshAsDefaultShell": true, + "configureZshAsDefaultShell": false, "installOhMyZsh": true, "username": "rstudio", "upgradePackages": false - }, "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} }, "init": true, "overrideCommand": false, - "postCreateCommand": { - "renv": "R -q -e 'renv::activate(profile = \"4.2\"); renv::restore(); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = \".\", verbose = 1), verbose = 1);'", - "rstudio": "jq --arg folder \"$(pwd)/\" '. + { \"initial_working_directory\": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json" - }, + "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", + + "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", "customizations": { "vscode": { @@ -69,7 +67,7 @@ "8787": { "label": "Rstudio", "requireLocalPort": true, - "onAutoForward": "ignore" + "onAutoForward": "openBrowser" } }, // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 2929310c..af6c75b9 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,7 +18,7 @@ "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, "ghcr.io/devcontainers/features/common-utils:2": { "installZsh": true, - "configureZshAsDefaultShell": true, + "configureZshAsDefaultShell": false, "installOhMyZsh": true, "username": "rstudio", "upgradePackages": false @@ -28,10 +28,9 @@ "init": true, "overrideCommand": false, - "postCreateCommand": { - "renv": "R -q -e 'renv::activate(profile = \"4.3\"); renv::restore(); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = \".\", verbose = 1), verbose = 1);'", - "rstudio": "jq --arg folder \"$(pwd)/\" '. + { \"initial_working_directory\": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json" - }, + "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", + + "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", "customizations": { "vscode": { @@ -68,7 +67,7 @@ "8787": { "label": "Rstudio", "requireLocalPort": true, - "onAutoForward": "ignore" + "onAutoForward": "openBrowser" } }, // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh new file mode 100644 index 00000000..9c6aec29 --- /dev/null +++ b/.devcontainer/postCreateCommand.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +R -q -e 'renv::activate(profile = paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")); renv::restore(); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);' + +jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json diff --git a/renv/activate.R b/renv/activate.R index 360dd528..cc742fc9 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,8 @@ local({ # the requested version of renv - version <- "0.17.0" + version <- "1.0.0" + attr(version, "sha") <- NULL # the project directory project <- getwd() @@ -60,21 +61,75 @@ local({ # load bootstrap tools `%||%` <- function(x, y) { - if (is.environment(x) || length(x)) x else y + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix } bootstrap <- function(version, library) { + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + # attempt to download renv - tarball <- tryCatch(renv_bootstrap_download(version), error = identity) - if (inherits(tarball, "error")) - stop("failed to download renv ", version) + 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 - status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) - if (inherits(status, "error")) - stop("failed to install renv ", version) + 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() { @@ -83,31 +138,32 @@ local({ 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)) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + return(repos) + } + # check for lockfile repositories repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) if (!inherits(repos, "error") && length(repos)) return(repos) - # if we're testing, re-use the test repositories - if (renv_bootstrap_tests_running()) { - repos <- getOption("renv.tests.repos") - if (!is.null(repos)) - return(repos) - } - # retrieve current repos repos <- getOption("repos") # ensure @CRAN@ entries are resolved - repos[repos == "@CRAN@"] <- getOption( - "renv.repos.cran", - "https://cloud.r-project.org" - ) + repos[repos == "@CRAN@"] <- cran # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") @@ -146,33 +202,34 @@ local({ renv_bootstrap_download <- function(version) { - # if the renv version number has 4 components, assume it must - # be retrieved via github - nv <- numeric_version(version) - components <- unclass(nv)[[1]] - - # if this appears to be a development version of 'renv', we'll - # try to restore from github - dev <- length(components) == 4L - - # begin collecting different methods for finding renv - methods <- c( - renv_bootstrap_download_tarball, - if (dev) - renv_bootstrap_download_github - else c( - renv_bootstrap_download_cran_latest, - renv_bootstrap_download_cran_archive + 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(version), error = identity) + path <- tryCatch(method(), error = identity) if (is.character(path) && file.exists(path)) return(path) } - stop("failed to download renv ", version) + stop("All download methods failed") } @@ -236,8 +293,6 @@ local({ type <- spec$type repos <- spec$repos - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - baseurl <- utils::contrib.url(repos = repos, type = type) ext <- if (identical(type, "source")) ".tar.gz" @@ -254,13 +309,10 @@ local({ condition = identity ) - if (inherits(status, "condition")) { - message("FAILED") + if (inherits(status, "condition")) return(FALSE) - } # report success and return - message("OK (downloaded ", type, ")") destfile } @@ -317,8 +369,6 @@ local({ urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - for (url in urls) { status <- tryCatch( @@ -326,14 +376,11 @@ local({ condition = identity ) - if (identical(status, 0L)) { - message("OK") + if (identical(status, 0L)) return(destfile) - } } - message("FAILED") return(FALSE) } @@ -356,7 +403,7 @@ local({ 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." + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." msg <- sprintf(fmt, tarball) warning(msg) @@ -365,10 +412,7 @@ local({ } - fmt <- "* Bootstrapping with tarball at path '%s'." - msg <- sprintf(fmt, tarball) - message(msg) - + catf("- Using local tarball '%s'.", tarball) tarball } @@ -395,8 +439,6 @@ local({ on.exit(do.call(base::options, saved), add = TRUE) } - message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) - url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) @@ -406,26 +448,105 @@ local({ condition = identity ) - if (!identical(status, 0L)) { - message("FAILED") + if (!identical(status, 0L)) return(FALSE) - } - message("OK") + 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 - message("* Installing renv ", version, " ... ", appendLF = FALSE) 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) + R <- file.path(bin, exe) args <- c( "--vanilla", "CMD", "INSTALL", "--no-multiarch", @@ -433,19 +554,7 @@ local({ shQuote(path.expand(tarball)) ) - output <- system2(r, args, stdout = TRUE, stderr = TRUE) - message("Done!") - - # check for successful install - status <- attr(output, "status") - if (is.numeric(status) && !identical(status, 0L)) { - header <- "Error installing renv:" - lines <- paste(rep.int("=", nchar(header)), collapse = "") - text <- c(header, lines, output) - writeLines(text, con = stderr()) - } - - status + system2(R, args, stdout = TRUE, stderr = TRUE) } @@ -655,34 +764,60 @@ local({ } - renv_bootstrap_validate_version <- function(version) { + renv_bootstrap_validate_version <- function(version, description = NULL) { - loadedversion <- utils::packageDescription("renv", fields = "Version") - if (version == loadedversion) - return(TRUE) + # resolve description file + description <- description %||% { + path <- getNamespaceInfo("renv", "path") + packageDescription("renv", lib.loc = dirname(path)) + } - # assume four-component versions are from GitHub; - # three-component versions are from CRAN - components <- strsplit(loadedversion, "[.-]")[[1]] - remote <- if (length(components) == 4L) - paste("rstudio/renv", loadedversion, sep = "@") + # 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 - paste("renv", loadedversion, sep = "@") + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + remote <- if (!is.null(description[["RemoteSha"]])) { + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + } else { + paste("renv", description[["Version"]], sep = "@") + } + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = description[["RemoteSha"]] + ) fmt <- paste( "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", + "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", + "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", sep = "\n" ) - - msg <- sprintf(fmt, loadedversion, version, remote) - warning(msg, call. = FALSE) + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE } + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + renv_bootstrap_hash_text <- function(text) { hashfile <- tempfile("renv-hash-") @@ -847,6 +982,40 @@ local({ } + renv_bootstrap_version_friendly <- function(version, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf("[sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = " ") + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + + renv_bootstrap_in_rstudio <- function() { + commandArgs()[[1]] == "RStudio" + } renv_json_read <- function(file = NULL, text = NULL) { @@ -990,31 +1159,23 @@ local({ if (renv_bootstrap_load(project, libpath, version)) return(TRUE) - # load failed; inform user we're about to bootstrap - prefix <- paste("# Bootstrapping renv", version) - postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") - header <- paste(prefix, postfix) - message(header) - - # 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) + if (renv_bootstrap_in_rstudio()) { + setHook("rstudio.sessionInit", function(...) { + renv_bootstrap_run(version, libpath) - # try again to load - if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - message("* Successfully installed and loaded renv ", version, ".") - return(renv::load()) + # Work around buglet in RStudio if hook uses readline + tryCatch( + { + tools <- as.environment("tools:rstudio") + tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE) + }, + error = function(cnd) {} + ) + }) + } else { + renv_bootstrap_run(version, libpath) } - # 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) + invisible() }) From 589a1b3ab8e0a84af316739d936d1c29a11d71eb Mon Sep 17 00:00:00 2001 From: galachad Date: Fri, 4 Aug 2023 15:44:09 +0000 Subject: [PATCH 10/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 51 +- renv.lock | 1599 +----------------------- renv/profiles/4.1/renv.lock | 1599 +----------------------- renv/profiles/4.1/renv/settings.dcf | 10 - renv/profiles/4.1/renv/settings.json | 24 + renv/profiles/4.2/renv.lock | 1682 +------------------------ renv/profiles/4.2/renv/settings.dcf | 10 - renv/profiles/4.2/renv/settings.json | 24 + renv/profiles/4.3/renv.lock | 1684 +------------------------- renv/profiles/4.3/renv/settings.dcf | 10 - renv/profiles/4.3/renv/settings.json | 24 + 11 files changed, 118 insertions(+), 6599 deletions(-) delete mode 100644 renv/profiles/4.1/renv/settings.dcf create mode 100644 renv/profiles/4.1/renv/settings.json delete mode 100644 renv/profiles/4.2/renv/settings.dcf create mode 100644 renv/profiles/4.2/renv/settings.json delete mode 100644 renv/profiles/4.3/renv/settings.dcf create mode 100644 renv/profiles/4.3/renv/settings.json diff --git a/.Rprofile b/.Rprofile index c57642c3..32e01deb 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,17 +1,48 @@ # Set renv profile base on R version. -renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") -if (file.exists("./renv/profiles")) { - message("Using renv profile from `renv/profile` file.") - if (renv_profile %in% c("4.1", "4.2", "4.3")) { - message("Set renv profile to `", renv_profile, "`") - Sys.setenv("RENV_PROFILE" = renv_profile) +.get_dependencies <- function(project_dir) { + + admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE) + adm_dev_suggests <- if(length(admdev_loc) != 0) { + renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests")) + } else { + data.frame(Packages = character(0)) + } + suggests_packages <- renv:::renv_dependencies_discover_description(project_dir, fields = "Suggests") + + packages <- names( + renv:::renv_package_dependencies( + unique(c( + project_dir, + adm_dev_suggests[["Package"]], + suggests_packages[["Package"]], + c("staged.dependencies", "renv", "styler") + )) + ) + ) + packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test"))] +} + +options(renv.snapshot.filter = .get_dependencies) + +.renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") +if (!file.exists("./renv/profile")) { + if (.renv_profile %in% c("4.1", "4.2", "4.3")) { + message("Set renv profile to `", .renv_profile, "`") + Sys.setenv("RENV_PROFILE" = .renv_profile) } else { - message("This repository do not contains the renv profile for your R version.") + message("This repository do not contains the renv profile for your R version.") } +} else { + message( + "Using renv profile from `renv/profile` file.\n", + "The `", readLines("./renv/profile"), "` profile will be used." + ) } if (Sys.getenv("GITHUB_ACTIONS") != "") { - options(repos = c(CRAN = "https://cran.rstudio.com")) - Sys.setenv(RENV_AUTOLOADER_ENABLED=FALSE) + options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest")) + Sys.setenv("RENV_AUTOLOADER_ENABLED" = FALSE) } -source("renv/activate.R") +Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE) +Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE) +# source("renv/activate.R") diff --git a/renv.lock b/renv.lock index 66174483..f21b8102 100644 --- a/renv.lock +++ b/renv.lock @@ -13,1612 +13,15 @@ ] }, "Packages": { - "DT": { - "Package": "DT", - "Version": "0.21", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "crosstalk", - "htmltools", - "htmlwidgets", - "jquerylib", - "jsonlite", - "magrittr", - "promises" - ], - "Hash": "45fa28dbf288cd606e13ca35d3d72437" - }, - "R.cache": { - "Package": "R.cache", - "Version": "0.15.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R.methodsS3", - "R.oo", - "R.utils", - "digest", - "utils" - ], - "Hash": "e92a8ea8388c47c82ed8aa435ed3be50" - }, - "R.methodsS3": { - "Package": "R.methodsS3", - "Version": "1.8.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "utils" - ], - "Hash": "4bf6453323755202d5909697b6f7c109" - }, - "R.oo": { - "Package": "R.oo", - "Version": "1.24.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R.methodsS3", - "methods", - "utils" - ], - "Hash": "5709328352717e2f0a9c012be8a97554" - }, - "R.utils": { - "Package": "R.utils", - "Version": "2.11.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R.methodsS3", - "R.oo", - "methods", - "tools", - "utils" - ], - "Hash": "a7ecb8e60815c7a18648e84cd121b23a" - }, - "R6": { - "Package": "R6", - "Version": "2.5.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "470851b6d5d0ac559e9d01bb352b4021" - }, - "Rcpp": { - "Package": "Rcpp", - "Version": "1.0.8", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "methods", - "utils" - ], - "Hash": "22b546dd7e337f6c0c58a39983a496bc" - }, - "askpass": { - "Package": "askpass", - "Version": "1.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "sys" - ], - "Hash": "e8a22846fff485f0be3770c2da758713" - }, - "backports": { - "Package": "backports", - "Version": "1.4.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "c39fbec8a30d23e721980b8afb31984c" - }, - "base64enc": { - "Package": "base64enc", - "Version": "0.1-3", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "543776ae6848fde2f48ff3816d0628bc" - }, - "brew": { - "Package": "brew", - "Version": "1.0-7", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "38875ea52350ff4b4c03849fc69736c8" - }, - "brio": { - "Package": "brio", - "Version": "1.1.3", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "976cf154dfb043c012d87cddd8bca363" - }, - "bslib": { - "Package": "bslib", - "Version": "0.3.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "grDevices", - "htmltools", - "jquerylib", - "jsonlite", - "rlang", - "sass" - ], - "Hash": "56ae7e1987b340186a8a5a157c2ec358" - }, - "cachem": { - "Package": "cachem", - "Version": "1.0.6", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "fastmap", - "rlang" - ], - "Hash": "648c5b3d71e6a37e3043617489a0a0e9" - }, - "callr": { - "Package": "callr", - "Version": "3.7.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "processx", - "utils" - ], - "Hash": "9b2191ede20fa29828139b9900922e51" - }, - "cli": { - "Package": "cli", - "Version": "3.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "0d297d01734d2bcea40197bd4971a764" - }, - "clipr": { - "Package": "clipr", - "Version": "0.8.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "utils" - ], - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" - }, - "codetools": { - "Package": "codetools", - "Version": "0.2-18", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "019388fc48e48b3da0d3a76ff94608a8" - }, - "commonmark": { - "Package": "commonmark", - "Version": "1.8.0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "2ba81b120c1655ab696c935ef33ea716" - }, - "covr": { - "Package": "covr", - "Version": "3.5.1", - "Source": "Repository", - "Repository": "RSPM", - 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"d98c94dacb7e0efcf83b0a133a705504" + "Hash": "c321cd99d56443dbffd1c9e673c0c1a2" } } } diff --git a/renv/profiles/4.3/renv/settings.dcf b/renv/profiles/4.3/renv/settings.dcf deleted file mode 100644 index fd205f80..00000000 --- a/renv/profiles/4.3/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: admiral, admiraldev, admiral.test, admiralci -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE diff --git a/renv/profiles/4.3/renv/settings.json b/renv/profiles/4.3/renv/settings.json new file mode 100644 index 00000000..2bbd9c3c --- /dev/null +++ b/renv/profiles/4.3/renv/settings.json @@ -0,0 +1,24 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [ + "admiral", + "admiraldev", + "admiral.test", + "admiralci" + ], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} From 8e09f46d9ef83e7a1f28dceb09cd60596db33377 Mon Sep 17 00:00:00 2001 From: galachad Date: Fri, 4 Aug 2023 16:12:06 +0000 Subject: [PATCH 11/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 2 +- renv.lock | 2 +- renv/profiles/4.1/renv.lock | 2 +- renv/profiles/4.2/renv.lock | 2 +- renv/profiles/4.2/renv/settings.json | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.Rprofile b/.Rprofile index 32e01deb..f8158967 100644 --- a/.Rprofile +++ b/.Rprofile @@ -45,4 +45,4 @@ if (Sys.getenv("GITHUB_ACTIONS") != "") { } Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE) Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE) -# source("renv/activate.R") +source("renv/activate.R") diff --git a/renv.lock b/renv.lock index f21b8102..93c400f4 100644 --- a/renv.lock +++ b/renv.lock @@ -4,7 +4,7 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://packagemanager.posit.co/cran/latest" }, { "Name": "RSPM", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index f21b8102..93c400f4 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -4,7 +4,7 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://packagemanager.posit.co/cran/latest" }, { "Name": "RSPM", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 8005c0f6..9fce578f 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -4,7 +4,7 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cloud.r-project.org" + "URL": "https://packagemanager.posit.co/cran/latest" }, { "Name": "RSPM", diff --git a/renv/profiles/4.2/renv/settings.json b/renv/profiles/4.2/renv/settings.json index 2bbd9c3c..3462f3b0 100644 --- a/renv/profiles/4.2/renv/settings.json +++ b/renv/profiles/4.2/renv/settings.json @@ -15,7 +15,7 @@ "ppm.enabled": null, "ppm.ignored.urls": [], "r.version": null, - "snapshot.type": "implicit", + "snapshot.type": "custom", "use.cache": true, "vcs.ignore.cellar": true, "vcs.ignore.library": true, From b8f5c766327684f38e49556ad0197e912e52c397 Mon Sep 17 00:00:00 2001 From: galachad Date: Fri, 4 Aug 2023 16:43:59 +0000 Subject: [PATCH 12/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rprofile b/.Rprofile index f8158967..51ad0fdc 100644 --- a/.Rprofile +++ b/.Rprofile @@ -19,7 +19,7 @@ )) ) ) - packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test"))] + packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", getwd()))] } options(renv.snapshot.filter = .get_dependencies) From f603b3b790b90a4ed00f40d9d668bb9c6070b0e8 Mon Sep 17 00:00:00 2001 From: galachad Date: Fri, 4 Aug 2023 17:19:45 +0000 Subject: [PATCH 13/22] renv / codespaces update from pharmaverse/admiralci --- renv.lock | 1597 ++++++++++++++++++++++++ renv/profiles/4.1/renv.lock | 1597 ++++++++++++++++++++++++ renv/profiles/4.2/renv.lock | 1680 +++++++++++++++++++++++++ renv/profiles/4.3/renv.lock | 1682 +++++++++++++++++++++++++- renv/profiles/4.3/renv/settings.json | 2 +- 5 files changed, 6556 insertions(+), 2 deletions(-) diff --git a/renv.lock b/renv.lock index 93c400f4..a2b111c3 100644 --- a/renv.lock +++ b/renv.lock @@ -13,6 +13,1055 @@ ] }, "Packages": { + "DT": { + "Package": "DT", + "Version": "0.21", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "crosstalk", + "htmltools", + "htmlwidgets", + "jquerylib", + "jsonlite", + "magrittr", + "promises" + ], + "Hash": "45fa28dbf288cd606e13ca35d3d72437" + }, + "R.cache": { + "Package": "R.cache", + "Version": "0.15.0", + 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mode 100644 renv/settings.json diff --git a/renv/settings.dcf b/renv/settings.dcf deleted file mode 100644 index fd205f80..00000000 --- a/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: admiral, admiraldev, admiral.test, admiralci -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 00000000..3462f3b0 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,24 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [ + "admiral", + "admiraldev", + "admiral.test", + "admiralci" + ], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "custom", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} From ed63cb5ce25ffed3fea3e3527e323460f19d9a56 Mon Sep 17 00:00:00 2001 From: galachad Date: Fri, 4 Aug 2023 18:55:21 +0000 Subject: [PATCH 15/22] renv / codespaces update from pharmaverse/admiralci --- renv.lock | 77 +++++++++++++++++++++++++++++++++++++ renv/profiles/4.1/renv.lock | 77 +++++++++++++++++++++++++++++++++++++ 2 files changed, 154 insertions(+) diff --git a/renv.lock b/renv.lock index a2b111c3..5801ed10 100644 --- a/renv.lock +++ b/renv.lock @@ -188,6 +188,18 @@ ], "Hash": "9b2191ede20fa29828139b9900922e51" }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "rematch", + "tibble" + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, "cli": { "Package": "cli", "Version": "3.4.1", @@ -219,6 +231,13 @@ ], "Hash": "019388fc48e48b3da0d3a76ff94608a8" }, + "collections": { + "Package": "collections", + "Version": "0.3.5", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "92537c684a3d2eaa6bd8f65c28ef97f0" + }, "commonmark": { "Package": "commonmark", "Version": "1.8.0", @@ -717,6 +736,30 @@ ], "Hash": "caea8b0f899a0b1738444b9bc47067e7" }, + "languageserver": { + "Package": "languageserver", + "Version": "0.3.12", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "callr", + "collections", + "fs", + "jsonlite", + "lintr", + "parallel", + "roxygen2", + "stringi", + "styler", + "tools", + "utils", + "xml2", + "xmlparsedata" + ], + "Hash": "f62ed8b09fd56cd70291bd077bc52c4b" + }, "later": { "Package": "later", "Version": "1.3.0", @@ -957,6 +1000,19 @@ ], "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6" }, + "progress": { + "Package": "progress", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R6", + "crayon", + "hms", + "prettyunits" + ], + "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + }, "promises": { "Package": "promises", "Version": "1.2.0.1", @@ -1038,6 +1094,27 @@ ], "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, + "readxl": { + "Package": "readxl", + "Version": "1.3.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Rcpp", + "cellranger", + "progress", + "tibble", + "utils" + ], + "Hash": "63537c483c2dbec8d9e3183b3735254a" + }, + "rematch": { + "Package": "rematch", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c66b930d20bb6d858cd18e1cebcfae5c" + }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index a2b111c3..5801ed10 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -188,6 +188,18 @@ ], "Hash": "9b2191ede20fa29828139b9900922e51" }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "rematch", + "tibble" + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, "cli": { "Package": "cli", "Version": "3.4.1", @@ -219,6 +231,13 @@ ], "Hash": "019388fc48e48b3da0d3a76ff94608a8" }, + "collections": { + "Package": "collections", + "Version": "0.3.5", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "92537c684a3d2eaa6bd8f65c28ef97f0" + }, "commonmark": { "Package": "commonmark", "Version": "1.8.0", @@ -717,6 +736,30 @@ ], "Hash": "caea8b0f899a0b1738444b9bc47067e7" }, + "languageserver": { + "Package": "languageserver", + "Version": "0.3.12", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "callr", + "collections", + "fs", + "jsonlite", + "lintr", + "parallel", + "roxygen2", + "stringi", + "styler", + "tools", + "utils", + "xml2", + "xmlparsedata" + ], + "Hash": "f62ed8b09fd56cd70291bd077bc52c4b" + }, "later": { "Package": "later", "Version": "1.3.0", @@ -957,6 +1000,19 @@ ], "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6" }, + "progress": { + "Package": "progress", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R6", + "crayon", + "hms", + "prettyunits" + ], + "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + }, "promises": { "Package": "promises", "Version": "1.2.0.1", @@ -1038,6 +1094,27 @@ ], "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, + "readxl": { + "Package": "readxl", + "Version": "1.3.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Rcpp", + "cellranger", + "progress", + "tibble", + "utils" + ], + "Hash": "63537c483c2dbec8d9e3183b3735254a" + }, + "rematch": { + "Package": "rematch", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c66b930d20bb6d858cd18e1cebcfae5c" + }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", From 35f03dff7c62ce23ecf5d4b44080c62790d72dd3 Mon Sep 17 00:00:00 2001 From: galachad Date: Fri, 4 Aug 2023 19:30:40 +0000 Subject: [PATCH 16/22] renv / codespaces update from pharmaverse/admiralci --- renv/profiles/4.2/renv.lock | 78 +++++++++++++++++++++++++++++++++++++ renv/profiles/4.3/renv.lock | 78 +++++++++++++++++++++++++++++++++++++ 2 files changed, 156 insertions(+) diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 7c5bc1b2..7661270b 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -192,6 +192,18 @@ ], "Hash": "9b2191ede20fa29828139b9900922e51" }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "rematch", + "tibble" + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, "cli": { "Package": "cli", "Version": "3.6.0", @@ -223,6 +235,13 @@ ], "Hash": "c089a619a7fae175d149d89164f8c7d8" }, + "collections": { + "Package": "collections", + "Version": "0.3.7", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "90a0eda114ab0bef170ddbf5ef0cd93f" + }, "commonmark": { "Package": "commonmark", "Version": "1.8.1", @@ -749,6 +768,30 @@ ], "Hash": "8329a9bcc82943c8069104d4be3ee22d" }, + "languageserver": { + "Package": "languageserver", + "Version": "0.3.15", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "callr", + "collections", + "fs", + "jsonlite", + "lintr", + "parallel", + "roxygen2", + "stringi", + "styler", + "tools", + "utils", + "xml2", + "xmlparsedata" + ], + "Hash": "fbea0dd12b4f5dedbe3654e4b9cbbddc" + }, "later": { "Package": "later", "Version": "1.3.0", @@ -1007,6 +1050,19 @@ ], "Hash": "e9d21e79848e02e524bea6f5bd53e7e4" }, + "progress": { + "Package": "progress", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R6", + "crayon", + "hms", + "prettyunits" + ], + "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + }, "promises": { "Package": "promises", "Version": "1.2.0.1", @@ -1091,6 +1147,28 @@ ], "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, + "readxl": { + "Package": "readxl", + "Version": "1.4.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "cellranger", + "cpp11", + "progress", + "tibble", + "utils" + ], + "Hash": "2e6020b1399d95f947ed867045e9ca17" + }, + "rematch": { + "Package": "rematch", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c66b930d20bb6d858cd18e1cebcfae5c" + }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", diff --git a/renv/profiles/4.3/renv.lock b/renv/profiles/4.3/renv.lock index c9604218..1ce40dba 100644 --- a/renv/profiles/4.3/renv.lock +++ b/renv/profiles/4.3/renv.lock @@ -192,6 +192,18 @@ ], "Hash": "9b2191ede20fa29828139b9900922e51" }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "rematch", + "tibble" + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, "cli": { "Package": "cli", "Version": "3.6.1", @@ -223,6 +235,13 @@ ], "Hash": "c089a619a7fae175d149d89164f8c7d8" }, + "collections": { + "Package": "collections", + "Version": "0.3.7", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "90a0eda114ab0bef170ddbf5ef0cd93f" + }, "commonmark": { "Package": "commonmark", "Version": "1.9.0", @@ -748,6 +767,30 @@ ], "Hash": "8329a9bcc82943c8069104d4be3ee22d" }, + "languageserver": { + "Package": "languageserver", + "Version": "0.3.15", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "callr", + "collections", + "fs", + "jsonlite", + "lintr", + "parallel", + "roxygen2", + "stringi", + "styler", + "tools", + "utils", + "xml2", + "xmlparsedata" + ], + "Hash": "fbea0dd12b4f5dedbe3654e4b9cbbddc" + }, "later": { "Package": "later", "Version": "1.3.0", @@ -1006,6 +1049,19 @@ ], "Hash": "e9d21e79848e02e524bea6f5bd53e7e4" }, + "progress": { + "Package": "progress", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R6", + "crayon", + "hms", + "prettyunits" + ], + "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061" + }, "promises": { "Package": "promises", "Version": "1.2.0.1", @@ -1090,6 +1146,28 @@ ], "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, + "readxl": { + "Package": "readxl", + "Version": "1.4.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "cellranger", + "cpp11", + "progress", + "tibble", + "utils" + ], + "Hash": "2e6020b1399d95f947ed867045e9ca17" + }, + "rematch": { + "Package": "rematch", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c66b930d20bb6d858cd18e1cebcfae5c" + }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", From dbb46a86ee9cf54f9678daeccf7c679d2cd5b851 Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 10 Aug 2023 16:21:14 +0000 Subject: [PATCH 17/22] renv / codespaces update from pharmaverse/admiralci --- .devcontainer/4.1/devcontainer.json | 3 ++- .devcontainer/4.2/devcontainer.json | 3 ++- .devcontainer/devcontainer.json | 3 ++- .devcontainer/postCreateCommand.sh | 2 +- 4 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json index f287993d..1d05f7fd 100644 --- a/.devcontainer/4.1/devcontainer.json +++ b/.devcontainer/4.1/devcontainer.json @@ -6,7 +6,8 @@ "containerEnv": { "ROOT": "true", "PASSWORD": "rstudio", - "DISABLE_AUTH": "true" + "DISABLE_AUTH": "true", + "RENV_AUTOLOADER_ENABLED": "false" }, "features": { "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { diff --git a/.devcontainer/4.2/devcontainer.json b/.devcontainer/4.2/devcontainer.json index 9878fa4b..f30486e0 100644 --- a/.devcontainer/4.2/devcontainer.json +++ b/.devcontainer/4.2/devcontainer.json @@ -6,7 +6,8 @@ "containerEnv": { "ROOT": "true", "PASSWORD": "rstudio", - "DISABLE_AUTH": "true" + "DISABLE_AUTH": "true", + "RENV_AUTOLOADER_ENABLED": "false" }, "features": { "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index af6c75b9..4f49db8f 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -6,7 +6,8 @@ "containerEnv": { "ROOT": "true", "PASSWORD": "rstudio", - "DISABLE_AUTH": "true" + "DISABLE_AUTH": "true", + "RENV_AUTOLOADER_ENABLED": "false" }, "features": { "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh index 9c6aec29..9b9db23a 100644 --- a/.devcontainer/postCreateCommand.sh +++ b/.devcontainer/postCreateCommand.sh @@ -1,5 +1,5 @@ #!/bin/bash -R -q -e 'renv::activate(profile = paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")); renv::restore(); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);' +R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$major, substr(R.version$minor, 1, 1), sep = "."), "renv.lock")); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);' jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json From 2f7c971be8122704618f0776b75cb49795b61295 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adam=20Fory=C5=9B?= Date: Mon, 14 Aug 2023 15:07:07 +0200 Subject: [PATCH 18/22] Update .Rbuildignore --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 3d27fcb3..c29a8462 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -32,3 +32,4 @@ ^admiralvaccine\.Rcheck$ ^admiralvaccine.*\.tar\.gz$ ^admiralvaccine.*\.tgz$ +^\.devcontainer$ From 561490692aec96637bca1e6f4549570ee6db1628 Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 15 Aug 2023 16:31:59 +0000 Subject: [PATCH 19/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rprofile b/.Rprofile index 51ad0fdc..d059c2fc 100644 --- a/.Rprofile +++ b/.Rprofile @@ -19,7 +19,7 @@ )) ) ) - packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", getwd()))] + packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))] } options(renv.snapshot.filter = .get_dependencies) From b4c172b78cfc7e64714d1b6484487fb1537d00a1 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 16 Aug 2023 14:29:55 +0000 Subject: [PATCH 20/22] renv / codespaces update from pharmaverse/admiralci --- renv/profiles/4.1/renv/settings.json | 3 ++- renv/profiles/4.2/renv/settings.json | 3 ++- renv/profiles/4.3/renv/settings.json | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/renv/profiles/4.1/renv/settings.json b/renv/profiles/4.1/renv/settings.json index 3462f3b0..4922677e 100644 --- a/renv/profiles/4.1/renv/settings.json +++ b/renv/profiles/4.1/renv/settings.json @@ -5,7 +5,8 @@ "admiral", "admiraldev", "admiral.test", - "admiralci" + "admiralci", + "pharmaversesdtm" ], "package.dependency.fields": [ "Imports", diff --git a/renv/profiles/4.2/renv/settings.json b/renv/profiles/4.2/renv/settings.json index 3462f3b0..4922677e 100644 --- a/renv/profiles/4.2/renv/settings.json +++ b/renv/profiles/4.2/renv/settings.json @@ -5,7 +5,8 @@ "admiral", "admiraldev", "admiral.test", - "admiralci" + "admiralci", + "pharmaversesdtm" ], "package.dependency.fields": [ "Imports", diff --git a/renv/profiles/4.3/renv/settings.json b/renv/profiles/4.3/renv/settings.json index 3462f3b0..4922677e 100644 --- a/renv/profiles/4.3/renv/settings.json +++ b/renv/profiles/4.3/renv/settings.json @@ -5,7 +5,8 @@ "admiral", "admiraldev", "admiral.test", - "admiralci" + "admiralci", + "pharmaversesdtm" ], "package.dependency.fields": [ "Imports", From 460130b5205c03628a1de07584a288a6fab0ff7e Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 21 Sep 2023 10:00:32 +0000 Subject: [PATCH 21/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 2 +- renv/profiles/4.1/renv/settings.json | 1 - renv/profiles/4.2/renv/settings.json | 1 - renv/profiles/4.3/renv/settings.json | 1 - renv/settings.json | 4 ++-- 5 files changed, 3 insertions(+), 6 deletions(-) diff --git a/.Rprofile b/.Rprofile index d059c2fc..51f55c19 100644 --- a/.Rprofile +++ b/.Rprofile @@ -19,7 +19,7 @@ )) ) ) - packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))] + packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "pharmaversesdtm", getwd()))] } options(renv.snapshot.filter = .get_dependencies) diff --git a/renv/profiles/4.1/renv/settings.json b/renv/profiles/4.1/renv/settings.json index 4922677e..0c8943c5 100644 --- a/renv/profiles/4.1/renv/settings.json +++ b/renv/profiles/4.1/renv/settings.json @@ -4,7 +4,6 @@ "ignored.packages": [ "admiral", "admiraldev", - "admiral.test", "admiralci", "pharmaversesdtm" ], diff --git a/renv/profiles/4.2/renv/settings.json b/renv/profiles/4.2/renv/settings.json index 4922677e..0c8943c5 100644 --- a/renv/profiles/4.2/renv/settings.json +++ b/renv/profiles/4.2/renv/settings.json @@ -4,7 +4,6 @@ "ignored.packages": [ "admiral", "admiraldev", - "admiral.test", "admiralci", "pharmaversesdtm" ], diff --git a/renv/profiles/4.3/renv/settings.json b/renv/profiles/4.3/renv/settings.json index 4922677e..0c8943c5 100644 --- a/renv/profiles/4.3/renv/settings.json +++ b/renv/profiles/4.3/renv/settings.json @@ -4,7 +4,6 @@ "ignored.packages": [ "admiral", "admiraldev", - "admiral.test", "admiralci", "pharmaversesdtm" ], diff --git a/renv/settings.json b/renv/settings.json index 3462f3b0..0c8943c5 100644 --- a/renv/settings.json +++ b/renv/settings.json @@ -4,8 +4,8 @@ "ignored.packages": [ "admiral", "admiraldev", - "admiral.test", - "admiralci" + "admiralci", + "pharmaversesdtm" ], "package.dependency.fields": [ "Imports", From f2119f9621aabce07834bc92ecbe245a3acfbda5 Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 21 Sep 2023 21:08:22 +0000 Subject: [PATCH 22/22] renv / codespaces update from pharmaverse/admiralci --- .Rprofile | 3 +-- .devcontainer/4.1/devcontainer.json | 2 +- .devcontainer/4.2/devcontainer.json | 2 +- .devcontainer/devcontainer.json | 2 +- .devcontainer/postCreateCommand.sh | 6 ++++++ .devcontainer/rstudio.sh | 5 +++++ 6 files changed, 15 insertions(+), 5 deletions(-) create mode 100644 .devcontainer/rstudio.sh diff --git a/.Rprofile b/.Rprofile index 51f55c19..6d46e675 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,8 +1,7 @@ # Set renv profile base on R version. .get_dependencies <- function(project_dir) { - admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE) - adm_dev_suggests <- if(length(admdev_loc) != 0) { + adm_dev_suggests <- if (length(admdev_loc) != 0) { renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests")) } else { data.frame(Packages = character(0)) diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json index 1d05f7fd..ab6ddfee 100644 --- a/.devcontainer/4.1/devcontainer.json +++ b/.devcontainer/4.1/devcontainer.json @@ -31,7 +31,7 @@ "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", - "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", + "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", "customizations": { "vscode": { diff --git a/.devcontainer/4.2/devcontainer.json b/.devcontainer/4.2/devcontainer.json index f30486e0..decbcca5 100644 --- a/.devcontainer/4.2/devcontainer.json +++ b/.devcontainer/4.2/devcontainer.json @@ -31,7 +31,7 @@ "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", - "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", + "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", "customizations": { "vscode": { diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4f49db8f..3f47589f 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -31,7 +31,7 @@ "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", - "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"", + "postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", "customizations": { "vscode": { diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh index 9b9db23a..8dfe4e23 100644 --- a/.devcontainer/postCreateCommand.sh +++ b/.devcontainer/postCreateCommand.sh @@ -1,5 +1,11 @@ #!/bin/bash +# move script rstudio into /usr/bin +sudo cp "$(pwd)/.devcontainer/rstudio.sh" /usr/bin/rstudio +sudo chmod +x /usr/bin/rstudio + +# Restore renv and install staged dependencies R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$major, substr(R.version$minor, 1, 1), sep = "."), "renv.lock")); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);' +# Define rstudio default working directory jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json diff --git a/.devcontainer/rstudio.sh b/.devcontainer/rstudio.sh new file mode 100644 index 00000000..053a247b --- /dev/null +++ b/.devcontainer/rstudio.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +$BROWSER "https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}" + +exit 1