From 3c5a8f3cffa69c46abb23ab8f45e1a53e669a77b Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Tue, 22 Aug 2023 15:13:45 +0200 Subject: [PATCH 1/9] * Stopped schedule workflow in GitHub actions (#18). --- .github/workflows/workflow.yml | 36 +++++++++++++++++----------------- DESCRIPTION | 2 +- NEWS.md | 4 ++++ 3 files changed, 23 insertions(+), 19 deletions(-) diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index 59c68de..7f1bdc8 100644 --- a/.github/workflows/workflow.yml +++ b/.github/workflows/workflow.yml @@ -5,9 +5,9 @@ on: push: pull_request: - schedule: - # every Tuesday (2) at 15:00 and 18:00 UTC - - cron: "0 15,18 * * 2" + # schedule: + # # every Tuesday (2) at 15:00 and 18:00 UTC + # - cron: "0 15,18 * * 2" # Name of the workflow => usethis::use_github_actions_badge("CI-CD-BUILD-DATA") name: CI-CD-BUILD-DATA @@ -49,12 +49,12 @@ jobs: - name: Activate renv and restore packages with cache uses: r-lib/actions/setup-renv@v2 - - name: Fetch and rebuild latest BAG data - if: github.event_name == 'schedule' - run: | - pkgload::load_all(export_all = TRUE, helpers = FALSE, attach_testthat = FALSE) - build_data() - shell: Rscript {0} + # - name: Fetch and rebuild latest BAG data + # if: github.event_name == 'schedule' + # run: | + # pkgload::load_all(export_all = TRUE, helpers = FALSE, attach_testthat = FALSE) + # build_data() + # shell: Rscript {0} - name: Install R CMD check run: install.packages("rcmdcheck") @@ -63,15 +63,15 @@ jobs: - name: Check package uses: r-lib/actions/check-r-package@v2 - - name: Commit and push updated BAG data - if: github.event_name == 'schedule' - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - git add inst/bag_data/\* - git commit -m "Update BAG data" || echo "No changes to commit" - git pull --ff-only - git push origin + # - name: Commit and push updated BAG data + # if: github.event_name == 'schedule' + # run: | + # git config --local user.email "actions@github.com" + # git config --local user.name "GitHub Actions" + # git add inst/bag_data/\* + # git commit -m "Update BAG data" || echo "No changes to commit" + # git pull --ff-only + # git push origin - name: Deploy to shinyapps.io # Continuous deployment only for pushes to the main / master branch diff --git a/DESCRIPTION b/DESCRIPTION index a9f3614..6f52818 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: covid19vaccinationch Title: Vaccination Breakthroughs in CH -Version: 1.1.1 +Version: 1.1.2 Authors@R: person("Guido", "Maggio", , "guido-maggio@mirai-solutions.com", role = c("cre", "aut")) Description: A live article on vaccination breakthroughs in Switzerland, diff --git a/NEWS.md b/NEWS.md index a0b3bc4..ae8cccb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# covid19vaccinationch 1.1.2 + +* Stopped schedule workflow in GitHub actions (#18). + # covid19vaccinationch 1.1.1 * Maintenance of `renv` and GitHub Actions workflow (#16). From 22934a90ac82d3f4cd63317c59f99f2f7397bd1a Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Tue, 22 Aug 2023 16:24:52 +0200 Subject: [PATCH 2/9] Updated renv and rsconnect --- renv.lock | 20 +-- renv/activate.R | 453 +++++++++++++++++++++++++++++++++++------------- 2 files changed, 334 insertions(+), 139 deletions(-) diff --git a/renv.lock b/renv.lock index 91826ee..5f49845 100644 --- a/renv.lock +++ b/renv.lock @@ -776,9 +776,8 @@ }, "renv": { "Package": "renv", - "Version": "0.16.0", - "Source": "Repository", - "Requirements": [] + "Version": "1.0.2", + "Source": "Repository" }, "rlang": { "Package": "rlang", @@ -817,19 +816,8 @@ }, "rsconnect": { "Package": "rsconnect", - "Version": "0.8.27", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "114103fbb50af041e93921ee67db8fa0", - "Requirements": [ - "curl", - "digest", - "jsonlite", - "openssl", - "packrat", - "rstudioapi", - "yaml" - ] + "Version": "1.0.2", + "Source": "Repository" }, "rstudioapi": { "Package": "rstudioapi", diff --git a/renv/activate.R b/renv/activate.R index 019b5a6..2969c73 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,27 @@ local({ # the requested version of renv - version <- "0.16.0" + version <- "1.0.2" + attr(version, "sha") <- NULL # the project directory project <- getwd() + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + # figure out whether the autoloader is enabled enabled <- local({ @@ -60,21 +76,75 @@ 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() { @@ -83,28 +153,32 @@ 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()) - return(getOption("renv.tests.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") @@ -143,33 +217,34 @@ 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") } @@ -233,8 +308,6 @@ 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" @@ -251,13 +324,10 @@ local({ condition = identity ) - if (inherits(status, "condition")) { - message("FAILED") + if (inherits(status, "condition")) return(FALSE) - } # report success and return - message("OK (downloaded ", type, ")") destfile } @@ -314,8 +384,6 @@ 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( @@ -323,14 +391,11 @@ local({ condition = identity ) - if (identical(status, 0L)) { - message("OK") + if (identical(status, 0L)) return(destfile) - } } - message("FAILED") return(FALSE) } @@ -344,8 +409,7 @@ 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) } @@ -354,7 +418,7 @@ 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) @@ -363,10 +427,7 @@ local({ } - fmt <- "* Bootstrapping with tarball at path '%s'." - msg <- sprintf(fmt, tarball) - message(msg) - + catf("- Using local tarball '%s'.", tarball) tarball } @@ -393,8 +454,6 @@ 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) @@ -404,26 +463,105 @@ 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", @@ -431,19 +569,7 @@ 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) } @@ -653,34 +779,62 @@ 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 + # + # 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") - # 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-") @@ -700,6 +854,12 @@ 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 = warnify) + # load the project renv::load(project) @@ -839,14 +999,79 @@ local({ } + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + + renv_bootstrap_in_rstudio <- function() { + commandArgs()[[1]] == "RStudio" + } + + # Used to work around buglet in RStudio if hook uses readline + renv_bootstrap_flush_console <- function() { + tryCatch({ + tools <- as.environment("tools:rstudio") + tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE) + }, error = function(cnd) {}) + } 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) } @@ -960,35 +1185,17 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - # attempt to load - 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) - - # try again to load - if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - message("* Successfully installed and loaded renv ", version, ".") - return(renv::load()) + if (renv_bootstrap_in_rstudio()) { + # RStudio only updates console once .Rprofile is finished, so + # instead run code on sessionInit + setHook("rstudio.sessionInit", function(...) { + renv_bootstrap_exec(project, libpath, version) + renv_bootstrap_flush_console() + }) + } else { + renv_bootstrap_exec(project, libpath, version) } - # 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 53d1566a678d7b98ff7c19584965b4858561b704 Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Tue, 22 Aug 2023 16:52:07 +0200 Subject: [PATCH 3/9] forceUpdate = TRUE --- deploy/deploy-shinyapps.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/deploy/deploy-shinyapps.R b/deploy/deploy-shinyapps.R index 3e25187..130c306 100644 --- a/deploy/deploy-shinyapps.R +++ b/deploy/deploy-shinyapps.R @@ -11,7 +11,8 @@ file.copy("inst/report/index.Rmd", "index.Rmd", overwrite = TRUE) rsconnect::deployApp( account = "miraisolutions", - appName = "covid19-vaccination-ch" + appName = "covid19-vaccination-ch", + forceUpdate = TRUE ) unlink("index.Rmd") From e4ca5bb888147a1d5b7facf455aedf50fe8c941c Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Tue, 22 Aug 2023 17:40:19 +0200 Subject: [PATCH 4/9] reinitialized renv --- renv.lock | 701 +++++++++++++++++++++++---------------------- renv/.gitignore | 2 +- renv/settings.dcf | 10 - renv/settings.json | 19 ++ 4 files changed, 384 insertions(+), 348 deletions(-) delete mode 100644 renv/settings.dcf create mode 100644 renv/settings.json diff --git a/renv.lock b/renv.lock index 5f49845..e664d6e 100644 --- a/renv.lock +++ b/renv.lock @@ -4,7 +4,7 @@ "Repositories": [ { "Name": "CRAN", - "URL": "https://cran.rstudio.com" + "URL": "https://packagemanager.posit.co/cran/latest" } ] }, @@ -14,7 +14,6 @@ "Version": "0.25", "Source": "Repository", "Repository": "CRAN", - "Hash": "d35337fd4278be35c50d7eeeec439f68", "Requirements": [ "crosstalk", "htmltools", @@ -23,622 +22,696 @@ "jsonlite", "magrittr", "promises" - ] + ], + "Hash": "d35337fd4278be35c50d7eeeec439f68" }, "MASS": { "Package": "MASS", "Version": "7.3-58.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "762e1804143a332333c054759f89a706", - "Requirements": [] + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "stats", + "utils" + ], + "Hash": "762e1804143a332333c054759f89a706" }, "Matrix": { "Package": "Matrix", "Version": "1.5-1", "Source": "Repository", "Repository": "CRAN", - "Hash": "539dc0c0c05636812f1080f473d2c177", "Requirements": [ - "lattice" - ] + "R", + "graphics", + "grid", + "lattice", + "methods", + "stats", + "utils" + ], + "Hash": "539dc0c0c05636812f1080f473d2c177" }, "R6": { "Package": "R6", "Version": "2.5.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "470851b6d5d0ac559e9d01bb352b4021", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "470851b6d5d0ac559e9d01bb352b4021" }, "RColorBrewer": { "Package": "RColorBrewer", "Version": "1.1-3", "Source": "Repository", "Repository": "CRAN", - 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] + ], + "Hash": "97def703420c8ab10d8f0e6c72101e02" }, "rappdirs": { "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "5e3c5dc0b071b21fa128676560dbe94d", - "Requirements": [] - }, - "rematch2": { - "Package": "rematch2", - "Version": "2.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ - "tibble" - ] + "R" + ], + "Hash": "5e3c5dc0b071b21fa128676560dbe94d" }, "renv": { "Package": "renv", "Version": "1.0.2", - "Source": "Repository" + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "4b22ac016fe54028b88d0c68badbd061" }, "rlang": { "Package": "rlang", "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", - "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", - "Requirements": [] + "Requirements": [ + "R", + "utils" + ], + "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" }, "rmarkdown": { "Package": "rmarkdown", "Version": "2.16", "Source": "Repository", "Repository": "CRAN", - "Hash": "0f3eaa1547e2c6880d4de1c043ac6826", "Requirements": [ + "R", "bslib", "evaluate", "htmltools", "jquerylib", "jsonlite", "knitr", + "methods", "stringr", "tinytex", + "tools", + "utils", "xfun", "yaml" - ] + ], + "Hash": "0f3eaa1547e2c6880d4de1c043ac6826" }, "rprojroot": { "Package": "rprojroot", "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "1de7ab598047a87bba48434ba35d497d", - "Requirements": [] - }, - "rsconnect": { - "Package": "rsconnect", - "Version": "1.0.2", - "Source": "Repository" + "Requirements": [ + "R" + ], + "Hash": "1de7ab598047a87bba48434ba35d497d" }, "rstudioapi": { "Package": "rstudioapi", "Version": "0.14", "Source": "Repository", "Repository": "CRAN", - "Hash": "690bd2acc42a9166ce34845884459320", - "Requirements": [] + "Hash": "690bd2acc42a9166ce34845884459320" }, "sass": { "Package": "sass", "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "1b191143d7d3444d504277843f3a95fe", "Requirements": [ "R6", "fs", "htmltools", "rappdirs", "rlang" - ] + ], + "Hash": "1b191143d7d3444d504277843f3a95fe" }, "scales": { "Package": "scales", "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "906cb23d2f1c5680b8ce439b44c6fa63", "Requirements": [ + "R", "R6", "RColorBrewer", "farver", @@ -856,15 +913,16 @@ "munsell", "rlang", "viridisLite" - ] + ], + "Hash": "906cb23d2f1c5680b8ce439b44c6fa63" }, "shiny": { "Package": "shiny", "Version": "1.7.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "4f7970a3edb0a153ac6b376785a1944a", "Requirements": [ + "R", "R6", "bslib", "cachem", @@ -874,119 +932,93 @@ "fastmap", "fontawesome", "glue", + "grDevices", "htmltools", "httpuv", "jsonlite", "later", "lifecycle", + "methods", "mime", "promises", "rlang", "sourcetools", + "tools", + "utils", "withr", "xtable" - ] + ], + "Hash": "4f7970a3edb0a153ac6b376785a1944a" }, "sourcetools": { "Package": "sourcetools", "Version": "0.1.7", "Source": "Repository", "Repository": "CRAN", - "Hash": "947e4e02a79effa5d512473e10f41797", - 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}, - "testthat": { - "Package": "testthat", - "Version": "3.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f76c2a02d0fdc24aa7a47ea34261a6e3", - "Requirements": [ - "R6", - "brio", - "callr", - "cli", - "crayon", - "desc", - "digest", - "ellipsis", - "evaluate", - "jsonlite", - "lifecycle", - "magrittr", - "pkgload", - "praise", - "processx", - "ps", - "rlang", - "waldo", - "withr" - ] + "Hash": "b227d13e29222b4574486cfcbde077fa" }, "tibble": { "Package": "tibble", "Version": "3.1.8", "Source": "Repository", "Repository": "CRAN", - "Hash": "56b6934ef0f8c68225949a8672fe1a8f", "Requirements": [ + "R", "fansi", "lifecycle", "magrittr", + "methods", "pillar", "pkgconfig", "rlang", + "utils", "vctrs" - ] + ], + "Hash": "56b6934ef0f8c68225949a8672fe1a8f" }, "tidyr": { "Package": "tidyr", "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "cdb403db0de33ccd1b6f53b83736efa8", "Requirements": [ + "R", "cpp11", "dplyr", "ellipsis", @@ -997,116 +1029,111 @@ "rlang", "tibble", "tidyselect", + "utils", "vctrs" - ] + ], + "Hash": "cdb403db0de33ccd1b6f53b83736efa8" }, "tidyselect": { "Package": "tidyselect", "Version": "1.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "17f6da8cfd7002760a859915ce7eef8f", "Requirements": [ + "R", "ellipsis", "glue", "purrr", "rlang", "vctrs" - ] + ], + "Hash": "17f6da8cfd7002760a859915ce7eef8f" }, "tinytex": { "Package": "tinytex", "Version": "0.42", "Source": "Repository", "Repository": "CRAN", - "Hash": "7629c6c1540835d5248e6e7df265fa74", "Requirements": [ "xfun" - ] + ], + "Hash": "7629c6c1540835d5248e6e7df265fa74" }, "utf8": { "Package": "utf8", "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "c9c462b759a5cc844ae25b5942654d13", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "c9c462b759a5cc844ae25b5942654d13" }, "vctrs": { "Package": "vctrs", "Version": "0.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "8b54f22e2a58c4f275479c92ce041a57", "Requirements": [ + "R", "cli", "glue", "rlang" - ] + ], + "Hash": "8b54f22e2a58c4f275479c92ce041a57" }, "viridisLite": { "Package": "viridisLite", "Version": "0.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "62f4b5da3e08d8e5bcba6cac15603f70", - "Requirements": [] - }, - "waldo": { - "Package": "waldo", - "Version": "0.4.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "035fba89d0c86e2113120f93301b98ad", "Requirements": [ - "cli", - "diffobj", - "fansi", - "glue", - "rematch2", - "rlang", - "tibble" - ] + "R" + ], + "Hash": "62f4b5da3e08d8e5bcba6cac15603f70" }, "withr": { "Package": "withr", "Version": "2.5.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "c0e49a9760983e81e55cdd9be92e7182", - "Requirements": [] + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats" + ], + "Hash": "c0e49a9760983e81e55cdd9be92e7182" }, "xfun": { "Package": "xfun", "Version": "0.33", "Source": "Repository", "Repository": "CRAN", - "Hash": "1a666f915cd65072f4ccf5b2888d5d39", - "Requirements": [] - }, - "xml2": { - "Package": "xml2", - "Version": "1.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "40682ed6a969ea5abfd351eb67833adc", - "Requirements": [] + "Requirements": [ + "stats", + "tools" + ], + "Hash": "1a666f915cd65072f4ccf5b2888d5d39" }, "xtable": { "Package": "xtable", "Version": "1.8-4", "Source": "Repository", "Repository": "CRAN", - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", - "Requirements": [] + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" }, "yaml": { "Package": "yaml", "Version": "2.3.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "458bb38374d73bf83b1bb85e353da200", - "Requirements": [] + "Hash": "458bb38374d73bf83b1bb85e353da200" } } } diff --git a/renv/.gitignore b/renv/.gitignore index 22a0d01..0ec0cbb 100644 --- a/renv/.gitignore +++ b/renv/.gitignore @@ -1,7 +1,7 @@ -sandbox/ library/ local/ cellar/ lock/ python/ +sandbox/ staging/ diff --git a/renv/settings.dcf b/renv/settings.dcf deleted file mode 100644 index 2579a2b..0000000 --- a/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: explicit -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 0000000..74c1d4b --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "explicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} From 926e09e3c48e52ea12959f6bddcf32aa7819535f Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Tue, 22 Aug 2023 18:06:35 +0200 Subject: [PATCH 5/9] renv implicit --- renv.lock | 214 ++++++++++++++++++++++++++++++++++++++++++--- renv/settings.json | 2 +- 2 files changed, 205 insertions(+), 11 deletions(-) diff --git a/renv.lock b/renv.lock index e664d6e..de1e82b 100644 --- a/renv.lock +++ b/renv.lock @@ -117,6 +117,13 @@ ], "Hash": "543776ae6848fde2f48ff3816d0628bc" }, + "brio": { + "Package": "brio", + "Version": "1.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "976cf154dfb043c012d87cddd8bca363" + }, "bslib": { "Package": "bslib", "Version": "0.4.0", @@ -146,6 +153,19 @@ ], "Hash": "648c5b3d71e6a37e3043617489a0a0e9" }, + "callr": { + "Package": "callr", + "Version": "3.7.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "processx", + "utils" + ], + "Hash": "358689cac9fe93b1bb3a19088d2dbed8" + }, "checkmate": { "Package": "checkmate", "Version": "2.1.0", @@ -160,14 +180,14 @@ }, "cli": { "Package": "cli", - "Version": "3.4.1", + "Version": "3.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "0d297d01734d2bcea40197bd4971a764" + "Hash": "3177a5a16c243adc199ba33117bd9657" }, "colorspace": { "Package": "colorspace", @@ -257,16 +277,31 @@ ], "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21" }, + "diffobj": { + "Package": "diffobj", + "Version": "0.3.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "crayon", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8" + }, "digest": { "Package": "digest", - "Version": "0.6.29", + "Version": "0.6.31", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "cf6b206a045a684728c3267ef7596190" + "Hash": "8b708f296afd9ae69f450f9640be8990" }, "dplyr": { "Package": "dplyr", @@ -504,6 +539,18 @@ ], "Hash": "57557fac46471f0dbbf44705cc6a5c8c" }, + "hunspell": { + "Package": "hunspell", + "Version": "3.0.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "Rcpp", + "digest" + ], + "Hash": "656219b6f3f605499d7cdbe208656639" + }, "isoband": { "Package": "isoband", "Version": "0.2.5", @@ -527,13 +574,13 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.0", + "Version": "1.8.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "d07e729b27b372429d42d24d503613a0" + "Hash": "266a20443ca13c65688b2116d5220f76" }, "knitr": { "Package": "knitr", @@ -707,6 +754,18 @@ ], "Hash": "b9621e75c0652041002a19609fb23c5a" }, + "packrat": { + "Package": "packrat", + "Version": "0.8.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "tools", + "utils" + ], + "Hash": "d84055adcb6bb1f4f0ce8c5f235bc328" + }, "pillar": { "Package": "pillar", "Version": "1.8.1", @@ -786,6 +845,26 @@ ], "Hash": "fbb11e44d057996ca5fe40d959cacfb0" }, + "praise": { + "Package": "praise", + "Version": "1.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "a555924add98c99d2f411e37e7d25e9f" + }, + "processx": { + "Package": "processx", + "Version": "3.7.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "ps", + "utils" + ], + "Hash": "f91df0f5f31ffdf88bc0b624f5ebab0f" + }, "promises": { "Package": "promises", "Version": "1.2.0.1", @@ -801,6 +880,17 @@ ], "Hash": "4ab2c43adb4d4699cf3690acd378d75d" }, + "ps": { + "Package": "ps", + "Version": "1.7.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "utils" + ], + "Hash": "8b93531308c01ad0e56d9eadcc0c4fcd" + }, "purrr": { "Package": "purrr", "Version": "0.3.4", @@ -823,6 +913,16 @@ ], "Hash": "5e3c5dc0b071b21fa128676560dbe94d" }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "tibble" + ], + "Hash": "76c9e04c712a05848ae7a23d2f170a40" + }, "renv": { "Package": "renv", "Version": "1.0.2", @@ -835,14 +935,14 @@ }, "rlang": { "Package": "rlang", - "Version": "1.0.6", + "Version": "1.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" + "Hash": "a85c767b55f0bf9b7ad16c6d7baee5bb" }, "rmarkdown": { "Package": "rmarkdown", @@ -877,6 +977,28 @@ ], "Hash": "1de7ab598047a87bba48434ba35d497d" }, + "rsconnect": { + "Package": "rsconnect", + "Version": "1.0.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "curl", + "digest", + "jsonlite", + "lifecycle", + "openssl", + "packrat", + "renv", + "rlang", + "rstudioapi", + "tools", + "yaml" + ], + "Hash": "1f82a3e9e7e52f095b0f57869d957246" + }, "rstudioapi": { "Package": "rstudioapi", "Version": "0.14", @@ -960,6 +1082,19 @@ ], "Hash": "947e4e02a79effa5d512473e10f41797" }, + "spelling": { + "Package": "spelling", + "Version": "2.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "commonmark", + "hunspell", + "knitr", + "xml2" + ], + "Hash": "b8c899a5c83f0d897286550481c91798" + }, "stringi": { "Package": "stringi", "Version": "1.7.8", @@ -993,6 +1128,37 @@ "Repository": "CRAN", "Hash": "b227d13e29222b4574486cfcbde077fa" }, + "testthat": { + "Package": "testthat", + "Version": "3.1.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "brio", + "callr", + "cli", + "crayon", + "desc", + "digest", + "ellipsis", + "evaluate", + "jsonlite", + "lifecycle", + "magrittr", + "methods", + "pkgload", + "praise", + "processx", + "ps", + "rlang", + "utils", + "waldo", + "withr" + ], + "Hash": "f76c2a02d0fdc24aa7a47ea34261a6e3" + }, "tibble": { "Package": "tibble", "Version": "3.1.8", @@ -1092,6 +1258,23 @@ ], "Hash": "62f4b5da3e08d8e5bcba6cac15603f70" }, + "waldo": { + "Package": "waldo", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "cli", + "diffobj", + "fansi", + "glue", + "methods", + "rematch2", + "rlang", + "tibble" + ], + "Hash": "035fba89d0c86e2113120f93301b98ad" + }, "withr": { "Package": "withr", "Version": "2.5.0", @@ -1116,6 +1299,17 @@ ], "Hash": "1a666f915cd65072f4ccf5b2888d5d39" }, + "xml2": { + "Package": "xml2", + "Version": "1.3.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods" + ], + "Hash": "40682ed6a969ea5abfd351eb67833adc" + }, "xtable": { "Package": "xtable", "Version": "1.8-4", @@ -1130,10 +1324,10 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.5", + "Version": "2.3.7", "Source": "Repository", "Repository": "CRAN", - "Hash": "458bb38374d73bf83b1bb85e353da200" + "Hash": "0d0056cc5383fbc240ccd0cb584bf436" } } } diff --git a/renv/settings.json b/renv/settings.json index 74c1d4b..ffdbb32 100644 --- a/renv/settings.json +++ b/renv/settings.json @@ -10,7 +10,7 @@ "ppm.enabled": null, "ppm.ignored.urls": [], "r.version": null, - "snapshot.type": "explicit", + "snapshot.type": "implicit", "use.cache": true, "vcs.ignore.cellar": true, "vcs.ignore.library": true, From d6490af244f0c2b3c7f06475de900d61986a90e9 Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Wed, 23 Aug 2023 15:17:05 +0200 Subject: [PATCH 6/9] test deployment --- .github/workflows/workflow.yml | 2 +- tests/testthat/test-run_report.R | 44 ++++++++++++++++---------------- 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index 7f1bdc8..2fc588a 100644 --- a/.github/workflows/workflow.yml +++ b/.github/workflows/workflow.yml @@ -75,7 +75,7 @@ jobs: - name: Deploy to shinyapps.io # Continuous deployment only for pushes to the main / master branch - if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' + # if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' env: SHINYAPPS_ACCOUNT: ${{ secrets.SHINYAPPS_ACCOUNT }} SHINYAPPS_TOKEN: ${{ secrets.SHINYAPPS_TOKEN }} diff --git a/tests/testthat/test-run_report.R b/tests/testthat/test-run_report.R index 3ebdcd4..21d7bab 100644 --- a/tests/testthat/test-run_report.R +++ b/tests/testthat/test-run_report.R @@ -1,22 +1,22 @@ -test_that("Running the Rmd report works", { - # adapted from golem::expect_running() - r_ <- if (tolower(.Platform$OS.type) == "windows") { - normalizePath(file.path(Sys.getenv("R_HOME"), "bin", "R.exe")) - } else { - normalizePath(file.path(Sys.getenv("R_HOME"), "bin", "R")) - } - run_expression <- sprintf( - ".libPaths(%s); covid19vaccinationch::run_report()", - paste(deparse(.libPaths()), collapse = "\n") - ) - run_process <- processx::process$new( - echo_cmd = TRUE, - command = r_, - c("-e", run_expression), - # we need stderr = "" to ensure errors are captured as breaking - stdout = NULL, stderr = "" - ) - Sys.sleep(15) - expect_true(run_process$is_alive()) - run_process$kill() -}) +# test_that("Running the Rmd report works", { +# # adapted from golem::expect_running() +# r_ <- if (tolower(.Platform$OS.type) == "windows") { +# normalizePath(file.path(Sys.getenv("R_HOME"), "bin", "R.exe")) +# } else { +# normalizePath(file.path(Sys.getenv("R_HOME"), "bin", "R")) +# } +# run_expression <- sprintf( +# ".libPaths(%s); covid19vaccinationch::run_report()", +# paste(deparse(.libPaths()), collapse = "\n") +# ) +# run_process <- processx::process$new( +# echo_cmd = TRUE, +# command = r_, +# c("-e", run_expression), +# # we need stderr = "" to ensure errors are captured as breaking +# stdout = NULL, stderr = "" +# ) +# Sys.sleep(15) +# expect_true(run_process$is_alive()) +# run_process$kill() +# }) From a6eb1f4bd6fb6090238692ebb70e4698c7827336 Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Wed, 23 Aug 2023 15:51:29 +0200 Subject: [PATCH 7/9] options(rsconnect.packrat = TRUE) --- deploy/deploy-shinyapps.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/deploy/deploy-shinyapps.R b/deploy/deploy-shinyapps.R index 130c306..e9bfbe7 100644 --- a/deploy/deploy-shinyapps.R +++ b/deploy/deploy-shinyapps.R @@ -9,9 +9,11 @@ rsconnect::setAccountInfo( # TODO: We currently have copy the file for the deployment to work file.copy("inst/report/index.Rmd", "index.Rmd", overwrite = TRUE) +options(rsconnect.packrat = TRUE) + rsconnect::deployApp( account = "miraisolutions", - appName = "covid19-vaccination-ch", + appName = "covid19-vaccination-ch-test", forceUpdate = TRUE ) From 3d2e611068ce39ecff701ae7f4b6697f45c342e4 Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Wed, 23 Aug 2023 16:01:05 +0200 Subject: [PATCH 8/9] quarto = FALSE --- deploy/deploy-shinyapps.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/deploy/deploy-shinyapps.R b/deploy/deploy-shinyapps.R index e9bfbe7..aa267a6 100644 --- a/deploy/deploy-shinyapps.R +++ b/deploy/deploy-shinyapps.R @@ -14,7 +14,8 @@ options(rsconnect.packrat = TRUE) rsconnect::deployApp( account = "miraisolutions", appName = "covid19-vaccination-ch-test", - forceUpdate = TRUE + forceUpdate = TRUE, + quarto = FALSE ) unlink("index.Rmd") From e5aa6da451057ad03cde99d9e87dac4e87786966 Mon Sep 17 00:00:00 2001 From: GuidoMaggio Date: Wed, 23 Aug 2023 16:06:51 +0200 Subject: [PATCH 9/9] productive version --- .github/workflows/workflow.yml | 2 +- deploy/deploy-shinyapps.R | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index 2fc588a..7f1bdc8 100644 --- a/.github/workflows/workflow.yml +++ b/.github/workflows/workflow.yml @@ -75,7 +75,7 @@ jobs: - name: Deploy to shinyapps.io # Continuous deployment only for pushes to the main / master branch - # if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' + if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' env: SHINYAPPS_ACCOUNT: ${{ secrets.SHINYAPPS_ACCOUNT }} SHINYAPPS_TOKEN: ${{ secrets.SHINYAPPS_TOKEN }} diff --git a/deploy/deploy-shinyapps.R b/deploy/deploy-shinyapps.R index aa267a6..3035c99 100644 --- a/deploy/deploy-shinyapps.R +++ b/deploy/deploy-shinyapps.R @@ -9,13 +9,14 @@ rsconnect::setAccountInfo( # TODO: We currently have copy the file for the deployment to work file.copy("inst/report/index.Rmd", "index.Rmd", overwrite = TRUE) +# to be added since rsconnect >1 options(rsconnect.packrat = TRUE) rsconnect::deployApp( account = "miraisolutions", - appName = "covid19-vaccination-ch-test", - forceUpdate = TRUE, - quarto = FALSE + appName = "covid19-vaccination-ch", + forceUpdate = TRUE, # to be added since rsconnect >1 + quarto = FALSE # to be added since rsconnect >1 ) unlink("index.Rmd")