Respect renv lockfiles

NEWS.md

@@ -1,5 +1,10 @@
 # rsconnect (development version)
 
+* `deployApp()` and friends will now respect packrat and renv lock files,
+  if present. If you don't want to use these lockfiles, and instead return
+  the previous behaviour of snapshotting on every deploy, add your
+  lockfiles to `.rscignore` (#671).
+
 * New `rsconnect.http.headers` and `rsconnect.http.cookies` allow you to
   set extra arbitrary additional headers/cookies on each request (#405).
   Their use is documented in the new `vignette("custom-http")`.

R/bundleFiles.R

@@ -178,8 +178,6 @@ ignoreBundleFiles <- function(dir, contents) {
   ignore <- c(
     # rsconnect packages
     "rsconnect", "rsconnect-python", "manifest.json",
-    # packrat + renv,
-    "renv", "renv.lock", "packrat",
     # version control
     ".git", ".gitignore", ".svn",
     # R/RStudio

R/bundlePackage.R

@@ -15,7 +15,7 @@ bundlePackages <- function(bundleDir,
     unclass(utils::packageDescription(nm))
   })
 
-  # Connect prefers that packrat/packrat.lock file, but will use the manifest
+  # Connect prefers the packrat/packrat.lock file, but will use the manifest
   # if needed. shinyapps.io only uses the manifest, and only supports Github
   # remotes, not Bitbucket or Gitlab.
   github_cols <- grep("Github", colnames(deps), perl = TRUE, value = TRUE)
@@ -68,15 +68,21 @@ copyPackageDescriptions <- function(bundleDir, packages) {
   invisible()
 }
 
-snapshotRDependencies <- function(appDir,
+snapshotRDependencies <- function(bundleDir,
                                   implicit_dependencies = c(),
                                   verbose = FALSE) {
 
-  # create a packrat "snapshot"
-  addPackratSnapshot(appDir, implicit_dependencies, verbose = verbose)
+  if (file.exists(renvLockFile(bundleDir))) {
+    # Translate renv lock file to packrat lock file
+    translateRenvToPackrat(bundleDir)
+  } else if (file.exists(packratLockFile(bundleDir))) {
+    # Packrat lock file already exists; no action needed
+  } else {
+    # Find and snapshot current dependencies
+    addPackratSnapshot(bundleDir, implicit_dependencies, verbose = verbose)
+  }
 
-  # TODO: should we care about lockfile version or packrat version?
-  lockFilePath <- snapshotLockFile(appDir)
+  lockFilePath <- packratLockFile(bundleDir)
   df <- as.data.frame(read.dcf(lockFilePath), stringsAsFactors = FALSE)
 
   # get repos defined in the lockfile
@@ -270,6 +276,6 @@ performPackratSnapshot <- function(bundleDir, verbose = FALSE) {
   invisible()
 }
 
-snapshotLockFile <- function(appDir) {
-  file.path(appDir, "packrat", "packrat.lock")
+packratLockFile <- function(bundleDir) {
+  file.path(bundleDir, "packrat", "packrat.lock")
 }

R/renv.R

@@ -0,0 +1,86 @@
+translateRenvToPackrat <- function(bundleDir) {
+  renv <- jsonlite::read_json(renvLockFile(bundleDir))
+  packrat <- packratFromRenv(renv)
+
+  packratPath <- packratLockFile(bundleDir)
+  dir.create(dirname(packratPath), showWarnings = FALSE)
+  write.dcf(packrat, packratPath)
+}
+
+packratFromRenv <- function(renv) {
+  meta <- packratMeta(renv)
+  packages <- packratPackages(renv$Packages)
+  rbind_fill(list(meta, packages))
+}
+
+packratMeta <- function(renv) {
+  repos <- vapply(
+    renv$R$Repositories,
+    function(x) paste0(x$Name, "=", x$URL),
+    character(1)
+  )
+  data.frame(
+    PackratFormat = NA,
+    PackratVersion = NA,
+    RVersion = renv$R$Version,
+    Repos = paste(repos, collapse = ",")
+  )
+}
+
+packratPackages <- function(packages) {
+  out <- lapply(packages, packratPackage)
+  names(out) <- NULL
+  out <- compact(out)
+  out <- lapply(out, as.data.frame, stringsAsFactors = FALSE)
+  rbind_fill(out)
+}
+
+packratPackage <- function(pkg) {
+  # Don't include renv itself
+  if (identical(pkg$Package, "renv")) {
+    return(NULL)
+  }
+
+  # Convert renv sources to packrat sources
+  # https://github.com/rstudio/renv/blob/0.17.2/R/snapshot.R
+  if (identical(pkg$Repository, "CRAN")) {
+    pkg$Source <- "CRAN"
+  } else if (pkg$Source == "unknown") {
+    pkg$Source <- "source"
+  }
+
+  # Remove Remote fields that renv adds for "standard" installs from CRAN
+  if (identical(pkg$RemoteType, "standard")) {
+    pkg <- pkg[!grepl("^Remote", names(pkg))]
+  }
+
+  # Drop hash since packrat hash != renv hash
+  pkg$Hash <- NULL
+
+  # Convert Requirements to Requires, a comma separated list
+  if (length(pkg$Requirements) > 0) {
+    pkg$Requires <- paste0(unlist(pkg$Requirements), collapse = ", ")
+  }
+  pkg$Requirements <- NULL
+
+  pkg
+}
+
+renvLockFile <- function(bundleDir) {
+  file.path(bundleDir, "renv.lock")
+}
+
+showPackratTranslation <- function(path) {
+  renv <- jsonlite::read_json(renvLockFile(path))
+  packrat <- packratFromRenv(renv)
+  showDcf(packrat)
+}
+
+showDcf <- function(df) {
+  path <- tempfile()
+  on.exit(path, add = TRUE)
+
+  write.dcf(df, path)
+  writeLines(readLines(path))
+  invisible()
+}

tests/testthat/_snaps/renv.md

@@ -0,0 +1,46 @@
+# generates expected packrat file
+
+    Code
+      showPackratTranslation(test_path("renv-cran"))
+    Output
+      RVersion: 4.2.1
+      Repos: CRAN=https://cran.rstudio.com
+
+      Package: cli
+      Version: 3.6.0
+      Source: CRAN
+      Repository: CRAN
+    Code
+      showPackratTranslation(test_path("renv-github"))
+    Output
+      RVersion: 4.2.1
+      Repos: CRAN=https://cran.rstudio.com
+
+      Package: withr
+      Version: 2.5.0.9000
+      Source: GitHub
+      RemoteType: github
+      RemoteHost: api.github.com
+      RemoteUsername: r-lib
+      RemoteRepo: withr
+      RemoteRef: main
+      RemoteSha: 3b01a2bef7b17bf2f82d94be58a2d4287827fa21
+    Code
+      showPackratTranslation(test_path("renv-bioc"))
+    Output
+      RVersion: 4.2.1
+      Repos: CRAN=https://cran.rstudio.com
+
+      Package: BiocGenerics
+      Version: 0.44.0
+      Source: Bioconductor
+      git_url: https://git.bioconductor.org/packages/BiocGenerics
+      git_branch: RELEASE_3_16
+      git_last_commit: d7cd9c1
+      git_last_commit_date: 2022-11-01
+
+      Package: BiocManager
+      Version: 1.30.20
+      Source: CRAN
+      Repository: CRAN
+

tests/testthat/renv-bioc/dependences.R

@@ -0,0 +1 @@
+library(bioBase)

tests/testthat/renv-bioc/renv.lock

@@ -0,0 +1,46 @@
+{
+  "R": {
+    "Version": "4.2.1",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cran.rstudio.com"
+      }
+    ]
+  },
+  "Packages": {
+    "BiocGenerics": {
+      "Package": "BiocGenerics",
+      "Version": "0.44.0",
+      "Source": "Bioconductor",
+      "git_url": "https://git.bioconductor.org/packages/BiocGenerics",
+      "git_branch": "RELEASE_3_16",
+      "git_last_commit": "d7cd9c1",
+      "git_last_commit_date": "2022-11-01",
+      "Hash": "0de19224c2cd94f48fbc0d0bc663ce3b",
+      "Requirements": []
+    },
+    "BiocManager": {
+      "Package": "BiocManager",
+      "Version": "1.30.20",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "a7fca16a50b6ef7771b49d636dd54b57",
+      "Requirements": []
+    },
+    "renv": {
+      "Package": "renv",
+      "Version": "0.16.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "RemoteType": "standard",
+      "RemotePkgRef": "renv",
+      "RemoteRef": "renv",
+      "RemoteRepos": "https://cran.rstudio.com",
+      "RemotePkgPlatform": "aarch64-apple-darwin20",
+      "RemoteSha": "0.16.0",
+      "Hash": "c9e8442ab69bc21c9697ecf856c1e6c7",
+      "Requirements": []
+    }
+  }
+}

tests/testthat/renv-cran/dependences.R

@@ -0,0 +1 @@
+library(cli)

tests/testthat/renv-cran/renv.lock

@@ -0,0 +1,41 @@
+{
+  "R": {
+    "Version": "4.2.1",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cran.rstudio.com"
+      }
+    ]
+  },
+  "Packages": {
+    "cli": {
+      "Package": "cli",
+      "Version": "3.6.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "RemoteType": "standard",
+      "RemotePkgRef": "cli",
+      "RemoteRef": "cli",
+      "RemoteRepos": "https://cran.rstudio.com",
+      "RemotePkgPlatform": "aarch64-apple-darwin20",
+      "RemoteSha": "3.6.0",
+      "Hash": "3177a5a16c243adc199ba33117bd9657",
+      "Requirements": []
+    },
+    "renv": {
+      "Package": "renv",
+      "Version": "0.16.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "RemoteType": "standard",
+      "RemotePkgRef": "renv",
+      "RemoteRef": "renv",
+      "RemoteRepos": "https://cran.rstudio.com",
+      "RemotePkgPlatform": "aarch64-apple-darwin20",
+      "RemoteSha": "0.16.0",
+      "Hash": "c9e8442ab69bc21c9697ecf856c1e6c7",
+      "Requirements": []
+    }
+  }
+}

tests/testthat/renv-github/dependences.R

@@ -0,0 +1 @@
+library(withr)

tests/testthat/renv-github/renv.lock

@@ -0,0 +1,40 @@
+{
+  "R": {
+    "Version": "4.2.1",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cran.rstudio.com"
+      }
+    ]
+  },
+  "Packages": {
+    "renv": {
+      "Package": "renv",
+      "Version": "0.16.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "RemoteType": "standard",
+      "RemotePkgRef": "renv",
+      "RemoteRef": "renv",
+      "RemoteRepos": "https://cran.rstudio.com",
+      "RemotePkgPlatform": "aarch64-apple-darwin20",
+      "RemoteSha": "0.16.0",
+      "Hash": "c9e8442ab69bc21c9697ecf856c1e6c7",
+      "Requirements": []
+    },
+    "withr": {
+      "Package": "withr",
+      "Version": "2.5.0.9000",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteUsername": "r-lib",
+      "RemoteRepo": "withr",
+      "RemoteRef": "main",
+      "RemoteSha": "3b01a2bef7b17bf2f82d94be58a2d4287827fa21",
+      "Hash": "a5b00ca54909a1dd45d6f6f148887c64",
+      "Requirements": []
+    }
+  }
+}

tests/testthat/test-bundleFiles.R

@@ -107,7 +107,7 @@ test_that("ignores knitr cache directories", {
 test_that("ignores files anywhere in path", {
   dir <- withr::local_tempdir()
   dir.create(file.path(dir, "a/b/c"), recursive = TRUE)
-  file.create(file.path(dir, c("x", "a/renv", "a/b/.gitignore", "a/b/c/.DS_Store")))
+  file.create(file.path(dir, c("x", "a/b/.gitignore", "a/b/c/.DS_Store")))
 
   expect_equal(bundleFiles(dir), "x")
 })

tests/testthat/test-renv.R

@@ -0,0 +1,30 @@
+#' @examples
+#' makeRenvSnapshot(test_path("renv-cran"), "cli")
+#' makeRenvSnapshot(test_path("renv-bioc"), "bioBase", "bioc::Biobase")
+#' makeRenvSnapshot(test_path("renv-github"), "withr", "r-lib/withr")
+makeRenvSnapshot <- function(path, name, package = name) {
+  dir.create(path, showWarnings = FALSE)
+
+  withr::local_dir(path)
+  writeLines(paste0("library(", name, ")"), "dependences.R")
+
+  callr::r(args = list(package = package), function(package) {
+    renv::activate()
+    renv::install(package)
+    renv::snapshot(prompt = FALSE)
+  })
+
+  unlink(c(".Rprofile", ".gitignore", "renv"), recursive = TRUE)
+
+  invisible()
+}
+
+# -------------------------------------------------------------------------
+
+test_that("generates expected packrat file", {
+  expect_snapshot({
+    showPackratTranslation(test_path("renv-cran"))
+    showPackratTranslation(test_path("renv-github"))
+    showPackratTranslation(test_path("renv-bioc"))
+  })
+})