support reporting + checking of R system requirements (#2101)

* begin supporting R system requirements

* support for redhat

* tweak display

* [WIP]

* tweaks

* add some tests

* update NEWS

* simplify a bit

* tweak resolution of sysreqs

* more refinement

* [WIP]

* more work

* resolve package aliases

* tweaks

* try to resolve packages

* check system requirements for other distros

* rename

* move sysreqs to single file

* tidy up

* add collapse arg

* add to pkgdown

* formatting

* try to resolve virtual packages on debian systems

* allow alias to accept vector text

* handle virtual packages on rpm in a similar way

* fixes

* tweaks

NAMESPACE

@@ -42,6 +42,7 @@ export(scaffold)
 export(settings)
 export(snapshot)
 export(status)
+export(sysreqs)
 export(update)
 export(upgrade)
 export(use)

NEWS.md

@@ -1,6 +1,15 @@
 
 # renv (development version)
 
+* `renv` gains the `sysreqs()` function, which can be used to query the system
+  packages required by a set of R packages. Functionality is currently available
+  for Debian-based distributions, as well as Red Hat distributions.
+
+* On Linux, `renv` now uses the database from
+  <https://github.com/rstudio/r-system-requirements> when determining if
+  an R package's required system libraries are installed, and notifies
+  the user which packages (if any) are missing during install / restore.
+
 * Fixed an issue where `renv` could fail to retrieve credentials registered
   for 'github.com' when querying URLs at 'api.github.com'.
 

R/abi.R

@@ -45,7 +45,7 @@ renv_abi_check <- function(packages = NULL,
   reasons <- unique(tbl$reason)
   if ("Rcpp_precious_list" %in% reasons) {
     packages <- sort(unique(tbl$package[tbl$reason == "Rcpp_precious_list"]))
-    caution_bullets(
+    bulletin(
       "The following packages were built against a newer version of Rcpp than is currently available:",
       packages,
       c(
@@ -61,7 +61,7 @@ renv_abi_check <- function(packages = NULL,
   if ("missing" %in% reasons) {
 
     missing <- tbl[tbl$reason == "missing", ]
-    caution_bullets(
+    bulletin(
       "The following required system libraries are unavailable:",
       unique(missing$dependency),
       c(

R/aliases.R

@@ -1,6 +1,6 @@
 
 # aliases used primarily for nicer / normalized text output
-the$aliases <- list(
+the$aliases <- c(
   bioc         = "Bioconductor",
   bioconductor = "Bioconductor",
   bitbucket    = "Bitbucket",
@@ -16,6 +16,8 @@ the$aliases <- list(
   xgit         = "Git"
 )
 
-alias <- function(text) {
-  the$aliases[[text]] %||% text
+alias <- function(text, aliases = the$aliases) {
+  matches <- text %in% names(aliases)
+  text[matches] <- aliases[text[matches]]
+  text
 }

R/available-packages.R

@@ -95,7 +95,7 @@ renv_available_packages_query <- function(type, repos, quiet = FALSE) {
     paste(c(header(url), msgs, ""), collapse = "\n")
   })
 
-  caution_bullets(header, msgs)
+  bulletin(header, msgs)
   filter(dbs, Negate(is.null))
 
 }

R/cache.R

@@ -275,7 +275,7 @@ renv_cache_diagnose_corrupt_metadata <- function(paths, problems, verbose) {
 
     # nocov start
     if (verbose) {
-      caution_bullets(
+      bulletin(
         "The following package(s) are missing 'Meta/package.rds':",
         renv_cache_format_path(bad),
         "These packages should be purged and reinstalled."
@@ -304,7 +304,7 @@ renv_cache_diagnose_corrupt_metadata <- function(paths, problems, verbose) {
 
     # nocov start
     if (verbose) {
-      caution_bullets(
+      bulletin(
         "The following package(s) have corrupt 'Meta/package.rds' files:",
         renv_cache_format_path(bad),
         "These packages should be purged and reinstalled."
@@ -335,7 +335,7 @@ renv_cache_diagnose_missing_descriptions <- function(paths, problems, verbose) {
 
   # nocov start
   if (verbose) {
-    caution_bullets(
+    bulletin(
       "The following packages are missing DESCRIPTION files in the cache:",
       renv_cache_format_path(bad),
       "These packages should be purged and reinstalled."
@@ -369,7 +369,7 @@ renv_cache_diagnose_bad_hash <- function(paths, problems, verbose) {
     fmt <- "%s %s [Hash: %s != %s]"
     entries <- sprintf(fmt, lhs$Package, lhs$Version, lhs$Hash, rhs$Hash)
 
-    caution_bullets(
+    bulletin(
       "The following packages have incorrect hashes:",
       entries,
       "Consider using `renv::rehash()` to re-hash these packages."
@@ -412,7 +412,7 @@ renv_cache_diagnose_wrong_built_version <- function(paths, problems, verbose) {
     # nocov start
     if (verbose) {
 
-      caution_bullets(
+      bulletin(
         "The following packages have no 'Built' field recorded in their DESCRIPTION file:",
         paths[isna],
         "renv is unable to validate the version of R this package was built for."
@@ -450,7 +450,7 @@ renv_cache_diagnose_wrong_built_version <- function(paths, problems, verbose) {
   # nocov start
   if (verbose) {
 
-    caution_bullets(
+    bulletin(
       "The following packages in the cache were built for a different version of R:",
       renv_cache_format_path(paths[wrong]),
       "These packages will need to be purged and reinstalled."

R/caution.R

@@ -5,20 +5,20 @@ caution <- function(fmt = "", ..., con = stdout()) {
     writeLines(sprintf(fmt, ...), con = con)
 }
 
-caution_bullets <- function(preamble = NULL,
-                            values = NULL,
-                            postamble = NULL,
-                            ...,
-                            bullets = TRUE,
-                            emitter = NULL)
+bulletin <- function(preamble = NULL,
+                     values = NULL,
+                     postamble = NULL,
+                     ...,
+                     bullets = TRUE,
+                     emitter = NULL)
 {
   if (empty(values))
     return(invisible())
 
   renv_dots_check(...)
 
   lines <- c(
-    if (length(preamble))  paste(preamble, collapse = "\n"),
+    if (length(preamble)) paste(preamble, collapse = "\n"),
     if (bullets)
       paste("-", values, collapse = "\n")
     else

R/clean.R

@@ -131,7 +131,7 @@ renv_clean_library_tempdirs <- function(project, prompt) {
   # nocov start
   if (prompt || renv_verbose()) {
 
-    caution_bullets("The following directories will be removed:", bad)
+    bulletin("The following directories will be removed:", bad)
 
     if (prompt && !proceed())
       cancel()
@@ -177,7 +177,7 @@ renv_clean_system_library <- function(project, prompt) {
   # nocov start
   if (prompt || renv_verbose()) {
 
-    caution_bullets(
+    bulletin(
       "The following non-system packages are installed in the system library:",
       packages,
       c(
@@ -227,7 +227,7 @@ renv_clean_unused_packages <- function(project, prompt) {
   # nocov start
   if (prompt || renv_verbose()) {
 
-    caution_bullets(
+    bulletin(
       c(
         "The following packages are installed in the project library,",
         "but appear to be no longer used in your project."
@@ -272,7 +272,7 @@ renv_clean_package_locks <- function(project, prompt) {
   # nocov start
   if (prompt || renv_verbose()) {
 
-    caution_bullets(
+    bulletin(
       "The following stale package locks were discovered in your library:",
       basename(old),
       "These locks will be removed."
@@ -306,7 +306,7 @@ renv_clean_cache <- function(project, prompt) {
   missing <- !file.exists(projlist)
   if (any(missing)) {
 
-    caution_bullets(
+    bulletin(
       "The following projects are monitored by renv, but no longer exist:",
       projlist[missing],
       "These projects will be removed from renv's project list."
@@ -342,7 +342,7 @@ renv_clean_cache <- function(project, prompt) {
 
   if (prompt || renv_verbose()) {
 
-    caution_bullets(
+    bulletin(
       "The following packages are installed in the cache but no longer used:",
       renv_cache_format_path(diff),
       "These packages will be removed."

R/config-defaults.R

@@ -339,6 +339,15 @@ config <- list(
     )
   },
 
+  sysreqs.check = function(..., default = TRUE) {
+    renv_config_get(
+      name    = "sysreqs.check",
+      type    = "logical[1]",
+      default = default,
+      args    = list(...)
+    )
+  },
+
   updates.check = function(..., default = FALSE) {
     renv_config_get(
       name    = "updates.check",

R/dependencies.R

@@ -1883,7 +1883,7 @@ renv_dependencies_report <- function(errors) {
     paste(c(header(file), messages, ""), collapse = "\n")
   })
 
-  caution_bullets(
+  bulletin(
     "WARNING: One or more problems were discovered while enumerating dependencies.",
     c("", lines),
     "Please see `?renv::dependencies` for more information.",

R/diagnostics.R

@@ -29,6 +29,7 @@ diagnostics <- function(project = NULL) {
     renv_diagnostics_project,
     renv_diagnostics_status,
     renv_diagnostics_packages,
+    renv_diagnostics_sysreqs,
     renv_diagnostics_abi,
     renv_diagnostics_profile,
     renv_diagnostics_settings,
@@ -145,6 +146,21 @@ renv_diagnostics_packages <- function(project) {
 
 }
 
+renv_diagnostics_sysreqs <- function(project) {
+
+  if (!renv_platform_linux())
+    return()
+
+  writef(header("R System Requirements"))
+
+  lockfile <- renv_lockfile_create(project)
+  records <- renv_lockfile_records(lockfile)
+  sysreqs <- map(records, `[[`, "SystemRequirements")
+  ok <- renv_sysreqs_check(sysreqs, prompt = FALSE)
+  invisible(ok)
+
+}
+
 renv_diagnostics_packages_version <- function(lockfile, all) {
 
   data <- rep.int(NA_character_, length(all))

R/equip-macos.R

@@ -80,7 +80,7 @@ renv_equip_macos_toolchain <- function() {
     return(TRUE)
 
   command <- paste("sudo /usr/sbin/installer -pkg", shQuote(destfile), "-target /")
-  caution_bullets(
+  bulletin(
     "The R LLVM toolchain has been successfully downloaded. Please execute:",
     command,
     "in a separate terminal to complete installation."
@@ -123,7 +123,7 @@ renv_equip_macos_rstudio <- function(spec, destfile) {
   if (!installed)
     return(FALSE)
 
-  caution_bullets(
+  bulletin(
     "The R LLVM toolchain has been downloaded and installed to:",
     spec$dst,
     "This toolchain will be used by renv when installing packages from source."

R/extsoft.R

@@ -31,7 +31,7 @@ renv_extsoft_install <- function(quiet = FALSE) {
 
   if (interactive()) {
 
-    caution_bullets(
+    bulletin(
       "The following external software tools will be installed:",
       files,
       sprintf("Tools will be installed into %s.", renv_path_pretty(extsoft))
@@ -135,7 +135,7 @@ renv_extsoft_use <- function(quiet = FALSE) {
 
   if (interactive()) {
 
-    caution_bullets(
+    bulletin(
       "The following entries will be added to ~/.R/Makevars:",
       c(localsoft, libxml, localcpp, locallibs),
       "These tools will be used when compiling R packages from source."

R/hydrate.R

@@ -366,7 +366,7 @@ renv_hydrate_resolve_missing <- function(project, library, remotes, missing) {
       sprintf("[%s]: %s", package, short)
     })
 
-    caution_bullets(
+    bulletin(
       "The following package(s) were not installed successfully:",
       text,
       "You may need to manually download and install these packages."
@@ -416,7 +416,7 @@ renv_hydrate_report <- function(packages, na, linkable) {
   }
 
   if (length(na)) {
-    caution_bullets(
+    bulletin(
       "The following packages are used in this project, but not available locally:",
       csort(names(na)),
       "renv will attempt to download and install these packages."

R/install.R

@@ -227,6 +227,14 @@ install <- function(packages = NULL,
     cancel_if(prompt && !proceed())
   }
 
+  # check for installed dependencies
+  if (config$sysreqs.check(default = renv_platform_linux())) {
+    paths <- map(records, `[[`, "Path")
+    sysreqs <- map(paths, renv_sysreqs_read)
+    renv_sysreqs_check(sysreqs, prompt = prompt)
+  }
+
+
   # install retrieved records
   before <- Sys.time()
   renv_install_impl(records)
@@ -766,7 +774,7 @@ renv_install_preflight_requirements <- function(records) {
   fmt <- "Package '%s' requires '%s', but '%s' will be installed"
   text <- sprintf(fmt, format(package), format(requires), format(actual))
   if (renv_verbose()) {
-    caution_bullets(
+    bulletin(
       "The following issues were discovered while preparing for installation:",
       text,
       "Installation of these packages may not succeed."
@@ -789,7 +797,7 @@ renv_install_postamble <- function(packages) {
   installed <- map_chr(packages, renv_package_version)
   loaded <- map_chr(packages, renv_namespace_version)
 
-  caution_bullets(
+  bulletin(
     c("", "The following loaded package(s) have been updated:"),
     packages[installed != loaded],
     "Restart your R session to use the new versions."
@@ -826,7 +834,7 @@ renv_install_preflight_permissions <- function(library) {
     postamble <- sprintf(fmt, info$effective_user %||% info$user)
 
     # print it
-    caution_bullets(
+    bulletin(
       preamble = preamble,
       values = library,
       postamble = postamble

R/library.R

@@ -22,7 +22,7 @@ renv_library_diagnose <- function(project, libpath) {
   # if only some symlinks are broken, report to user
   if (any(missing)) {
 
-    caution_bullets(
+    bulletin(
       "The following package(s) are missing entries in the cache:",
       basename(children[missing]),
       "These packages will need to be reinstalled."

R/load.R

@@ -766,7 +766,7 @@ renv_load_check_description <- function(project) {
 
   values <- sprintf("[line %i is blank]", bad)
 
-  caution_bullets(
+  bulletin(
     sprintf("%s contains blank lines:", renv_path_pretty(descpath)),
     values,
     c(

R/lockfile-read.R

@@ -76,7 +76,7 @@ renv_lockfile_read_preflight <- function(contents) {
 
     all <- unlist(parts, recursive = TRUE, use.names = FALSE)
 
-    caution_bullets(
+    bulletin(
       "The lockfile contains one or more merge conflict markers:",
       head(all, n = -1L),
       "You will need to resolve these merge conflicts before the file can be read."

R/migrate.R

@@ -321,7 +321,7 @@ renv_migrate_packrat_cache_impl <- function(targets) {
   if (nrow(bad) == 0)
     return(TRUE)
 
-  caution_bullets(
+  bulletin(
     "The following packages could not be copied from the Packrat cache:",
     with(bad, sprintf("%s [%s]", format(source), reason)),
     "These packages may need to be reinstalled and re-cached."