REVDEP: modernize [ci skip]

Author: HenrikBengtsson

revdep/run.R

@@ -1,4 +1,7 @@
 #!/usr/bin/env Rscript
+if (!requireNamespace("revdepcheck")) {
+  stop('Install revdepcheck: remotes::install_github("r-lib/revdepcheck")')
+}
 library("revdepcheck")
 options(warn = 1L)
 
@@ -96,38 +99,69 @@ revdep_children <- local({
   }
 })
 
-revdep_pkgs_with_status <- function(status = "error") {
+revdep_pkgs_with_status <- function(status = c("error", "failure")) {
   status <- match.arg(status)
   res <- revdepcheck::revdep_summary()
-  field <- switch(status, error = "errors")
-  has_status <- vapply(res, FUN = function(x) {
-    z <- x[["new"]][[field]]
-    is.character(z) && any(nchar(z) > 0)
-  }, FUN.VALUE = NA, USE.NAMES = TRUE)
-  has_status <- !is.na(has_status) & has_status
-  names(has_status)[has_status]
+  if (status == "failure") {
+    names(which(sapply(res, FUN = .subset2, "status") == "E"))
+  } else if (status == "error") {
+    field <- switch(status, error = "errors")
+    has_status <- vapply(res, FUN = function(x) {
+      z <- x[["new"]][[field]]
+      is.character(z) && any(nchar(z) > 0)
+    }, FUN.VALUE = NA, USE.NAMES = TRUE)
+    has_status <- !is.na(has_status) & has_status
+    names(has_status)[has_status]
+  }
 }
 
-revdep_preinstall <- function(pkgs) {
-  pkgs <- unique(pkgs)
-  lib_paths_org <- lib_paths <- .libPaths()
-  on.exit(.libPaths(lib_paths_org))
+revdep_preinstall_libs <- function() {
+  lib_paths <- .libPaths()
   lib_paths[1] <- sprintf("%s-revdepcheck", lib_paths[1])
   dir.create(lib_paths[1], recursive = TRUE, showWarnings = FALSE)
-  .libPaths(lib_paths)
+  lib_paths
+}
+
+revdep_preinstall <- function(pkgs) {
+  oopts <- options(Ncpus = available_cores())
+  lib_paths_org <- .libPaths()
+  on.exit({
+    .libPaths(lib_paths_org)
+    options(oopts)
+  })
+  .libPaths(revdep_preinstall_libs())
+  
+  pkgs <- unique(pkgs)
   message(sprintf("Triggering crancache builds by pre-installing %d packages: %s", length(pkgs), paste(sQuote(pkgs), collapse = ", ")))
   message(".libPaths():")
   message(paste(paste0(" - ", .libPaths()), collapse = "\n"))
   ## Install one-by-one to update cache sooner
   for (kk in seq_along(pkgs)) {
     pkg <- pkgs[kk]
-    message(sprintf("Pre-installing package %d of %d: %s",
-                    kk, length(pkgs), pkg))
-    crancache::install_packages(pkg)
+    message(sprintf("Pre-installing package %d of %d: %s (Ncpus = %d)",
+                    kk, length(pkgs), pkg, getOption("Ncpus", 1L)))
+    crancache::install_packages(pkg, dependencies = c("Depends", "Imports", "LinkingTo", "Suggests"))
   }
 }
 
-args <- base::commandArgs()
+revdep_preinstall_update <- function() {
+  oopts <- options(Ncpus = available_cores())
+  lib_paths_org <- .libPaths()
+  on.exit({
+    .libPaths(lib_paths_org)
+    options(oopts)
+  })
+  .libPaths(revdep_preinstall_libs())
+  
+  message("Update crancache for all pre-installing packages:")
+  message(".libPaths():")
+  message(paste(paste0(" - ", .libPaths()), collapse = "\n"))
+  message(sprintf("Ncpus=%d", getOption("Ncpus", 1L)))
+  crancache::update_packages(ask = FALSE)
+}
+
+
+args <- base::commandArgs(trailingOnly = TRUE)
 if ("--reset" %in% args) {
   revdep_reset()
 } else if ("--todo-reset" %in% args) {
@@ -137,17 +171,25 @@ if ("--reset" %in% args) {
   todo()
 } else if ("--add" %in% args) {
   pos <- which("--add" == args)
+  if (pos == length(args)) stop("Missing value for option '--add'")
   pkgs <- parse_pkgs(args[seq(from = pos + 1L, to = length(args))])
   revdep_add(packages = pkgs)
   todo()
 } else if ("--rm" %in% args) {
   pos <- which("--rm" == args)
+  if (pos == length(args)) stop("Missing value for option '--rm'")
   pkgs <- parse_pkgs(args[seq(from = pos + 1L, to = length(args))])
   revdep_rm(packages = pkgs)
   todo()
 } else if ("--add-broken" %in% args) {
   revdep_add_broken()
   todo()
+} else if ("--add-error" %in% args) {
+#  res <- revepcheck::revdep_summary()
+  pkgs <- revdep_pkgs_with_status("error")
+  str(pkgs)
+  revdep_add(packages = pkgs)
+  todo()
 } else if ("--add-all" %in% args) {
   revdep_init()
   pkgs <- revdep_children()
@@ -168,6 +210,7 @@ if ("--reset" %in% args) {
   todo()
 } else if ("--show-check" %in% args) {
   pos <- which("--show-check" == args)
+  if (pos == length(args)) stop("Missing value for option '--show-check")
   pkgs <- parse_pkgs(args[seq(from = pos + 1L, to = length(args))])
   for (pkg in pkgs) {
     for (dir in c("old", "new")) {
@@ -188,20 +231,34 @@ if ("--reset" %in% args) {
   cat(sprintf("[n=%d] %s\n", length(pkgs), paste(pkgs, collapse = " ")))
 } else if ("--list-error" %in% args) {
   cat(paste(revdep_pkgs_with_status("error"), collapse = " "), "\n", sep="")
+} else if ("--list-failure" %in% args) {
+  cat(paste(revdep_pkgs_with_status("failure"), collapse = " "), "\n", sep="")
 } else if ("--add-error" %in% args) {
   revdepcheck::revdep_add(packages = revdep_pkgs_with_status("error"))
+} else if ("--add-failure" %in% args) {
+  revdepcheck::revdep_add(packages = revdep_pkgs_with_status("failure"))
+} else if ("--preinstall-update" %in% args) {
+  revdep_preinstall_update()
 } else if ("--preinstall-children" %in% args) {
   pkg <- revdep_this_package()
   pkgs <- revdepcheck:::cran_revdeps(pkg)
   revdep_preinstall(pkgs)
 } else if ("--preinstall-error" %in% args) {
   res <- revdepcheck::revdep_summary()
   revdep_preinstall(revdep_pkgs_with_status("error"))
+} else if ("--preinstall-failure" %in% args) {
+  res <- revdepcheck::revdep_summary()
+  revdep_preinstall(revdep_pkgs_with_status("failure"))
+} else if ("--preinstall-todo" %in% args) {
+  todo <- revdep_todo()
+  revdep_preinstall(todo$package)
 } else if ("--preinstall" %in% args) {
   pos <- which("--preinstall" == args)
+  if (pos == length(args)) stop("Missing value for option '--preinstall'")
   pkgs <- parse_pkgs(args[seq(from = pos + 1L, to = length(args))])
   revdep_preinstall(pkgs)
 } else {
+  stopifnot(length(args) == 0L)
   check()
   revdep_report(all = TRUE)
 }

revdep/run.sge

@@ -14,23 +14,15 @@
 
 ## SPECIAL: On Wynton HPC
 if [[ $SGE_CLUSTER_NAME == *wynton* ]]; then
-    module load CBI
-    module load r
-#    module load r/4.0.0-alpha
-
-    ## Some packages need a more modern version of gcc, e.g. 'balvaan'
-    module load scl-devtoolset/4
-
-    ## Some packages require non-default system libraries
-    module load gdal geos gsl hdf5 jags
+    module load CBI r
 
     ## Install all packages to toward $TMPDIR, if revdep/library doesn't already exist.
     ## This will avoid some of the slowness on the global file system
-    #if [[ ! -d revdep/library ]]; then
-    #    tmpdir=$(mktemp -d)
-    #    ln -fs "$tmpdir" revdep/library
-    #    [[ -d revdep/library ]] || { >&2 echo "ERROR: Failed to link revdep/library/ to $tmpdir"; exit 1; }
-    #fi
+    if [[ ! -d revdep/library ]]; then
+        tmpdir=$(mktemp -d)
+        ln -fs "$tmpdir" revdep/library
+        [[ -d revdep/library ]] || { >&2 echo "ERROR: Failed to link revdep/library/ to $tmpdir"; exit 1; }
+    fi
 
     ## To check in on revdep/library/ on the running host (see below), submit a job like:
     ##   echo "ls -lR revdep/library/" | qsub -cwd -j yes -l hostname=<hostname>