gistfile.patch

diff --git a/lib/arborist/load-virtual.js b/lib/arborist/load-virtual.js
index f03bd80..6bb07af 100644
--- a/lib/arborist/load-virtual.js
+++ b/lib/arborist/load-virtual.js
@@ -24,6 +24,7 @@ const loadWorkspacesVirtual = Symbol.for('loadWorkspacesVirtual')
 const flagsSuspect = Symbol.for('flagsSuspect')
 const reCalcDepFlags = Symbol('reCalcDepFlags')
 const checkRootEdges = Symbol('checkRootEdges')
+const rootOptionProvided = Symbol('rootOptionProvided')
 
 const depsToEdges = (type, deps) =>
   Object.entries(deps).map(d => [type, ...d])
@@ -63,6 +64,8 @@ module.exports = cls => class VirtualLoader extends cls {
       root = await this[loadRoot](s),
     } = options
 
+    this[rootOptionProvided] = !!options.root
+
     await this[loadFromShrinkwrap](s, root)
     return treeCheck(this.virtualTree)
   }
@@ -74,13 +77,15 @@ module.exports = cls => class VirtualLoader extends cls {
   }
 
   async [loadFromShrinkwrap] (s, root) {
-    // root is never any of these things, but might be a brand new
-    // baby Node object that never had its dep flags calculated.
-    root.extraneous = false
-    root.dev = false
-    root.optional = false
-    root.devOptional = false
-    root.peer = false
+    if (!this[rootOptionProvided]) {
+      // root is never any of these things, but might be a brand new
+      // baby Node object that never had its dep flags calculated.
+      root.extraneous = false
+      root.dev = false
+      root.optional = false
+      root.devOptional = false
+      root.peer = false
+    }
     this[checkRootEdges](s, root)
     root.meta = s
     this.virtualTree = root
@@ -101,7 +106,7 @@ module.exports = cls => class VirtualLoader extends cls {
       node.devOptional = true
       node.peer = true
     }
-    calcDepFlags(this.virtualTree, true)
+    calcDepFlags(this.virtualTree, !this[rootOptionProvided])
   }
 
   // check the lockfile deps, and see if they match.  if they do not