[BUG] Need to run `npm install` twice to fix `npm ci` command

[Saibamen]

Is there an existing issue for this?

• I have searched the existing issues

This issue exists in the latest npm version

• I am using the latest npm

Current Behavior

npm error `npm ci` can only install packages when your package.json and package-lock.json or npm-shrinkwrap.json are in sync. Please update your lock file with `npm install` before continuing.
npm error
npm error Invalid: lock file's yaml@1.10.2 does not satisfy yaml@2.5.1
npm error Missing: yaml@1.10.2 from lock file

Expected Behavior

npm ci should install packages without exception

Steps To Reproduce

Download repro repository: https://github.com/Saibamen/npm-double-install-bug

1. Delete package-lock.json
2. npm install
3. npm ci

See errors

Building with commited lock file (created on Windows) and npm ci:

Building with fresh lock file, npm install and then npm ci

Annoying workarounds

Workaround v1

1. npm install
2. Delete node_modules
3. npm install
4. npm ci

Workaround v2

Just run npm install twice, no need to delete node_modules.

1. npm install
2. npm install
3. npm ci

Environment

• npm: 10.8.3
• Node.js: 20.17.0
• OS Name: Windows 10
• System Model Name: 10.0.19045.4894
• npm config:

; node bin location = C:\Program Files\nodejs\node.exe
; node version = v20.17.0
; npm local prefix = C:\XXX\npm-double-install-bug
; npm version = 10.8.3
; cwd = C:\XXX\npm-double-install-bug
; HOME = C:\Users\YYY
; Run `npm config ls -l` to show all defaults.

Diff after running npm install second time:

diff --git a/package-lock.json b/package-lock.json
index 07842ff..4823f0c 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1606,6 +1606,16 @@
         }
       }
     },
+    "node_modules/eslint-plugin-svelte/node_modules/yaml": {
+      "version": "1.10.2",
+      "resolved": "https://registry.npmjs.org/yaml/-/yaml-1.10.2.tgz",
+      "integrity": "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==",
+      "dev": true,
+      "license": "ISC",
+      "engines": {
+        "node": ">= 6"
+      }
+    },
     "node_modules/eslint-scope": {
       "version": "7.2.2",
       "resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.2.2.tgz",
@@ -3528,21 +3538,6 @@
         }
       }
     },
-    "node_modules/svelte-check/node_modules/yaml": {
-      "version": "2.5.1",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.5.1.tgz",
-      "integrity": "sha512-bLQOjaX/ADgQ20isPJRvF0iRUHIxVhYvr53Of7wGcWlO2jvtUlH5m87DsmulFVxRpNLOnI4tB6p/oh8D7kpn9Q==",
-      "dev": true,
-      "license": "ISC",
-      "optional": true,
-      "peer": true,
-      "bin": {
-        "yaml": "bin.mjs"
-      },
-      "engines": {
-        "node": ">= 14"
-      }
-    },
     "node_modules/svelte-eslint-parser": {
       "version": "0.41.1",
       "resolved": "https://registry.npmjs.org/svelte-eslint-parser/-/svelte-eslint-parser-0.41.1.tgz",
@@ -3737,19 +3732,6 @@
         "url": "https://github.com/sponsors/antonk52"
       }
     },
-    "node_modules/tailwindcss/node_modules/yaml": {
-      "version": "2.5.1",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.5.1.tgz",
-      "integrity": "sha512-bLQOjaX/ADgQ20isPJRvF0iRUHIxVhYvr53Of7wGcWlO2jvtUlH5m87DsmulFVxRpNLOnI4tB6p/oh8D7kpn9Q==",
-      "dev": true,
-      "license": "ISC",
-      "bin": {
-        "yaml": "bin.mjs"
-      },
-      "engines": {
-        "node": ">= 14"
-      }
-    },
     "node_modules/text-table": {
       "version": "0.2.0",
       "resolved": "https://registry.npmjs.org/text-table/-/text-table-0.2.0.tgz",
@@ -4067,13 +4049,16 @@
       "license": "ISC"
     },
     "node_modules/yaml": {
-      "version": "1.10.2",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-1.10.2.tgz",
-      "integrity": "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==",
+      "version": "2.5.1",
+      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.5.1.tgz",
+      "integrity": "sha512-bLQOjaX/ADgQ20isPJRvF0iRUHIxVhYvr53Of7wGcWlO2jvtUlH5m87DsmulFVxRpNLOnI4tB6p/oh8D7kpn9Q==",
       "dev": true,
       "license": "ISC",
+      "bin": {
+        "yaml": "bin.mjs"
+      },
       "engines": {
-        "node": ">= 6"
+        "node": ">= 14"
       }
     },
     "node_modules/yocto-queue": {

[milaninfy]

Closing: this looks to be similar if not a duplicate of an existing issue, #6787. If you believe your instance is unique, please provide further clarifying details.