[Bug?]: Very slow Link step on 4.9.0 when `nodeLinker: pnpm`

[tienipia]

Self-service

• I'd be willing to implement a fix

Describe the bug

After upgrading from Yarn 4.8.1 to Yarn 4.9.0 in an environment where nodeLinker is set to pnpm only, running yarn install stalls for an extended period during the Link step. Below is the console output for reference:

.yarnrc.yml

nodeLinker: pnpm

yarn install output

➤ YN0000: · Yarn 4.9.0
➤ YN0000: ┌ Resolution step
➤ YN0000: └ Completed
➤ YN0000: ┌ Post-resolution validation
➤ YN0060: │ ical.js is listed by your project with version 2.1.0 (pda334), which doesn't satisfy what @fullcalendar/icalendar requests (^1.4.0).
➤ YN0060: │ vite is listed by your project with version 6.2.5 (p3789c), which doesn't satisfy what vite-plugin-vue-layouts and other dependencies request (^5.0.0).
➤ YN0002: │ saeroun-helpdesk-web@workspace:. doesn't provide @schedule-x/date-picker (p9f559), requested by @schedule-x/vue.
➤ YN0086: │ Some peer dependencies are incorrectly met by your project; run yarn explain peer-requirements <hash> for details, where <hash> is the six-letter p-prefixed code.
➤ YN0086: │ Some peer dependencies are incorrectly met by dependencies; run yarn explain peer-requirements for details.
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0000: └ Completed in 1s 499ms
➤ YN0000: ┌ Link step
➤ YN0007: │ ttf2woff2@npm:5.0.0 must be built because it never has been before or the last one failed
➤ YN0007: │ core-js-pure@npm:3.38.1 must be built because it never has been before or the last one failed
➤ YN0007: │ @parcel/watcher@npm:2.5.1 must be built because it never has been before or the last one failed
➤ YN0007: │ vue-demi@npm:0.14.10 [02956] must be built because it never has been before or the last one failed
➤ YN0007: │ esbuild@npm:0.25.0 must be built because it never has been before or the last one failed
➤ YN0007: │ esbuild@npm:0.21.5 must be built because it never has been before or the last one failed
➤ YN0000: └ Completed in 3m 15s
➤ YN0000: · Done with warnings in 3m 17s

same yarn install with 4.8.1

➤ YN0000: · Yarn 4.8.1
➤ YN0000: ┌ Resolution step
➤ YN0000: └ Completed in 0s 239ms
➤ YN0000: ┌ Post-resolution validation
➤ YN0060: │ @schedule-x/calendar is listed by your project with version 2.27.2 (p8d391), which doesn't satisfy what @schedule-x/vue requests (2.27.0).
➤ YN0060: │ ical.js is listed by your project with version 2.1.0 (pda334), which doesn't satisfy what @fullcalendar/icalendar requests (^1.4.0).
➤ YN0060: │ vite is listed by your project with version 6.2.5 (p3789c), which doesn't satisfy what vite-plugin-vue-layouts and other dependencies request (^5.0.0).
➤ YN0002: │ saeroun-helpdesk-web@workspace:. doesn't provide @schedule-x/date-picker (p9f559), requested by @schedule-x/vue.
➤ YN0086: │ Some peer dependencies are incorrectly met by your project; run yarn explain peer-requirements <hash> for details, where <hash> is the six-letter p-prefixed code.
➤ YN0086: │ Some peer dependencies are incorrectly met by dependencies; run yarn explain peer-requirements for details.
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0000: └ Completed in 1s 512ms
➤ YN0000: ┌ Link step
➤ YN0000: └ Completed in 5s 325ms
➤ YN0000: · Done with warnings in 7s 153ms

To reproduce

simply run

yarn set version stable
yarn install

removing node_modules to make clean doesn't resolve issue.

Environment

System:
  OS: Linux 6.13 Fedora Linux 41 (Workstation Edition)
  CPU: (6) x64 AMD Ryzen 5 3500X 6-Core Processor
Binaries:
  Node: 22.14.0 - /tmp/xfs-e749689b/node
  Yarn: 4.8.1 - /tmp/xfs-e749689b/yarn
  npm: 10.9.2 - /usr/bin/npm

Additional context

No response

[arcanis]

Is it always reproducible? The only change I see that could be related is #6688, but it shouldn't be enabled by default (and it should only impact PnP).

[tienipia]

@arcanis
In projects with minimal dependencies, the difference isn’t very noticeable (though it is indeed slower). For example, with SvelteKit and a few libraries, what previously took around 1 second on version 4.8.1 now takes 4–5 seconds.

When using Vue, Vuetify, and many additional libraries, a process that used to take about 10 seconds on 4.8.1 now exceeds 3 minutes.

This behavior clearly isn’t limited to my own environment, as builds on CircleCI also fail at the yarn install step due to timeouts.

[tienipia]

nodeLinker with pnp or node-modules does not have issue.
this issue is limited to nodeLinker with pnpm

what I want to know is why it does getting slower after upgrade 4.8.1 to 4.9.0.

[arcanis]

No idea, it shouldn't have changed. What you can try is to run yarn set version from sources --branch <commit id> on each commit between the two commits to try to bisect the one that would have added the regression.

[clemyan]

Based on your output, build scripts were run during your 4.9.0 install but not during your 4.8.1 install. Did you do something between upgrading and running install? Simply upgrading Yarn should no trigger rebuilds

> yarn config set nodeLinker pnpm
➤ YN0000: Successfully set nodeLinker to 'pnpm'

> yarn add core-js-pure
➤ YN0000: · Yarn 4.8.1
➤ YN0000: ┌ Resolution step
➤ YN0085: │ + core-js-pure@npm:3.41.0
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0013: │ A package was added to the project (+ 1.72 MiB).
➤ YN0000: └ Completed in 0s 444ms
➤ YN0000: ┌ Link step
➤ YN0007: │ core-js-pure@npm:3.41.0 must be built because it never has been before or the last one failed
➤ YN0000: └ Completed in 7s 537ms
➤ YN0000: · Done in 8s 15ms

> yarn set version 4.9.0
➤ YN0000: Done in 0s 6ms

> yarn
➤ YN0000: · Yarn 4.9.0
➤ YN0000: ┌ Resolution step
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0000: └ Completed
➤ YN0000: ┌ Link step
➤ YN0000: └ Completed in 0s 364ms
➤ YN0000: · Done in 0s 408ms

[tienipia]

@arcanis @clemyan Here's clear reproduction package.json

package.json

{
  "name": "issue-pnpm",
  "version": "1.0.0",
  "type": "module",
  "license": "MIT",
  "dependencies": {
    "@iconify/json": "^2.2.324",
    "@intlify/unplugin-vue-i18n": "^6.0.5",
    "@trivago/prettier-plugin-sort-imports": "^5.2.2",
    "@vueuse/components": "13.1.0",
    "@vueuse/core": "13.1.0",
    "@vueuse/head": "2.0.0",
    "@vueuse/router": "13.1.0",
    "@vueuse/sound": "2.1.3",
    "ag-grid-community": "32.3.3",
    "ag-grid-vue3": "32.3.3",
    "awesome-phonenumber": "7.4.0",
    "axios": "1.8.4",
    "crypto-js": "4.2.0",
    "dayjs": "1.11.13",
    "dompurify": "3.2.5",
    "exceljs": "^4.4.0",
    "flag-icons": "7.3.2",
    "howler": "2.2.4",
    "human-format": "1.2.1",
    "ical.js": "2.1.0",
    "js-cookie": "3.0.5",
    "jszip": "3.10.1",
    "lz-string": "1.5.0",
    "maska": "3.1.1",
    "nanoid": "5.1.5",
    "overlayscrollbars": "2.11.1",
    "overlayscrollbars-vue": "0.5.9",
    "pinia": "3.0.2",
    "pinia-plugin-persistedstate": "4.2.0",
    "vue": "3.5.13",
    "xlsx": "0.18.5",
    "xlsx-js-style": "1.2.0",
    "zod": "3.24.2"
  },
  "devDependencies": {
    "autoprefixer": "^10.4.21",
    "postcss": "^8.5.3",
    "postcss-import": "^16.1.0",
    "prettier": "^3.5.3",
    "prettier-plugin-organize-attributes": "^1.0.0",
    "prettier-plugin-tailwindcss": "^0.6.11",
    "tailwindcss": "^4.1.3",
    "typescript": "^5.8.3",
    "unplugin-auto-import": "^19.1.2",
    "unplugin-icons": "^22.1.0",
    "unplugin-vue-components": "^28.4.1",
    "unplugin-vue-router": "^0.12.0",
    "vite": "^6.2.5",
    "vite-plugin-minify": "^2.1.0",
    "vite-plugin-pwa": "^1.0.0",
    "vite-plugin-static-copy": "^2.3.1",
    "vite-plugin-vue-layouts": "^0.11.0",
    "vite-plugin-vuetify": "^2.1.1",
    "vitepress": "^1.6.3",
    "workbox-window": "^7.3.0"
  }
}

common test precedure

1. copy&paste package.json to empty folder package.json
2. yarn set version <4.8.1 or 4.9.0>
3. yarn install twice

Scenario 1 - Yarn 4.8.1 + pnpm with clean state

rm -rf node_modules
rm -rf .yarn .yarnrc.yml yarn.lock
yarn set version 4.8.1
yarn config set nodeLinker pnpm
yarn install

bash output

tienipia@fedora:~/Repository/issue-pnpm$ yarn install
➤ YN0000: · Yarn 4.8.1
➤ YN0000: ┌ Resolution step
➤ YN0085: │ + @iconify/json@npm:2.2.325, @intlify/unplugin-vue-i18n@npm:6.0.5, @trivago/prettier-plugin-sort-imports@npm:5.2.2, @vueuse/components@npm:13.1.0, and 872 more.
➤ YN0000: └ Completed in 3s 707ms
➤ YN0000: ┌ Post-resolution validation
➤ YN0060: │ vite is listed by your project with version 6.2.6 (pceb72), which doesn't satisfy what vite-plugin-vue-layouts and other dependencies request (^5.0.0).
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vue-router (pd250b), requested by @vueuse/router and other dependencies.
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vuetify (p7e95c), requested by vite-plugin-vuetify.
➤ YN0086: │ Some peer dependencies are incorrectly met by your project; run yarn explain peer-requirements <hash> for details, where <hash> is the six-letter p-prefixed code.
➤ YN0086: │ Some peer dependencies are incorrectly met by dependencies; run yarn explain peer-requirements for details.
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0000: └ Completed in 0s 717ms
➤ YN0000: ┌ Link step
➤ YN0007: │ vue-demi@npm:0.14.10 [16098] must be built because it never has been before or the last one failed
➤ YN0007: │ esbuild@npm:0.25.2 must be built because it never has been before or the last one failed
➤ YN0007: │ esbuild@npm:0.21.5 must be built because it never has been before or the last one failed
➤ YN0000: └ Completed in 2s 361ms
➤ YN0000: · Done with warnings in 6s 851ms
tienipia@fedora:~/Repository/issue-pnpm$ yarn install
➤ YN0000: · Yarn 4.8.1
➤ YN0000: ┌ Resolution step
➤ YN0000: └ Completed
➤ YN0000: ┌ Post-resolution validation
➤ YN0060: │ vite is listed by your project with version 6.2.6 (pceb72), which doesn't satisfy what vite-plugin-vue-layouts and other dependencies request (^5.0.0).
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vue-router (pd250b), requested by @vueuse/router and other dependencies.
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vuetify (p7e95c), requested by vite-plugin-vuetify.
➤ YN0086: │ Some peer dependencies are incorrectly met by your project; run yarn explain peer-requirements <hash> for details, where <hash> is the six-letter p-prefixed code.
➤ YN0086: │ Some peer dependencies are incorrectly met by dependencies; run yarn explain peer-requirements for details.
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0000: └ Completed in 0s 691ms
➤ YN0000: ┌ Link step
➤ YN0000: └ Completed in 1s 948ms
➤ YN0000: · Done with warnings in 2s 802ms

---

Scenario 2 - Yarn 4.9.0 + pnpm with clean state

rm -rf node_modules
rm -rf .yarn .yarnrc.yml yarn.lock
yarn set version 4.9.0
yarn config set nodeLinker pnpm
yarn install

bash output

tienipia@fedora:~/Repository/issue-pnpm$ yarn install
➤ YN0000: · Yarn 4.9.0
➤ YN0000: ┌ Resolution step
➤ YN0085: │ + @iconify/json@npm:2.2.325, @intlify/unplugin-vue-i18n@npm:6.0.5, @trivago/prettier-plugin-sort-imports@npm:5.2.2, @vueuse/components@npm:13.1.0, and 872 more.
➤ YN0000: └ Completed in 5s 452ms
➤ YN0000: ┌ Post-resolution validation
➤ YN0060: │ vite is listed by your project with version 6.2.6 (pceb72), which doesn't satisfy what vite-plugin-vue-layouts and other dependencies request (^5.0.0).
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vue-router (pd250b), requested by @vueuse/router and other dependencies.
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vuetify (p7e95c), requested by vite-plugin-vuetify.
➤ YN0086: │ Some peer dependencies are incorrectly met by your project; run yarn explain peer-requirements <hash> for details, where <hash> is the six-letter p-prefixed code.
➤ YN0086: │ Some peer dependencies are incorrectly met by dependencies; run yarn explain peer-requirements for details.
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0000: └ Completed in 0s 748ms
➤ YN0000: ┌ Link step
➤ YN0007: │ vue-demi@npm:0.14.10 [16098] must be built because it never has been before or the last one failed
➤ YN0007: │ esbuild@npm:0.25.2 must be built because it never has been before or the last one failed
➤ YN0007: │ esbuild@npm:0.21.5 must be built because it never has been before or the last one failed
➤ YN0000: └ Completed in 2m 29s
➤ YN0000: · Done with warnings in 2m 35s
tienipia@fedora:~/Repository/issue-pnpm$ yarn install
➤ YN0000: · Yarn 4.9.0
➤ YN0000: ┌ Resolution step
➤ YN0000: └ Completed
➤ YN0000: ┌ Post-resolution validation
➤ YN0060: │ vite is listed by your project with version 6.2.6 (pceb72), which doesn't satisfy what vite-plugin-vue-layouts and other dependencies request (^5.0.0).
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vue-router (pd250b), requested by @vueuse/router and other dependencies.
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vuetify (p7e95c), requested by vite-plugin-vuetify.
➤ YN0086: │ Some peer dependencies are incorrectly met by your project; run yarn explain peer-requirements <hash> for details, where <hash> is the six-letter p-prefixed code.
➤ YN0086: │ Some peer dependencies are incorrectly met by dependencies; run yarn explain peer-requirements for details.
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0000: └ Completed in 0s 699ms
➤ YN0000: ┌ Link step
➤ YN0000: └ Completed in 2m 28s
➤ YN0000: · Done with warnings in 2m 29s

This issue must be reproducible. I've tried over 10 times.
My home desktop, office desktop, cci build server, jenkins nodes, all environments have same issue.

[clemyan]

Found the culprit: #6688 removed caching for ZipFS#getFileSource. This actually affects all node linkers because we read from the cache via ZipFS, but pnpm is disproportionately affected because it needs to read every single file to get their path in the global CAS

[arcanis]

cc @goloveychuk - I thought we only removed caching for the js backend?

[goloveychuk]

This is true. Need to debug

[goloveychuk]

Will check in two hours

[goloveychuk]

please try this branch #6760
yarn set version from sources --branch 6760

@arcanis It appears, I've removed read cache from libzip impl also, leaving only written files cache to overcome a libzip bug.
I've reverted that commit. And added new implementation, where implementations explicitly says cache or not.
It's possible to add additional heuristics for jszip impl.
E.g. if compression != STORE and requestNumber is 3 then cache

[tienipia]

@goloveychuk it seems to work fine. (tested on above issue-pnpm package.json)

yarn set version from sources --branch 6760
yarn config set nodeLinker pnpm
yarn install

bash output

tienipia@tienipia-fedora:~/issue-pnpm$ yarn install
➤ YN0000: · Yarn 4.9.0-git.20250410.hash-7153c3e
➤ YN0000: ┌ Resolution step
➤ YN0085: │ + @iconify/json@npm:2.2.325, @intlify/unplugin-vue-i18n@npm:6.0.5, @trivago/prettier-plugin-sort-imports@npm:5.2.2, @vueuse/components@npm:13.1.0, @vueuse/core@npm:13.1.0, @vueuse/head@npm:2.0.0, and 870 more.
➤ YN0000: └ Completed in 4s 489ms
➤ YN0000: ┌ Post-resolution validation
➤ YN0060: │ vite is listed by your project with version 6.2.6 (pceb72), which doesn't satisfy what vite-plugin-vue-layouts and other dependencies request (^5.0.0).
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vue-router (pd250b), requested by @vueuse/router and other dependencies.
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vuetify (p7e95c), requested by vite-plugin-vuetify.
➤ YN0086: │ Some peer dependencies are incorrectly met by your project; run yarn explain peer-requirements <hash> for details, where <hash> is the six-letter p-prefixed code.
➤ YN0086: │ Some peer dependencies are incorrectly met by dependencies; run yarn explain peer-requirements for details.
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0013: │ 254 packages were added to the project (+ 451.93 MiB).
➤ YN0000: └ Completed in 6s 336ms
➤ YN0000: ┌ Link step
➤ YN0007: │ vue-demi@npm:0.14.10 [16098] must be built because it never has been before or the last one failed
➤ YN0007: │ esbuild@npm:0.25.2 must be built because it never has been before or the last one failed
➤ YN0007: │ esbuild@npm:0.21.5 must be built because it never has been before or the last one failed
➤ YN0000: └ Completed in 3s 607ms
➤ YN0000: · Done with warnings in 14s 543ms
tienipia@tienipia-fedora:~/issue-pnpm$ yarn install
➤ YN0000: · Yarn 4.9.0-git.20250410.hash-7153c3e
➤ YN0000: ┌ Resolution step
➤ YN0000: └ Completed
➤ YN0000: ┌ Post-resolution validation
➤ YN0060: │ vite is listed by your project with version 6.2.6 (pceb72), which doesn't satisfy what vite-plugin-vue-layouts and other dependencies request (^5.0.0).
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vue-router (pd250b), requested by @vueuse/router and other dependencies.
➤ YN0002: │ issue-pnpm@workspace:. doesn't provide vuetify (p7e95c), requested by vite-plugin-vuetify.
➤ YN0086: │ Some peer dependencies are incorrectly met by your project; run yarn explain peer-requirements <hash> for details, where <hash> is the six-letter p-prefixed code.
➤ YN0086: │ Some peer dependencies are incorrectly met by dependencies; run yarn explain peer-requirements for details.
➤ YN0000: └ Completed
➤ YN0000: ┌ Fetch step
➤ YN0000: └ Completed in 1s 47ms
➤ YN0000: ┌ Link step
➤ YN0000: └ Completed in 2s 956ms
➤ YN0000: · Done with warnings in 4s 277ms