Root binaries get removed after installing a Workspace dependency

[ovidiuch]

Reproducing on Yarn 1.20 and 1.21.

Minimal reproducible demo at skidding/yarn-bin-missing

Steps to reproduce:

Step 1: Jest is installed in workspace root and binary is present after running yarn

> yarn
> ls node_modules/.bin/jest
# node_modules/.bin/jest

Step 2: Go to foo workspace and install Lodash

> cd cd packages/foo
> yarn add lodash

Step 3: Go to back to root and 💨 node_modules/.bin is gone.

> cd -
> ls node_modules/.bin/jest
ls: node_modules/.bin/jest: No such file or directory

[milesj]

Also encountering this. Running yarn install in the root temporarily fixes the issue.

[ovidiuch]

Running yarn install in the root temporarily fixes the issue.

Hmm. It doesn't for me. I have to remove node_modules and install from scratch or add a new root dep to get the binaries back.

[panrafal]

Same here.
I will add, that it also happens if yarn add (or yarn install for that matter) are called inside the workspace.
The bin files are actually removed from the root, but show up (all of them) in the said workspace.

@skidding Try runnin yarn install --force

[ovidiuch]

@skidding Try runnin yarn install --force

Thanks. I remember trying this to not avail.

What works for me:

• rm -rf node_modules && yarn
• yarn add fooPackageIDontReallyNeed && yarn remove fooPackageIDontReallyNeed

Hope somebody finds the root cause for this though 🙏

[edmorley]

The log output for the yarn add lodash step when using --verbose includes many lines of form:

verbose 2.385 Removing extraneous file "C:\\Users\\Ed\\src\\yarn-bin-missing\\node_modules\\.bin".
verbose 2.402 Removing extraneous file "C:\\Users\\Ed\\src\\yarn-bin-missing\\node_modules\\acorn-globals\\node_modules".
verbose 2.404 Removing extraneous file "C:\\Users\\Ed\\src\\yarn-bin-missing\\node_modules\\babel-core\\node_modules".
...
verbose 2.439 Removing extraneous file "C:\\Users\\Ed\\src\\yarn-bin-missing\\node_modules\\jest\\node_modules\\.bin".

Looking at the Git log shows #4630 made some changes to the extraneous file removal code:
https://github.com/yarnpkg/yarn/pull/4630/files#diff-306a2caea89d886b11134fb770d1ebf6

@arcanis I don't suppose you might know what's happening in this case? :-)
(Also CC @jgoz)

[edmorley]

I wonder if this is related to:

2. it installs all other dependencies of my-workspace to /my-workspace/node_modules

(From #4513)

In this case, the workspace package has zero dependencies, so if it was overwriting the root node_modules I guess that would explain why the .bin was seen as extraneous.

There's also #4359 about issues with binary linking.

[jgoz]

I wonder if the root cause is that the bin links are being incorrectly determined after extraneous files are being removed (i.e., starting here: https://github.com/arcanis/yarn/blob/8ba49660fd96c4155af29e784a4891e2c263ce03/src/package-linker.js#L393).

Removing the bin links shouldn't be a problem as long as they are re-created properly, which isn't happening.

[bestander]

@jgoz you are on the right path.
I think this code has an error when determining the right set of top level binaries.
A PR is welcome