npm update seems to collide with itself

[aredridel]

:; npm update tap
npm ERR! gentlyRm containing path /Users/aredridel/Projects/npm/newww/node_modules/nyc/node_modules/rimraf isn't under npm's control
- minimatch@2.0.10 node_modules/nyc/node_modules/minimatch
- glob@5.0.14 node_modules/nyc/node_modules/glob
- minimist@0.0.8 node_modules/nyc/node_modules/minimist
- mkdirp@0.5.1 node_modules/nyc/node_modules/mkdirp
- nyc@2.4.0 node_modules/nyc
rimraf@2.4.3 node_modules/nyc/node_modules/rimraf -> node_modules/tap/node_modules/rimraf
newww@2.1.0 /Users/aredridel/Projects/npm/newww
├── gulp@3.9.0
├── gulp-nodemon@1.0.5
├── imagemin-pngcrush@1.0.0
├── numbat-emitter@1.1.3
├── numbat-process@2.0.7
└── request@2.60.0

npm ERR! Darwin 15.0.0
npm ERR! argv "node" "/usr/local/bin/npm" "update" "tap"
npm ERR! node v0.12.7
npm ERR! npm  v3.3.1
npm ERR! path /Users/aredridel/Projects/npm/newww/node_modules/nyc/node_modules/.bin/rimraf
npm ERR! code EEXIST

npm ERR! Refusing to delete: /Users/aredridel/Projects/npm/newww/node_modules/nyc/node_modules/.bin/rimraf not in /Users/aredridel/Projects/npm/newww/node_modules/nyc/node_modules/rimraf
File exists: /Users/aredridel/Projects/npm/newww/node_modules/nyc/node_modules/.bin/rimraf
Move it away, and try again.

npm ERR! Please include the following file with any support request:
npm ERR!     /Users/aredridel/Projects/npm/newww/npm-debug.log

Debug log:

https://gist.github.com/iarna/14edc840c236b7b872ec

[othiym23]

I would really love to get the install and update code paths unified (which really means unifying ls and outdated, at least in part). Based on what @iarna has shown me of the code, I believe I know what's going on here, but I'm not sure. This too is an issue for her, and this one feels higher-priority to me than #9473. We'll decide during our next triage meeting whether it's a blocker or not. Thanks for filing these, @aredridel!

[othiym23]

@aredridel your good friend and mine @iarna is going to dig into this further. For now, I'm marking this as a blocker, and leaving it to Rebecca's discretion to remove the label once she's got a feeling for how severe an issue this is. How many times have you run into this? / How reproducible is this?

[iarna]

I thought I had an idea on how to make this happen. I saw this happen once. But now, no, nope, no can reproduce, grr.

[iarna]

This may or may not be related to #9198. I mean, it's in the same code space.

[iarna]

Next up, to manufacture a tree that results in the same diff-set as the log... 😒

[ADTC]

My whole repo broke because of such complaints. Why can't npm delete the file? It's Windows btw, I hardly think permissions play a role here. What is the meaning of "file isn't under npm's control"?

It's always some file in a .bin folder, either a shell script or a .bat file.

npm-debug.log

[radekholy24]

I hit this always when deploying to Azure. My deployment script includes npm prune --production which fails with this error. The simplest reproducer is to create a new Azure App Service instance, log in using the Kudu's console, run npm install mkdirp and then npm rm mkdirp.
The version of NPM is supposedly 3.5.1 thus #9198 probably did not fix this.

[iarna]

This is/was an issue in gently-rm. We had additional fixes to it in v3.6.0` (from January 2016), so a further repro with a current version of npm would be much appreciated.

[npm-robot]

We're closing this issue as it has gone thirty days without activity. In our experience if an issue has gone thirty days without any activity then it's unlikely to be addressed. In the case of bug reports, often the underlying issue will be addressed but finding related issues is quite difficult and often incomplete.

If this was a bug report and it is still relevant then we encourage you to open it again as a new issue. If this was a feature request then you should feel free to open it again, or even better open a PR.

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