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jupyter / atom-notebook

[Deprecated] Jupyter Notebook, but inside Atom.
MIT License
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Install Failed, #32

Closed alexkowalenko closed 8 years ago

alexkowalenko commented 8 years ago

Attempted to install the plugin for atom, but it failed. The following is the log.

runas@3.1.1 install /private/var/folders/1q/d5rjn3_s18n7_14kf_h7f2gh0000gn/T/apm-install-dir-11611-60365-igono9/node_modules/jupyter-notebook/node_modules/pathwatcher/node_modules/runas node-gyp rebuild

CXX(target) Release/obj.target/runas/src/main.o CXX(target) Release/obj.target/runas/src/runas_darwin.o CXX(target) Release/obj.target/runas/src/fork.o SOLINK_MODULE(target) Release/runas.node

bufferutil@1.2.1 install /private/var/folders/1q/d5rjn3_s18n7_14kf_h7f2gh0000gn/T/apm-install-dir-11611-60365-igono9/node_modules/jupyter-notebook/node_modules/ws/node_modules/bufferutil node-gyp rebuild

CXX(target) Release/obj.target/bufferutil/src/bufferutil.o SOLINK_MODULE(target) Release/bufferutil.node

utf-8-validate@1.2.1 install /private/var/folders/1q/d5rjn3_s18n7_14kf_h7f2gh0000gn/T/apm-install-dir-11611-60365-igono9/node_modules/jupyter-notebook/node_modules/ws/node_modules/utf-8-validate node-gyp rebuild

CXX(target) Release/obj.target/validation/src/validation.o SOLINK_MODULE(target) Release/validation.node

jupyter-js-utils@0.2.17 postinstall /private/var/folders/1q/d5rjn3_s18n7_14kf_h7f2gh0000gn/T/apm-install-dir-11611-60365-igono9/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils npm dedupe

pathwatcher@6.3.1 install /private/var/folders/1q/d5rjn3_s18n7_14kf_h7f2gh0000gn/T/apm-install-dir-11611-60365-igono9/node_modules/jupyter-notebook/node_modules/pathwatcher node-gyp rebuild

CXX(target) Release/obj.target/pathwatcher/src/main.o CXX(target) Release/obj.target/pathwatcher/src/common.o CXX(target) Release/obj.target/pathwatcher/src/handle_map.o CXX(target) Release/obj.target/pathwatcher/src/pathwatcher_unix.o SOLINK_MODULE(target) Release/pathwatcher.node

sh: npm: command not found npm ERR! Darwin 15.3.0 npm ERR! argv "/Applications/Atom.app/Contents/Resources/app/apm/bin/node" "/Applications/Atom.app/Contents/Resources/app/apm/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/Users/alex/.atom/.apm/.apmrc" "--userconfig" "/Users/alex/.atom/.apmrc" "install" "/private/var/folders/1q/d5rjn3_s18n7_14kf_h7f2gh0000gn/T/d-11611-60365-1gvbub4/package.tgz" "--target=0.34.5" "--arch=x64" npm ERR! node v0.10.40 npm ERR! npm v2.13.3 npm ERR! file sh npm ERR! code ELIFECYCLE npm ERR! errno ENOENT npm ERR! syscall spawn

npm ERR! jupyter-js-utils@0.2.17 postinstall: npm dedupe npm ERR! spawn ENOENT npm ERR! npm ERR! Failed at the jupyter-js-utils@0.2.17 postinstall script 'npm dedupe'. npm ERR! This is most likely a problem with the jupyter-js-utils package, npm ERR! not with npm itself. npm ERR! Tell the author that this fails on your system: npm ERR! npm dedupe npm ERR! You can get their info via: npm ERR! npm owner ls jupyter-js-utils npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request: npm ERR! /private/var/folders/1q/d5rjn3_s18n7_14kf_h7f2gh0000gn/T/apm-install-dir-11611-60365-igono9/npm-debug.log

johnxllis commented 8 years ago

Same issue here on both OS X El Captian and Ubuntu 14.04.

gnestor commented 8 years ago

Try PYTHON=python2 apm install

kfix commented 8 years ago

Atom 1.5.3 on OSX 10.11.3

$ apm -v
apm  1.6.0
npm  2.13.3
node 0.10.40
python 2.7.10
git 2.7.0

$ apm install jupyter-notebook
Installing jupyter-notebook to /Users/jkorkames/.atom/packages ✗

> runas@3.1.1 install /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/pathwatcher/node_modules/runas
> node-gyp rebuild

  CXX(target) Release/obj.target/runas/src/main.o
  CXX(target) Release/obj.target/runas/src/runas_darwin.o
  CXX(target) Release/obj.target/runas/src/fork.o
  SOLINK_MODULE(target) Release/runas.node

> bufferutil@1.2.1 install /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/ws/node_modules/bufferutil
> node-gyp rebuild

  CXX(target) Release/obj.target/bufferutil/src/bufferutil.o
  SOLINK_MODULE(target) Release/bufferutil.node

> utf-8-validate@1.2.1 install /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/ws/node_modules/utf-8-validate
> node-gyp rebuild

  CXX(target) Release/obj.target/validation/src/validation.o
  SOLINK_MODULE(target) Release/validation.node

> jupyter-js-utils@0.3.2 postinstall /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils
> npm dedupe

> pathwatcher@6.3.1 install /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/pathwatcher
> node-gyp rebuild

  CXX(target) Release/obj.target/pathwatcher/src/main.o
  CXX(target) Release/obj.target/pathwatcher/src/common.o
  CXX(target) Release/obj.target/pathwatcher/src/handle_map.o
  CXX(target) Release/obj.target/pathwatcher/src/pathwatcher_unix.o
  SOLINK_MODULE(target) Release/pathwatcher.node

> jupyter-js-services@0.5.1 postinstall /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services
> npm dedupe

minimist@1.2.0 node_modules/jupyter-js-utils/node_modules/minimist -> node_modules/minimist
requirejs@2.1.22 node_modules/jupyter-js-utils/node_modules/requirejs -> node_modules/requirejs

npm ERR! Darwin 15.3.0
npm ERR! argv "node" "/usr/local/bin/npm" "dedupe"
npm ERR! node v0.10.40
npm ERR! npm  v3.5.3
npm ERR! path /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils/node_modules/.bin/r.js
npm ERR! code EEXIST

npm ERR! Refusing to delete /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils/node_modules/.bin/r.js: containing path /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils/node_modules/requirejs isn't under npm's control
npm ERR! File exists: /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils/node_modules/.bin/r.js
npm ERR! Move it away, and try again.

npm ERR! Please include the following file with any support request:
npm ERR!     /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services/npm-debug.log
npm ERR! Darwin 15.3.0
npm ERR! argv "/opt/homebrew-cask/Caskroom/atom/1.0.2/Atom.app/Contents/Resources/app/apm/bin/node" "/opt/homebrew-cask/Caskroom/atom/1.0.2/Atom.app/Contents/Resources/app/apm/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/Users/jkorkames/.atom/.apm/.apmrc" "--userconfig" "/Users/jkorkames/.atom/.apmrc" "install" "/private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/d-116116-9700-ksanl3/package.tgz" "--target=0.34.5" "--arch=x64"
npm ERR! node v0.10.40
npm ERR! npm  v2.13.3
npm ERR! code ELIFECYCLE

npm ERR! jupyter-js-services@0.5.1 postinstall: `npm dedupe`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the jupyter-js-services@0.5.1 postinstall script 'npm dedupe'.
npm ERR! This is most likely a problem with the jupyter-js-services package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     npm dedupe
npm ERR! You can get their info via:
npm ERR!     npm owner ls jupyter-js-services
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR!     /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/npm-debug.log```
kfix commented 8 years ago

& within Atom's installer GUI:

> runas@3.1.1 install /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-8859-wynld/node_modules/jupyter-notebook/node_modules/pathwatcher/node_modules/runas
> node-gyp rebuild

  CXX(target) Release/obj.target/runas/src/main.o
  CXX(target) Release/obj.target/runas/src/runas_darwin.o
  CXX(target) Release/obj.target/runas/src/fork.o
  SOLINK_MODULE(target) Release/runas.node

> utf-8-validate@1.2.1 install /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-8859-wynld/node_modules/jupyter-notebook/node_modules/ws/node_modules/utf-8-validate
> node-gyp rebuild

  CXX(target) Release/obj.target/validation/src/validation.o
  SOLINK_MODULE(target) Release/validation.node

> bufferutil@1.2.1 install /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-8859-wynld/node_modules/jupyter-notebook/node_modules/ws/node_modules/bufferutil
> node-gyp rebuild

  CXX(target) Release/obj.target/bufferutil/src/bufferutil.o
  SOLINK_MODULE(target) Release/bufferutil.node

> jupyter-js-utils@0.3.2 postinstall /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-8859-wynld/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils
> npm dedupe

> pathwatcher@6.3.1 install /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-8859-wynld/node_modules/jupyter-notebook/node_modules/pathwatcher
> node-gyp rebuild

  CXX(target) Release/obj.target/pathwatcher/src/main.o
  CXX(target) Release/obj.target/pathwatcher/src/common.o
  CXX(target) Release/obj.target/pathwatcher/src/handle_map.o
  CXX(target) Release/obj.target/pathwatcher/src/pathwatcher_unix.o
  SOLINK_MODULE(target) Release/pathwatcher.node

sh: npm: command not found
npm ERR! Darwin 15.3.0
npm ERR! argv "/opt/homebrew-cask/Caskroom/atom/1.0.2/Atom.app/Contents/Resources/app/apm/bin/node" "/opt/homebrew-cask/Caskroom/atom/1.0.2/Atom.app/Contents/Resources/app/apm/node_modules/npm/bin/npm-cli.js" "--globalconfig" "/Users/jkorkames/.atom/.apm/.apmrc" "--userconfig" "/Users/jkorkames/.atom/.apmrc" "install" "/private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/d-116116-8859-xbypvv/package.tgz" "--target=0.34.5" "--arch=x64"
npm ERR! node v0.10.40
npm ERR! npm  v2.13.3
npm ERR! file sh
npm ERR! code ELIFECYCLE
npm ERR! errno ENOENT
npm ERR! syscall spawn

npm ERR! jupyter-js-utils@0.3.2 postinstall: `npm dedupe`
npm ERR! spawn ENOENT
npm ERR! 
npm ERR! Failed at the jupyter-js-utils@0.3.2 postinstall script 'npm dedupe'.
npm ERR! This is most likely a problem with the jupyter-js-utils package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     npm dedupe
npm ERR! You can get their info via:
npm ERR!     npm owner ls jupyter-js-utils
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR!     /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-8859-wynld/npm-debug.log
gnestor commented 8 years ago

This looks like a relevant line: 

npm ERR! File exists: /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils/node_modules/.bin/r.js
npm ERR! Move it away, and try again.

Try removing that file using rm /private/var/folders/m8/l0gl08bj0zn4zpck62hn3yv40000gp/T/apm-install-dir-116116-9700-1f2m3ac/node_modules/jupyter-notebook/node_modules/jupyter-js-services/node_modules/jupyter-js-utils/node_modules/.bin/r.js and reinstalling.

If that doesn't work, we should probably open an issue on jupyter-js-utils: npm ERR! Failed at the jupyter-js-utils@0.3.2 postinstall script 'npm dedupe'.

kfix commented 8 years ago

the /tmp folder is created and destroyed with each apm install run, nothing I can clean up for it. npm v2 is so old that I'm not surprised that npm-dedupe is being buggy. its a :imp: move for jupyter-js-utils's postinstall to use it, but maybe atom/apm should upgrade its npm.

rgbkrk commented 8 years ago

its a :imp: move for jupyter-js-utils's postinstall to use it

Agreed.

blink1073 commented 8 years ago

This looks like a permissions issue, where npm dedupe isn't being allowed to run properly. We are using npm dedupe specifically to overcome limitations in npm resolution logic in older versions.

kfix commented 8 years ago

I used TMPDIR=~/.atom/.apm-tmp apm install jupyter-notebook to try and get better perms. no change. additionally, all the debug logs still get blown away from that TMPDIR. npm's log dir is completely unconfigurable. @blink1073 what are the limitations that dedupe is being utilized to work around?

blink1073 commented 8 years ago

Dedupe avoids having duplicate versions of libraries in node_modules, and is a standard npm command.

rgbkrk commented 8 years ago

While npm dedupe saves disk space, it is currently causing friction with users. Putting commands in postinstall tends to be bad practice for userland as well.

Options:

  1. Rely on peerDependencies. End user applications have to list these peer deps within their primary dependencies.
  2. Use dedupe only at the stage of live code/user space (server, command line tool, stitched together front end).
  3. Use a different package that doesn't bother with the dedupe.
blink1073 commented 8 years ago

@rgbkrk, the reason we need dedupe is not to save disk space, but to ensure that isinstance Foo works, which is not the case if you have different versions of the same library loaded with different versions of the same class.

rgbkrk commented 8 years ago

Oh, ok. Peer deps would be the idiomatic and safe way of handling that then.

blink1073 commented 8 years ago

Thanks Kyle, I'll give that a try on Monday.

Ken0sis commented 8 years ago

I just tried to install this package and having the same error. This package looks great, and hope next update will address issue.

blink1073 commented 8 years ago

I released jupyter-js-utils@0.3.3, which avoids npm dedupe.

Ken0sis commented 8 years ago

Thank you for the update. It fixed the problem and allowed me to install. I just can't get it to open .ipynb files right now because it keeps complaining about not having jupyter session (which I did run from terminal). Probably just something on my end and I need to learn how this jupyter package works.

Thanks again for the work on update!

gnestor commented 8 years ago

Now you need to make sure that the path to your Jupyter binary is in Atom's path or in the jupyter-notebook settings. The package will run an instance of Jupyter Kernel Gateway for you, so you don't need to run an instance of it or Jupyter Notebook yourself.

kfix commented 8 years ago

jupyter-notebook Installs and runs for me now. Thanks @blink1073 @rgbkrk @gnestor !

gnestor commented 8 years ago

Good news! 👍👍