Uncaught Error: toString failed

[dnowacki-usgs]

I'm getting this error when trying to print a (rather large) variable. After the error, trying to run other lines gives a checkmark but no actual output.

Atom Version: 1.11.2
Electron Version: 0.37.8
System: Mac OS X 10.10.5
Thrown From: Hydrogen package, v0.15.0

Stack Trace

Uncaught Error: toString failed

At events.js:154

Error: toString failed
    at Buffer.toString (buffer.js:490:11)
    at toJSON (/Users/dnowacki/.atom/packages/Hydrogen/node_modules/jmp/index.js:225:33)
    at Function.Message._decode (/Users/dnowacki/.atom/packages/Hydrogen/node_modules/jmp/index.js:217:18)
    at Socket.<anonymous> (/Users/dnowacki/.atom/packages/Hydrogen/node_modules/jmp/index.js:330:35)
    at emitMany (events.js:121:13)
    at Socket.emit (events.js:195:7)
    at Socket._flushRead (/Users/dnowacki/.atom/packages/Hydrogen/node_modules/zmq/lib/index.js:638:15)
    at Socket._flushReads (/Users/dnowacki/.atom/packages/Hydrogen/node_modules/zmq/lib/index.js:676:23)
    at _zmq.onReadReady (/Users/dnowacki/.atom/packages/Hydrogen/node_modules/zmq/lib/index.js:297:10)

Commands

     -1:41.3.0 core:backspace (atom-text-editor.editor.is-focused)
     -1:40.9.0 hydrogen:run-and-move-down (atom-text-editor.editor.is-focused)
     -1:39.6.0 editor:newline (atom-text-editor.editor.is-focused)
     -1:37.5.0 hydrogen:run-and-move-down (atom-text-editor.editor.is-focused.autocomplete-active)
  9x -1:35.4.0 core:move-left (atom-text-editor.editor.is-focused)
     -1:32.6.0 editor:move-to-end-of-screen-line (atom-text-editor.editor.is-focused)
  2x -1:31.7.0 hydrogen:run-and-move-down (atom-text-editor.editor.is-focused)
  4x -1:04.6.0 core:move-up (atom-text-editor.editor.is-focused)
  5x -1:01.3.0 core:move-right (atom-text-editor.editor.is-focused)
     -1:00.2.0 core:move-left (atom-text-editor.editor.is-focused)
 18x -0:59.9.0 core:move-right (atom-text-editor.editor.is-focused)
  2x -0:54.8.0 core:backspace (atom-text-editor.editor.is-focused)
     -0:54.1.0 editor:move-to-first-character-of-line (atom-text-editor.editor.is-focused)
  4x -0:53.8.0 core:select-right (atom-text-editor.editor.is-focused)
     -0:52.8.0 core:backspace (atom-text-editor.editor.is-focused)
  2x -0:51.6.0 hydrogen:run-and-move-down (atom-text-editor.editor.is-focused)

Config

{
  "core": {
    "telemetryConsent": "no"
  },
  "Hydrogen": {
    "kernelspec": "{\"kernelspecs\":{\"python2\":{\"resource_dir\":\"/Users/dnowacki/anaconda/lib/python2.7/site-packages/ipykernel/resources\",\"spec\":{\"language\":\"python\",\"display_name\":\"Python 2\",\"env\":{},\"argv\":[\"/Users/dnowacki/anaconda/bin/python\",\"-m\",\"ipykernel\",\"-f\",\"{connection_file}\"]}}}}"
  }
}

Installed Packages

# User
Hydrogen, v0.15.0 (active)
atom-dark-syntax, v0.27.0 (inactive)
atom-dark-ui, v0.52.0 (inactive)
atom-light-syntax, v0.28.0 (inactive)
atom-light-ui, v0.44.0 (inactive)
base16-tomorrow-dark-theme, v1.2.0 (inactive)
base16-tomorrow-light-theme, v1.2.0 (inactive)
one-dark-ui, v1.6.0 (active)
one-light-ui, v1.6.0 (inactive)
one-dark-syntax, v1.3.0 (active)
one-light-syntax, v1.3.0 (inactive)
solarized-dark-syntax, v1.0.2 (inactive)
solarized-light-syntax, v1.0.2 (inactive)
about, v1.7.0 (active)
archive-view, v0.61.1 (active)
autocomplete-atom-api, v0.10.0 (active)
autocomplete-css, v0.11.2 (active)
autocomplete-html, v0.7.2 (active)
autocomplete-plus, v2.31.1 (active)
autocomplete-snippets, v1.11.0 (active)
autoflow, v0.27.0 (inactive)
autosave, v0.23.1 (active)
background-tips, v0.26.1 (active)
bookmarks, v0.42.0 (active)
bracket-matcher, v0.82.1 (active)
command-palette, v0.38.0 (inactive)
deprecation-cop, v0.54.1 (active)
dev-live-reload, v0.47.0 (active)
encoding-selector, v0.22.0 (active)
exception-reporting, v0.40.0 (active)
find-and-replace, v0.201.1 (inactive)
fuzzy-finder, v1.4.0 (active)
git-diff, v1.1.0 (active)
go-to-line, v0.31.0 (inactive)
grammar-selector, v0.48.2 (active)
image-view, v0.59.0 (active)
incompatible-packages, v0.26.1 (active)
keybinding-resolver, v0.35.0 (active)
line-ending-selector, v0.5.0 (active)
link, v0.31.1 (inactive)
markdown-preview, v0.158.0 (active)
metrics, v1.0.0 (active)
notifications, v0.65.1 (active)
open-on-github, v1.2.0 (inactive)
package-generator, v1.0.0 (inactive)
settings-view, v0.242.2-hotfix1 (active)
snippets, v1.0.2 (active)
spell-check, v0.68.2 (active)
status-bar, v1.4.1 (active)
styleguide, v0.47.0 (active)
symbols-view, v0.113.1 (inactive)
tabs, v0.101.0 (active)
timecop, v0.33.2 (active)
tree-view, v0.209.3 (active)
update-package-dependencies, v0.10.0 (active)
welcome, v0.35.1 (active)
whitespace, v0.33.0 (active)
wrap-guide, v0.38.2 (active)
language-c, v0.52.1 (active)
language-clojure, v0.21.0 (active)
language-coffee-script, v0.47.2 (active)
language-csharp, v0.12.1 (active)
language-css, v0.37.1 (active)
language-gfm, v0.88.0 (active)
language-git, v0.15.0 (active)
language-go, v0.42.1 (active)
language-html, v0.45.1 (active)
language-hyperlink, v0.16.0 (active)
language-java, v0.23.0 (active)
language-javascript, v0.119.0 (active)
language-json, v0.18.2 (active)
language-less, v0.29.5 (active)
language-make, v0.22.2 (active)
language-mustache, v0.13.0 (active)
language-objective-c, v0.15.1 (active)
language-perl, v0.35.0 (active)
language-php, v0.37.2 (active)
language-property-list, v0.8.0 (active)
language-python, v0.45.0 (active)
language-ruby, v0.69.0 (active)
language-ruby-on-rails, v0.25.0 (active)
language-sass, v0.56.0 (active)
language-shellscript, v0.22.4 (active)
language-source, v0.9.0 (active)
language-sql, v0.23.0 (active)
language-text, v0.7.1 (active)
language-todo, v0.28.0 (active)
language-toml, v0.18.0 (active)
language-xml, v0.34.9 (active)
language-yaml, v0.26.0 (active)

# Dev
No dev packages

[lgeiger]

@dnowacki-usgs Thanks for opening a issue.

This shouldn't happen but I can't reproduce it.

Could you post the exact command you are trying to run and a screenshot of the development console (cmd-alt-i)?

[n-riesco]

nodejs/node#4394

[dnowacki-usgs]

It may be some kind of timeout when printing a huge variable(?). In this case it's trying to print what was originally a Matlab .mat file. The file is loaded withscipy.io.loadmat, which results in a numpy.ndarray encapsulated in a dict or something like that. In any case, when trying to print one of the dict items, using say print matdata['dw1078araw'], does not do the typical "only print first/last few rows of huge array" behavior. Executing the same command in the Jupyter console requires several seconds before it spews out the result. Executing this command in Atom/hydrogen results in the toString error after several seconds.

Hopefully the development console screenshot below is helpful:

[n-riesco]

@dnowacki-usgs Node (and thus Atom) currently can't convert large buffers (larger than 192MB) into strings. See nodejs/node#4266 .

I've committed a workaround to the jmp repository, so that any messages that throw this exception are dropped. This change won't fix the issue with large buffers, but it should let you keep using Hydrogen.

I want to make a few more tests before making a new release of jmp with the workaround. Once I make the release, you'll have to reinstall Hydrogen, so that it picks up the latest version of jmp.

[n-riesco]

@dnowacki-usgs I've just published jmp@0.7.1 that works around this issue. If you have a chance to test it. Please, reinstall Hydrogen and post here whether printing a large output still renders the kernel unresponsive.

[dnowacki-usgs]

@n-riesco: Hmm, still throwing the error for me, and the kernel remains unresponsive. I uninstalled Hydrogen, restarted Atom, reinstalled Hydrogen, restarted Atom, and tested the same code with the same output. How can I test to make sure Hydrogen is using the latest jmp?

[lgeiger]

The latest version of jmp is only used in the development version of Hydrogen.

The fix will be released in Hydrogen 1.0.0 (soon). If you cannot wait, you can install the latest development version by following this steps: https://github.com/nteract/hydrogen#development.
Sorry for the confusion.