hydrogen: Can't update to 2.15.3 on Ubuntu

Prerequisites

Have you checked the solutions in our troubleshooting guide for common problems ?
- Enable Debug Messages isn’t useful in this case, is it?
Have you checked that your issue isn’t already filed ?
- #2090 is very similar, but IDK if it’s the same thing due to different distro and different Atom version. By all means, close this as a duplicate if needed.

Description

Can’t update to Hydrogen 2.15.3 on Linux

Steps to Reproduce

Try to update Hydrogen

Versions

OS version: Ubuntu 18.04.5 Kernel: Linux 4.15.0-142-generic Architecture: x86-64

$ atom --version
Atom    : 1.56.0
Electron: 9.4.4
Chrome  : 83.0.4103.122
Node    : 12.14.1

$ apm --version
apm  2.5.2
npm  6.14.8
node 12.4.0 x64
atom 1.56.0
python 2.7.17
git 2.17.1

Hydrogen version:

Atom says 2.14.7, but apm show hydrogen says 2.15.3.

Plugins

Have you installed and activated any of the Hydrogen plugins below ?

hydrogen-python
Hydrogen Launcher
Data Explorer

Logs

error.txt
- Part of it’s in French. “on entre dans le répertoire” means “entering directory” and “on quitte le répertoire” means “leaving directory”
2021-04-17T17_09_39_908Z-debug.log

Expected behavior

Update Hydrogen

Screenshots

Capture d’écran de 2021-04-17 13-45-02

Additional context

(none)

About this issue

Original URL
State: closed
Created 3 years ago
Comments: 22 (8 by maintainers)

Most upvoted comments

This looks like it has been resolved, but I get a similar error related to zeromq when trying to install Hydrogen on Manjaro (Linux 5.13.19-2-MANJARO and x86-64 architecture).

After re-installing zeromq with sudo pacman -S zeromq I ran

$ npm_config_zmq_external=true apm install hydrogen

which gave

Installing hydrogen to /home/julsy/.atom/packages [31m✗
[39m[31m
> @aminya/zeromq@5.2.16 install /tmp/apm-install-dir-20211115-89062-1taj1mg.0feo/node_modules/Hydrogen/node_modules/@aminya/zeromq
> node-gyp-build || npm run build:libzmq


> @aminya/zeromq@5.2.16 build:libzmq
> node-gyp rebuild


npm WARN deprecated uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
npm WARN deprecated json-parser@1.1.5: `json-parser` is deprecated. Please use `comment-json` instead
npm WARN deprecated popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
(node:89106) [DEP0150] DeprecationWarning: Setting process.config is deprecated. In the future the property will be read-only.
(Use `node --trace-deprecation ...` to show where the warning was created)
gyp: name 'openssl_fips' is not defined while evaluating condition 'openssl_fips != ""' in binding.gyp while trying to load binding.gyp
gyp ERR! configure error 
gyp ERR! stack Error: `gyp` failed with exit code: 1
gyp ERR! stack     at ChildProcess.onCpExit (/usr/lib/node_modules/atom-package-manager/node_modules/npm/node_modules/node-gyp/lib/configure.js:351:16)
gyp ERR! stack     at ChildProcess.emit (node:events:390:28)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (node:internal/child_process:290:12)
gyp ERR! System Linux 5.13.19-2-MANJARO
gyp ERR! command "/usr/bin/node" "/usr/lib/node_modules/atom-package-manager/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /tmp/apm-install-dir-20211115-89062-1taj1mg.0feo/node_modules/Hydrogen/node_modules/@aminya/zeromq
gyp ERR! node -v v17.1.0
gyp ERR! node-gyp -v v5.1.0
gyp ERR! not ok 
gyp: name 'openssl_fips' is not defined while evaluating condition 'openssl_fips != ""' in binding.gyp while trying to load binding.gyp
gyp ERR! configure error 
gyp ERR! stack Error: `gyp` failed with exit code: 1
gyp ERR! stack     at ChildProcess.onCpExit (/usr/lib/node_modules/node-gyp/lib/configure.js:353:16)
gyp ERR! stack     at ChildProcess.emit (node:events:390:28)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (node:internal/child_process:290:12)
gyp ERR! System Linux 5.13.19-2-MANJARO
gyp ERR! command "/usr/bin/node" "/usr/lib/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /tmp/apm-install-dir-20211115-89062-1taj1mg.0feo/node_modules/Hydrogen/node_modules/@aminya/zeromq
gyp ERR! node -v v17.1.0
gyp ERR! node-gyp -v v8.2.0
gyp ERR! not ok 
npm WARN enoent ENOENT: no such file or directory, open '/tmp/apm-install-dir-20211115-89062-1taj1mg.0feo/package.json'
npm WARN mobx-react@6.3.1 requires a peer of react@^16.8.0 || 16.9.0-alpha.0 but none is installed. You must install peer dependencies yourself.
npm WARN @nteract/markdown@4.6.2 requires a peer of react@^16.11.0 but none is installed. You must install peer dependencies yourself.
npm WARN @nteract/markdown@4.6.2 requires a peer of react-dom@^16.3.2 but none is installed. You must install peer dependencies yourself.
npm WARN @nteract/transform-vega@7.0.10 requires a peer of react@^16.3.2 but none is installed. You must install peer dependencies yourself.
npm WARN @nteract/outputs@3.0.11 requires a peer of react@^16.3.2 but none is installed. You must install peer dependencies yourself.
npm WARN react-table@6.11.5 requires a peer of react@^16.x.x but none is installed. You must install peer dependencies yourself.
npm WARN react-table@6.11.5 requires a peer of react-dom@^16.x.x but none is installed. You must install peer dependencies yourself.
npm WARN react-markdown@4.3.1 requires a peer of react@^15.0.0 || ^16.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN @nteract/presentational-components@3.4.12 requires a peer of react@^16.3.2 but none is installed. You must install peer dependencies yourself.
npm WARN react-json-tree@0.12.1 requires a peer of react@^16.3.0 but none is installed. You must install peer dependencies yourself.
npm WARN react-json-tree@0.12.1 requires a peer of react-dom@^16.3.0 but none is installed. You must install peer dependencies yourself.
npm WARN mobx-react-lite@2.2.2 requires a peer of react@^16.8.0 but none is installed. You must install peer dependencies yourself.
npm WARN apm-install-dir-20211115-89062-1taj1mg.0feo No description
npm WARN apm-install-dir-20211115-89062-1taj1mg.0feo No repository field.
npm WARN apm-install-dir-20211115-89062-1taj1mg.0feo No README data
npm WARN apm-install-dir-20211115-89062-1taj1mg.0feo No license field.

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! @aminya/zeromq@5.2.16 install: `node-gyp-build || npm run build:libzmq`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the @aminya/zeromq@5.2.16 install script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/julsy/.atom/.apm/_logs/2021-12-15T08_32_41_497Z-debug.log
[39m

The complete log is here: hydrogen-error.log

atom --version returns

Atom    : 1.58.0
Electron: 9.4.4
Chrome  : 83.0.4103.122
Node    : 12.14.1

and apm --version

apm  2.6.4
npm  6.14.9
node 17.1.0 x64
atom 1.58.0
python 3.9.7
git 2.34.1

I’m not really a JS aficionado. Any idea on how I can fix this?

julibeg on Dec 15, 2021

@n-riesco Could you remove hydrogen, and then clone the master branch, and try to run the tests?

git clone https://github.com/nteract/hydrogen.git
cd hydrogen
apm install --verbose
npm run build
npm run test

I think this time the source build passes, but still, it doesn’t find the correct prebuilds?

aminya on Apr 18, 2021

@aminya I’ve edited package.json so that install invokes node-gyp-build-test. This shows that we need the prebuilt for ABI 72 (Atom v1.56.0 comes with node v12.14.1, i.e. ABI 72).

$ apm install --verbose
Installing modules 
> @aminya/zeromq@5.2.15 install /home/nriesco/.atom/packages/Hydrogen/node_modules/@aminya/zeromq
> node-gyp-build-test || npm run build:libzmq

internal/modules/cjs/loader.js:815
  return process.dlopen(module, path.toNamespacedPath(filename));
                 ^

Error: The module '/home/nriesco/.atom/packages/Hydrogen/node_modules/@aminya/zeromq/build/Release/zmq.node'
was compiled against a different Node.js version using
NODE_MODULE_VERSION 80. This version of Node.js requires
NODE_MODULE_VERSION 72. Please try re-compiling or re-installing
the module (for instance, using `npm rebuild` or `npm install`).
    at Object.Module._extensions..node (internal/modules/cjs/loader.js:815:18)
    at Module.load (internal/modules/cjs/loader.js:641:32)
    at Function.Module._load (internal/modules/cjs/loader.js:556:12)
    at Module.require (internal/modules/cjs/loader.js:681:19)
    at require (internal/modules/cjs/helpers.js:16:16)
    at load (/home/nriesco/.atom/packages/Hydrogen/node_modules/@aminya/zeromq/node_modules/node-gyp-build/index.js:21:10)
    at Object.<anonymous> (/home/nriesco/.atom/packages/Hydrogen/node_modules/@aminya/zeromq/node_modules/node-gyp-build/build-test.js:19:19)
    at Module._compile (internal/modules/cjs/loader.js:774:30)
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:785:10)
    at Module.load (internal/modules/cjs/loader.js:641:32)

n-riesco on Apr 18, 2021