hydrogen 🚀 - Hydrogen crashes after updating Atom (ZeroMQ build fails on Electron 9)

hydrogen cannot be install after update atom to 1.56.0

asiloisad on 14 Apr 2021

Is that your observation or a known (recent) issue? Could you please give me some details ?

massimilianocomin on 14 Apr 2021

I don't know exactly what's wrong but I have kinda the same issue. I believe the problem is the last update of Atom in which they updated electron

jMazek on 14 Apr 2021

I have the same issue. Hydrogen won't install after updating Atom to 1.56.0 x64

[email protected] install C:\Users\lizmo\AppData\Local\Temp\apm-install-dir-2021314-4028-d9ufx7.ct94n\node_modules\Hydrogen\node_modules\zeromq
node scripts/prebuild-install.js || (node scripts/preinstall.js && node-gyp rebuild)

prebuild-install WARN install No prebuilt binaries found (target=9.4.4 runtime=electron arch=x64 libc= platform=win32)

Downloading libzmq for Windows
Download finished

C:\Users\lizmo\AppData\Local\Temp\apm-install-dir-2021314-4028-d9ufx7.ct94n\node_modules\Hydrogen\node_modules\zeromq>if not defined npm_config_node_gyp (node "C:\Users\lizmo\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modulesnpm-lifecycle\node-gyp-bin\....\node_modules\node-gyp\bin\node-gyp.js" rebuild ) else (node "C:\Users\lizmo\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\bin\node-gyp.js" rebuild )
Building the projects in this solution one at a time. To enable parallel build, please add the "-m" switch.
C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(439,5): error MSB8020: The build tools for Visual Studio 2015 (Platform Toolset = 'v140') cannot be found. To build using the v140 build tools, please install Visual Studio 2015 build tools. Alternatively, you may upgrade to the current Visual Studio tools by selecting the Project menu or right-click the solution, and then selecting "Retarget solution". [C:\Users\lizmo\AppData\Local\Temp\apm-install-dir-2021314-4028-d9ufx7.ct94n\node_modules\Hydrogen\node_modules\zeromq\build\zmq.vcxproj]

npm WARN deprecated [email protected]: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
npm WARN deprecated [email protected]: json-parser is deprecated. Please use comment-json instead
npm WARN deprecated popper.[email protected]: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
npm WARN deprecated highlight.[email protected]: Version no longer supported. Upgrade to @latest
gyp ERR! build error
gyp ERR! stack Error: C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\MSBuild\Current\Bin\MSBuild.exe failed with exit code: 1
gyp ERR! stack at ChildProcess.onExit (C:\Users\lizmo\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\lib\build.js:194:23)
gyp ERR! stack at ChildProcess.emit (events.js:200:13)
gyp ERR! stack at Process.ChildProcess._handle.onexit (internal/child_process.js:272:12)
gyp ERR! System Windows_NT 10.0.19042
gyp ERR! command "C:\Users\lizmo\AppData\Local\atom\app-1.56.0\resources\app\apm\bin\node.exe" "C:\Users\lizmo\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modules\npm\node_modules\node-gyp\bin\node-gyp.js" "rebuild"
gyp ERR! cwd C:\Users\lizmo\AppData\Local\Temp\apm-install-dir-2021314-4028-d9ufx7.ct94n\node_modules\Hydrogen\node_modules\zeromq
gyp ERR! node -v v12.4.0
gyp ERR! node-gyp -v v5.1.0
gyp ERR! not ok
npm WARN enoent ENOENT: no such file or directory, open 'C:\Users\lizmo\AppData\Local\Temp\apm-install-dir-2021314-4028-d9ufx7.ct94n\package.json'
npm WARN apm-install-dir-2021314-4028-d9ufx7.ct94n No description
npm WARN apm-install-dir-2021314-4028-d9ufx7.ct94n No repository field.
npm WARN apm-install-dir-2021314-4028-d9ufx7.ct94n No README data
npm WARN apm-install-dir-2021314-4028-d9ufx7.ct94n No license field.

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] install: node scripts/prebuild-install.js || (node scripts/preinstall.js && node-gyp rebuild)
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the [email protected] 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! C:\Users\lizmo.atom.apm_logs\2021-04-14T16_40_02_195Z-debug.log

liz-muehlmann on 14 Apr 2021

Getting a similar issue given the Atom update. Encountering an error when rebuilding Hydrogen. This has repeatedly occurred in the past whenever Atom updates and makes Atom unusable.

rhhyon on 14 Apr 2021

Same issue here.. =(

vandertilt on 14 Apr 2021

I`ve got the same error!
Looks like the electron update crash Hydrogen(Atom update 1.56.0)

OxQwerty on 14 Apr 2021

I have the same issue. Hydrogen will crash the editor whenever a new kernel is called on.
Mac OSX 11.1
% atom --version
Atom : 1.56.0
Electron: 9.4.4
Chrome : 83.0.4103.122
Node : 12.14.1

Hydrogen: 2.14.7

msw2171 on 14 Apr 2021

Same trouble here :(

Error report is the same as above for windows 10.

Curiously, installing an older version of atom doesn't work either... I guess if electron is the problem, older versions of atom/hydrogen don't default to a corresponding old release of electron?

I tried atom 15.0 and 14.0.

IanRMOReilly on 14 Apr 2021

after return to atom 1.55.0 x64 (https://github.com/atom/atom/releases/tag/v1.55.0) + hydrogen 2.14.7 everything work correctly. make sure you uncheck the auto-update atom options (Help/About Atom) and rebuild (or reinstall) hydrogen. we have to wait for fix for atom 1.56.0 :/

asiloisad on 14 Apr 2021

after return to atom 1.55.0 x64 (https://github.com/atom/atom/releases/tag/v1.55.0) + hydrogen 2.14.7 everything work correctly. make sure you uncheck the auto-update atom options (Help/About Atom) and rebuild (or reinstall) hydrogen. we have to wait for fix for atom 1.56.0 :/

Thanks for your help! Could you explain how to download atom 1.55.0?

rhhyon on 14 Apr 2021

@asiloisad I have the same versions listed, but still crashing. Any suggestions?

"""
gyp ERR! find VS
gyp ERR! find VS msvs_version not set from command line or npm config
gyp ERR! find VS VCINSTALLDIR not set, not running in VS Command Prompt
gyp ERR! find VS could not use PowerShell to find Visual Studio 2017 or newer
gyp ERR! find VS looking for Visual Studio 2015
gyp ERR! find VS - not found
gyp ERR! find VS not looking for VS2013 as it is only supported up to Node.js 8
gyp ERR! find VS
gyp ERR! find VS *******************
gyp ERR! find VS You need to install the latest version of Visual Studio
gyp ERR! find VS including the "Desktop development with C++" workload.
gyp ERR! find VS For more information consult the documentation at:
gyp ERR! find VS https://github.com/nodejs/node-gyp#on-windows
gyp ERR! find VS *******************
gyp ERR! find VS
gyp ERR! configure error
gyp ERR! stack Error: Could not find any Visual Studio installation to use
gyp ERR! stack at VisualStudioFinder.fail (C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\lib\find-visualstudio.js:121:47)
gyp ERR! stack at C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\lib\find-visualstudio.js:74:16
gyp ERR! stack at VisualStudioFinder.findVisualStudio2013 (C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\lib\find-visualstudio.js:351:14)
gyp ERR! stack at C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\lib\find-visualstudio.js:70:14
gyp ERR! stack at C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\lib\find-visualstudio.js:372:16
gyp ERR! stack at C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\lib\util.js:54:7
gyp ERR! stack at C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modulesnpm\node_modules\node-gyp\lib\util.js:33:16
gyp ERR! stack at ChildProcess.exithandler (child_process.js:297:5)
gyp ERR! stack at ChildProcess.emit (events.js:200:13)
gyp ERR! stack at maybeClose (internal/child_process.js:1021:16)
gyp ERR! System Windows_NT 10.0.17763
gyp ERR! command "C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\bin\node.exe" "C:\Users\FK143VT\AppData\Local\atom\app-1.56.0\resources\app\apm\node_modules\npm\node_modules\node-gyp\bin\node-gyp.js" "rebuild"
gyp ERR! cwd C:\Users\FK143VT.atom\packages\Hydrogen\node_modules\zeromq
gyp ERR! node -v v12.4.0
gyp ERR! node-gyp -v v5.1.0
gyp ERR! not ok
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] install: node scripts/prebuild-install.js || (node scripts/preinstall.js && node-gyp rebuild)
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the [email protected] 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! C:\Users\FK143VT.atom.apm_logs\2021-04-14T14_30_52_844Z-debug.log
"""

IanRMOReilly on 14 Apr 2021

Thanks for your help! Could you explain how to download atom 1.55.0?

Release is here:
https://github.com/atom/atom/releases/tag/v1.55.0

Download the appropriate setup script and run. If windows x64 like me it is AtomSetup-x64.exe.

However, this procedure did not work for me, so be warned.

IanRMOReilly on 14 Apr 2021

@IanRMOReilly the error message you posted is still 1.56.0.

And thanks for sharring the link to 1.55.0.

n-riesco on 14 Apr 2021

@n-riesco Aha! Good call, thanks for spotting that. After a fresh install you have to hit the "Rebuild package" button, otherwise it still thinks you are on 1.56.0.

All green for me. Thanks for the help

IanRMOReilly on 14 Apr 2021

I am still having hydrogen failures after going to 1.55.0, turning off auto-updates, and trying to reinstall hydrogen:

Installing “[email protected]” failed.Hide output…

> [email protected] install C:\Users\Andrew\AppData\Local\Temp\apm-install-dir-2021314-16432-1gou4ci.clin\node_modules\Hydrogen\node_modules\zeromq
> node scripts/prebuild-install.js || (node scripts/preinstall.js && node-gyp rebuild)


prebuild-install WARN install No prebuilt binaries found (target=6.1.12 runtime=electron arch=x64 libc= platform=win32)

Downloading libzmq for Windows
Download finished

(mcmc) C:\Users\Andrew\AppData\Local\Temp\apm-install-dir-2021314-16432-1gou4ci.clin\node_modules\Hydrogen\node_modules\zeromq>if not defined npm_config_node_gyp (node "C:\Users\Andrew\AppData\Local\atom\app-1.55.0\resources\app\apm\node_modules\npm\node_modules\npm-lifecycle\node-gyp-bin\\..\..\node_modules\node-gyp\bin\node-gyp.js" rebuild )  else (node "C:\Users\Andrew\AppData\Local\atom\app-1.55.0\resources\app\apm\node_modules\npm\node_modules\node-gyp\bin\node-gyp.js" rebuild ) 
Building the projects in this solution one at a time. To enable parallel build, please add the "/m" switch.
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Platforms\x64\PlatformToolsets\v140\Toolset.targets(36,5): error MSB8036: The Windows SDK version 8.1 was not found. Install the required version of Windows SDK or change the SDK version in the project property pages or by right-clicking the solution and selecting "Retarget solution". [C:\Users\Andrew\AppData\Local\Temp\apm-install-dir-2021314-16432-1gou4ci.clin\node_modules\Hydrogen\node_modules\zeromq\build\zmq.vcxproj]

npm WARN deprecated [email protected]: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
npm WARN deprecated [email protected]: `json-parser` is deprecated. Please use `comment-json` instead
npm WARN deprecated [email protected]: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
gyp ERR! build error 
gyp ERR! stack Error: `C:\Program Files (x86)\MSBuild\14.0\bin\MSBuild.exe` failed with exit code: 1
gyp ERR! stack     at ChildProcess.onExit (C:\Users\Andrew\AppData\Local\atom\app-1.55.0\resources\app\apm\node_modules\npm\node_modules\node-gyp\lib\build.js:194:23)
gyp ERR! stack     at ChildProcess.emit (events.js:200:13)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:272:12)
gyp ERR! System Windows_NT 10.0.19041
gyp ERR! command "C:\\Users\\Andrew\\AppData\\Local\\atom\\app-1.55.0\\resources\\app\\apm\\bin\\node.exe" "C:\\Users\\Andrew\\AppData\\Local\\atom\\app-1.55.0\\resources\\app\\apm\\node_modules\\npm\\node_modules\\node-gyp\\bin\\node-gyp.js" "rebuild"
gyp ERR! cwd C:\Users\Andrew\AppData\Local\Temp\apm-install-dir-2021314-16432-1gou4ci.clin\node_modules\Hydrogen\node_modules\zeromq
gyp ERR! node -v v12.4.0
gyp ERR! node-gyp -v v5.1.0
gyp ERR! not ok 
npm WARN enoent ENOENT: no such file or directory, open 'C:\Users\Andrew\AppData\Local\Temp\apm-install-dir-2021314-16432-1gou4ci.clin\package.json'
npm WARN apm-install-dir-2021314-16432-1gou4ci.clin No description
npm WARN apm-install-dir-2021314-16432-1gou4ci.clin No repository field.
npm WARN apm-install-dir-2021314-16432-1gou4ci.clin No README data
npm WARN apm-install-dir-2021314-16432-1gou4ci.clin No license field.

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] install: `node scripts/prebuild-install.js || (node scripts/preinstall.js && node-gyp rebuild)`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the [email protected] 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!     C:\Users\Andrew\.atom\.apm\_logs\2021-04-14T21_34_14_679Z-debug.log

afogarty85 on 14 Apr 2021

@afogarty85 The error message is too short. Please, could you share more? See the error messages already shared above.

n-riesco on 14 Apr 2021

Updated; any solutions yet?

afogarty85 on 15 Apr 2021

By the way, this is a duplicate of #2034.

The new ZeroMQ release has gone through, once this PR is merged the prebuilds will be uploaded:
https://github.com/zeromq/zeromq.js/pull/446

In the meantime, the solution is to use Atom 1.55:
https://github.com/nteract/hydrogen/issues/2034#issuecomment-819258884

aminya on 15 Apr 2021

By the way, this is a duplicate of #2034

1.55.0 is still failing for me and at least one other.

afogarty85 on 15 Apr 2021

1.55.0 is still failing for me and at least one other.

If you can't wait for the prebuilds, you can try to build ZeroMQ from the source. The above error message says that Windows 8.1 SDK is missing. You can download and install it from here:
https://go.microsoft.com/fwlink/p/?LinkId=323507

The SDK for the other Windows versions is available from here:
https://developer.microsoft.com/en-us/windows/downloads/sdk-archive/

aminya on 15 Apr 2021

I got it to work. Dragged Atom from Applications folder into the trash. Downloaded 1.55.0 (https://github.com/atom/atom/releases/tag/v1.55.0), rebuilt Hydrogen, and restarted Atom.

atom --version

apm --vAtom : 1.55.0
Electron: 6.1.12
Chrome : 76.0.3809.146
Node : 12.4.0

apm --version

apm 2.5.2
npm 6.14.8
node 12.4.0 x64
atom 1.55.0
python 3.6.4
git 2.30.0

apm show hydrogen

Hydrogen
├── 2.14.7

sw_vers

ProductName: Mac OS X
ProductVersion: 10.15.7
BuildVersion: 19H2

rhhyon on 15 Apr 2021

Looks like it is a windows 10 error, I have the same build and it fails (now trying older Atom versions):

apm --version
apm  2.5.2
npm  6.14.8
node 12.4.0 x64
atom 1.54.0
python 3.6.5
git 2.29.2.windows.3
visual studio 2015

afogarty85 on 15 Apr 2021

@rhhyon Glad you got it to work. Maybe I'm biased but this wouldn't be such a big deal if every other editor didn't suck so bad by comparison for python.

I tried switching to VS Code while we wait for a patch and wanted to die 😂

IanRMOReilly on 15 Apr 2021

If you want to use Atom 1.55, just run the following command:

C:/Users/YourUserName/AppData/Local/atom/app-1.55.0/resources/app/apm/bin/apm.cmd rebuild hydrogen

The issue is completely irrelevant to Atom.
@ZeroMQ which is failing to build has left our messages unanswered. Otherwise, I had fixed the issue a long time ago.
https://github.com/zeromq/zeromq.js/issues/442

aminya on 15 Apr 2021

Finally fixed! Thanks @aminya

Here is what I had to do since I already uninstalled Hydrogen.

# run
C:/Users/Andrew/AppData/Local/atom/app-1.54.0/resources/app/apm/bin/apm.cmd install hydrogen
# fails, it wants Windows 8.1 SDK
# follow instructions above to install Windows 8.1 SDK
https://stackoverflow.com/questions/43704734/how-to-fix-the-error-windows-sdk-version-8-1-was-not-found
# run again
C:/Users/Andrew/AppData/Local/atom/app-1.54.0/resources/app/apm/bin/apm.cmd install hydrogen
# rebuild
C:/Users/Andrew/AppData/Local/atom/app-1.54.0/resources/app/apm/bin/apm.cmd rebuild hydrogen
# load atom
# rebuild inside the GUI again
# reload atom

Working!

afogarty85 on 15 Apr 2021

👍1

Downgraded to Atom 1.55.0

Rebuilt Hydrogen

Editor still crashes when trying to initialize kernel and run python file.

On Apr 14, 2021, at 11:40 PM, Amin Yahyaabadi @.*> wrote:

Closed #2079 https://github.com/nteract/hydrogen/issues/2079 via #2082 https://github.com/nteract/hydrogen/pull/2082.

—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub https://github.com/nteract/hydrogen/issues/2079#event-4596889876, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATNAXMOCDJNAYBAC36MWPJLTIZN4VANCNFSM425OKJEA.

msw2171 on 15 Apr 2021

Hydrogen 2.15.0 is released. Now you can use Hydrogen on the latest Atom 🎉

aminya on 15 Apr 2021

👍1

And with Hydrogen 2.15.1 just now released a simple

apm uninstall hydrogen
apm install hydrogen

And I can get back to work!
Kudos @aminya, you rockstar! ;)

vandertilt on 15 Apr 2021

❤1

I'm unable to install Hydrogen 2.15.1 with Atom 1.56.0.

apm install hydrogen fails. Here is a snipped of the log:

npm WARN deprecated [email protected]: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
npm WARN deprecated [email protected]: `json-parser` is deprecated. Please use `comment-json` instead
npm WARN deprecated [email protected]: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
../binding.cc:28:10: fatal error: zmq.h: No such file or directory
 #include <zmq.h>
          ^~~~~~~
compilation terminated.
make: *** [Release/obj.target/zmq/binding.o] Error 1
gyp ERR! build error 
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/share/atom/resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/build.js:194:23)
gyp ERR! stack     at ChildProcess.emit (events.js:200:13)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:272:12)
gyp ERR! System Linux 5.4.0-71-generic
gyp ERR! command "/usr/share/atom/resources/app/apm/bin/node" "/usr/share/atom/resources/app/apm/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /tmp/apm-install-dir-2021315-15368-164j2v9.vdcr/node_modules/Hydrogen/node_modules/@aminya/zeromq
gyp ERR! node -v v12.4.0
gyp ERR! node-gyp -v v5.1.0
gyp ERR! not ok 
Failed to start child process.
child process exited with code -13
../binding.cc:28:10: fatal error: zmq.h: No such file or directory
 #include <zmq.h>
          ^~~~~~~
compilation terminated.
gyp ERR! build error 
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/share/atom/resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/build.js:194:23)
gyp ERR! stack     at ChildProcess.emit (events.js:200:13)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:272:12)
gyp ERR! System Linux 5.4.0-71-generic
gyp ERR! command "/usr/share/atom/resources/app/apm/bin/node" "/usr/share/atom/resources/app/apm/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /tmp/apm-install-dir-2021315-15368-164j2v9.vdcr/node_modules/Hydrogen/node_modules/@aminya/zeromq
gyp ERR! node -v v12.4.0
gyp ERR! node-gyp -v v5.1.0
gyp ERR! not ok 
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! @aminya/[email protected] build:libzmq: `node scripts/preinstall.js && node-gyp rebuild`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the @aminya/[email protected] build:libzmq script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.
npm WARN Local package.json exists, but node_modules missing, did you mean to install?

tom-andersson on 15 Apr 2021

@tom-andersson What is your operating system and processor architecture? No prebuilds are found for your system, and so the code is trying to build it from the source.

aminya on 15 Apr 2021

Thanks for quick reply @aminya
OS: Ubuntu 18.04.5 LTS
CPU arch: x86_64

How can I ensure the right prebuilds are in place? I'm not too familiar with Atom packages.

tom-andersson on 15 Apr 2021

@tom-andersson It should be picked up automatically. You can find them under

.atom/packages/hydrogen/node_modules/zeromq/prebuilds

I am also fixing the build-from-source script for the next version

aminya on 15 Apr 2021

Thanks @aminya. I don't have a .atom/packages/hydrogen folder since I uninstalled Hydrogen before attempting to reinstall (and reinstallation fails as above). Would you suggest I do anything or wait for your fix? Cheers

tom-andersson on 15 Apr 2021

I registered a new version now which fixes the building from the source.

Run the following command to ensure you are using the latest version:

apm uninstall hydrogen  # might fail if already uninstalled
apm install hydrogen

aminya on 15 Apr 2021

👍1

@aminya I'm still getting the following error from apm install hydrogen:

Installing hydrogen to /home/tomand/.atom/packages [31m✗
[39m[31m
> @aminya/[email protected] install /tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/node_modules/Hydrogen/node_modules/@aminya/zeromq
> node-gyp-build || npm run build:libzmq

make: Entering directory '/tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/node_modules/Hydrogen/node_modules/@aminya/zeromq/build'
  ACTION binding_gyp_libzmq_target_prepare_build libzmq/lib
Building libzmq for linux
  TOUCH Release/obj.target/libzmq.stamp
  CXX(target) Release/obj.target/zmq/binding.o
zmq.target.mk:116: recipe for target 'Release/obj.target/zmq/binding.o' failed
make: Leaving directory '/tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/node_modules/Hydrogen/node_modules/@aminya/zeromq/build'

> @aminya/[email protected] build:libzmq /tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/node_modules/Hydrogen/node_modules/@aminya/zeromq
> node-gyp rebuild

make: Entering directory '/tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/node_modules/Hydrogen/node_modules/@aminya/zeromq/build'
  ACTION binding_gyp_libzmq_target_prepare_build libzmq/lib
Building libzmq for linux
  TOUCH Release/obj.target/libzmq.stamp
  CXX(target) Release/obj.target/zmq/binding.o
zmq.target.mk:116: recipe for target 'Release/obj.target/zmq/binding.o' failed
make: Leaving directory '/tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/node_modules/Hydrogen/node_modules/@aminya/zeromq/build'

npm WARN deprecated [email protected]: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
npm WARN deprecated [email protected]: `json-parser` is deprecated. Please use `comment-json` instead
npm WARN deprecated [email protected]: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
Failed to start child process.
child process exited with code -13
../binding.cc:28:10: fatal error: zmq.h: No such file or directory
 #include <zmq.h>
          ^~~~~~~
compilation terminated.
make: *** [Release/obj.target/zmq/binding.o] Error 1
gyp ERR! build error 
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/share/atom/resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/build.js:194:23)
gyp ERR! stack     at ChildProcess.emit (events.js:200:13)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:272:12)
gyp ERR! System Linux 5.4.0-71-generic
gyp ERR! command "/usr/share/atom/resources/app/apm/bin/node" "/usr/share/atom/resources/app/apm/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/node_modules/Hydrogen/node_modules/@aminya/zeromq
gyp ERR! node -v v12.4.0
gyp ERR! node-gyp -v v5.1.0
gyp ERR! not ok 
../binding.cc:28:10: fatal error: zmq.h: No such file or directory
 #include <zmq.h>
          ^~~~~~~
compilation terminated.
make: *** [Release/obj.target/zmq/binding.o] Error 1
gyp ERR! build error 
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/share/atom/resources/app/apm/node_modules/npm/node_modules/node-gyp/lib/build.js:194:23)
gyp ERR! stack     at ChildProcess.emit (events.js:200:13)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:272:12)
gyp ERR! System Linux 5.4.0-71-generic
gyp ERR! command "/usr/share/atom/resources/app/apm/bin/node" "/usr/share/atom/resources/app/apm/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/node_modules/Hydrogen/node_modules/@aminya/zeromq
gyp ERR! node -v v12.4.0
gyp ERR! node-gyp -v v5.1.0
gyp ERR! not ok 
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! @aminya/[email protected] build:libzmq: `node-gyp rebuild`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the @aminya/[email protected] build:libzmq script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.
npm WARN Local package.json exists, but node_modules missing, did you mean to install?

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/tomand/.atom/.apm/_logs/2021-04-15T12_06_57_828Z-debug.log
npm WARN enoent ENOENT: no such file or directory, open '/tmp/apm-install-dir-2021315-8755-3q77tv.iw3u5/package.json'
npm WARN apm-install-dir-2021315-8755-3q77tv.iw3u5 No description
npm WARN apm-install-dir-2021315-8755-3q77tv.iw3u5 No repository field.
npm WARN apm-install-dir-2021315-8755-3q77tv.iw3u5 No README data
npm WARN apm-install-dir-2021315-8755-3q77tv.iw3u5 No license field.

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! @aminya/[email protected] install: `node-gyp-build || npm run build:libzmq`
npm ERR! Exit status 1
npm ERR! 
npm ERR! Failed at the @aminya/[email protected] 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/tomand/.atom/.apm/_logs/2021-04-15T12_06_58_467Z-debug.log
[39m

tom-andersson on 15 Apr 2021

Could you extract this zip file under .atom/packages/hydrogen/node_modules/zeromq/prebuilds?

prebuilds.zip

The prebuilds folder should look like the following.

 hydrogen
    |-prebuilds
         |_linux-x64
             |...
         |_darwin-x64
             |...
         |_win32-x64
             |...

aminya on 15 Apr 2021

@aminya I get what looks like the same error trace after extracting the zip file as suggested and running apm install hydrogen.

tom-andersson on 15 Apr 2021

That's strange!

Try cloning the repository, and running the following command

cd ~/.atom/packages
git clone https://github.com/nteract/hydrogen
cd hydrogen
apm install --production

If apm install failed, do this:

npm install --ignore-scripts

~~Then copy-paste the zip I gave you in this comment, under .atom/packages/hydrogen/node_modules/zeromq/prebuilds~~ -> Not needed.

Let me know how it goes.

aminya on 15 Apr 2021

Thank you for continued help @aminya. apm install --production produces the same error trace. I didn't have npm installed but after running sudo aptitude install npm and attempting npm install --ignore-scripts, I got the following error trace:

npm WARN deprecated [email protected]: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
npm WARN deprecated [email protected]: `json-parser` is deprecated. Please use `comment-json` instead
npm WARN deprecated [email protected]: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
npm WARN deprecated [email protected]: Version no longer supported. Upgrade to @latest
npm ERR! Linux 5.4.0-71-generic
npm ERR! argv "/usr/bin/node" "/usr/bin/npm" "install" "--ignore-scripts"
npm ERR! node v8.10.0
npm ERR! npm  v3.5.2
npm ERR! code EMISSINGARG

npm ERR! typeerror Error: Missing required argument #1
npm ERR! typeerror     at andLogAndFinish (/usr/share/npm/lib/fetch-package-metadata.js:31:3)
npm ERR! typeerror     at fetchPackageMetadata (/usr/share/npm/lib/fetch-package-metadata.js:51:22)
npm ERR! typeerror     at resolveWithNewModule (/usr/share/npm/lib/install/deps.js:456:12)
npm ERR! typeerror     at /usr/share/npm/lib/install/deps.js:457:7
npm ERR! typeerror     at /usr/share/npm/node_modules/iferr/index.js:13:50
npm ERR! typeerror     at /usr/share/npm/lib/fetch-package-metadata.js:37:12
npm ERR! typeerror     at addRequestedAndFinish (/usr/share/npm/lib/fetch-package-metadata.js:82:5)
npm ERR! typeerror     at returnAndAddMetadata (/usr/share/npm/lib/fetch-package-metadata.js:117:7)
npm ERR! typeerror     at pickVersionFromRegistryDocument (/usr/share/npm/lib/fetch-package-metadata.js:134:20)
npm ERR! typeerror     at /usr/share/npm/node_modules/iferr/index.js:13:50
npm ERR! typeerror This is an error with npm itself. Please report this error at:
npm ERR! typeerror     <http://github.com/npm/npm/issues>

npm ERR! Please include the following file with any support request:
npm ERR!     /home/tomand/.atom/packages/hydrogen/npm-debug.log

tom-andersson on 15 Apr 2021

No worries.

Npm comes with Atom. It is on some path like this:

path_to_your_atom_installation/atom/app-1.56.0/resources/app/apm/bin/npm

Just in case, are you using Atom downloaded from atom.io (deb file)? Atom installed from the package managers such as snapd is considered unofficial.
https://atom.io/

Your npm error is really strange. Something seems wrong with your system as npm isn't also working properly.

aminya on 15 Apr 2021

@aminya It was a while ago but I believe I would have installed atom with sudo apt-get install atom using the following instructions: https://flight-manual.atom.io/getting-started/sections/installing-atom/

I'll try reinstalling Atom from the .deb file.

Strangely, I don't have a .atom/atom/ folder which you say contains npm.

tom-andersson on 15 Apr 2021

Let us know. The path I mentioned in this comment isn't under .atom, but actually under the path which includes the atom binary.

path_to_your_atom_installation/atom is one folder above what the following returns

which atom # or apm

Also, feel free to join our Discord server to get more help from others.
https://discord.com/invite/R4KV8jTVpS

aminya on 15 Apr 2021

@aminya Running sudo apt-get remove atom followed by reinstalling Atom from the .deb file and running apm install hydrogen continues to fail.

which apm returns /usr/bin/apm and which atom returns /usr/bin/atom

To be clear, I've been using Atom and Hydrogen for work every day for a long time. I started noticing Hydrogen wasn't connecting to remote kernels after the latest Atom update. Then attempting to update Hydrogen led to these errors I'm having.

I may join the Discord server if you can't think of anything else at this point, thanks!

tom-andersson on 15 Apr 2021

Do you want to try using Atom 1.55 for now so you are not blocked? You can install the previous Hydrogen using:

apm install hydrogen#2.14.7

aminya on 15 Apr 2021

Thanks for the suggestion @aminya. After installing the .deb for Atom 1.55.0, running apm install hydrogen#2.14.7 still failed with the same error trace.

tom-andersson on 15 Apr 2021

../binding.cc:28:10: fatal error: zmq.h: No such file or directory in my error trace led me to https://github.com/JustinTulloss/zeromq.node/issues/596. I tried the suggested apt-get install libzmq3-dev and now I'm getting a new error trace from installing Hydrogen, this time including g++: error: ./Release/../../zmq/lib/libzmq.a: No such file or directory

tom-andersson on 15 Apr 2021

../binding.cc:28:10: fatal error: zmq.h: No such file or directory in my error trace led me to JustinTulloss/zeromq.node#596. I tried the suggested apt-get install libzmq3-dev and now I'm getting a new error trace from installing Hydrogen, this time including g++: error: ./Release/../../zmq/lib/libzmq.a: No such file or directory

Did you try my solution by chance? I also downgraded to Atom 1.54.0

https://github.com/nteract/hydrogen/issues/2079#issuecomment-819897668

afogarty85 on 15 Apr 2021

Thanks @afogarty85, I've just downgraded to Atom 1.54.0. How did you then install Hydrogen? apm install hydrogen#2.14.6? That still gives me a nasty error trace with g++: error: ./Release/../../zmq/lib/libzmq.a: No such file or directory.

tom-andersson on 15 Apr 2021

Finally got it working!
1) Downgraded to Atom 1.54.0 from the .deb file https://github.com/atom/atom/releases/tag/v1.54.0
2) Manually extracted the Hydrogen 2.14.6 .zip to my ~/.atom/packages/
3) cd ~/.atom/packages/hydrogen-2.14.6
4) apm install --production

Thanks @aminya and @afogarty85 for the help.

tom-andersson on 15 Apr 2021

I released 2.15.3 which includes some fixes for the builds on Linux. You might try this Hydrogen version, which should work with older Atom versions too.

apm install hydrogen

You can always downgrade to a lower version. For example: apm install hydrogen#2.14.7

aminya on 17 Apr 2021

Hydrogen: Hydrogen crashes after updating Atom (ZeroMQ build fails on Electron 9)

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