Neovim 0.7 crashes with "vim/_init_packages.lua: cannot load incompatible bytecode" #99630

madis · 2022-04-19T11:30:36Z

`brew gist-logs <formula>` link OR `brew config` AND `brew doctor` output

## Brew config

HOMEBREW_VERSION: 3.4.7
ORIGIN: https://github.com/Homebrew/brew
HEAD: 09e766f83c8a420cce9e2210c46a24ec3864a094
Last commit: 27 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 7a35c5eb9f9e81bbfd92654b8b9b7cc810511f05
Core tap last commit: 3 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_CORE_GIT_REMOTE: https://github.com/Homebrew/homebrew-core
HOMEBREW_DISPLAY: :1
HOMEBREW_MAKE_JOBS: 8
Homebrew Ruby: 2.6.8 => /home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/2.6.8/bin/ruby
CPU: octa-core 64-bit skylake
Clang: N/A
Git: 2.25.1 => /bin/git
Curl: 7.68.0 => /bin/curl
Kernel: Linux 5.13.0-37-generic x86_64 GNU/Linux
OS: Ubuntu 20.04.4 LTS (focal)
Host glibc: 2.31
/usr/bin/gcc: 9.4.0
/usr/bin/ruby: N/A
glibc: N/A
gcc@5: N/A
xorg: N/A

Brew doctor

Your system is ready to brew.

Verification

I ran brew update and am still able to reproduce my issue.
I have resolved all warnings from brew doctor and that did not fix my problem.

What were you trying to do (and why)?

Installing Neovim (both official latest and HEAD) via homebrew on Linux

What happened (include all command output)?

Installation ran normally. When starting Neovim, the following error is printed

$ /home/linuxbrew/.linuxbrew/bin/nvim --clean
vim/_init_packages.lua: cannot load incompatible bytecode
stack traceback:
	[C]: at 0x004f11c0
	[C]: at 0x7f3213850880
E970: Failed to initialize builtin lua modules

What did you expect to happen?

Expected Neovim to start normally (without crashing).

Googled a bit and these threads / commits may be useful (although didn't help in my case)

After installing neovim from https://github.com/neovim/neovim/releases/tag/v0.7.0 nvim-linux64.tar.gz, it started normally. So maybe it's more of a homebrew (/linux) issue?

Step-by-step reproduction instructions (by running `brew` commands)

brew install neovim
/home/linuxbrew/.linuxbrew/bin/nvim --clean

to run it without any extra config, i.e. factory defaults

System:
Terminal: GNOME Terminal 3.36.2 using VTE 0.60.3 +BIDI +GNUTLS +ICU +SYSTEMD
OS: 20.04.4 LTS (Focal Fossa) x86-64
$SHELL: xterm-256color

The text was updated successfully, but these errors were encountered:

clason · 2022-04-19T11:40:40Z

This is due to Neovim linking against PUC Lua 5.4 at runtime instead of the recommended LuaJIT (as it does on macOS, so this is purely a linuxbrew issue). In particular, Lua 5.4 is not compatible with 5.1, which Neovim targets, and should never be used.

Can you show the output of brew list?

clason · 2022-04-19T11:41:04Z

@carlocab

carlocab · 2022-04-19T11:47:59Z

Odd. @madis what is the output of brew linkage neovim?

madis · 2022-04-19T11:57:31Z

Odd. @madis what is the output of brew linkage neovim?

Warning: linkage is a developer command, so
Homebrew's developer mode has been automatically turned on.
To turn developer mode off, run brew developer off

System libraries:
  /lib/x86_64-linux-gnu/libc.so.6
  /lib/x86_64-linux-gnu/libm.so.6
  /lib/x86_64-linux-gnu/libpthread.so.0
  /lib/x86_64-linux-gnu/libutil.so.1
Homebrew libraries:
  /home/linuxbrew/.linuxbrew/lib/libtermkey.so.1 (libtermkey)
  /home/linuxbrew/.linuxbrew/lib/libuv.so.1 (libuv)
  /home/linuxbrew/.linuxbrew/lib/libluajit-5.1.so.2 (luajit)
  /home/linuxbrew/.linuxbrew/lib/libluv.so.1 (luv)
  /home/linuxbrew/.linuxbrew/lib/libmsgpackc.so.2 (msgpack)
  /home/linuxbrew/.linuxbrew/lib/libtree-sitter.so.0 (tree-sitter)
  /home/linuxbrew/.linuxbrew/lib/libunibilium.so.4 (unibilium)
Undeclared dependencies with linkage:
  luajit
Dependencies with no linkage:
  libnsl

clason · 2022-04-19T12:00:46Z

Can you try nvim -u NONE --version (which should skip bundled plugins as well)?

Also, what's the LuaJIT version here? Shouldn't Neovim link again against luajit-openresty?

carlocab · 2022-04-19T12:03:54Z

This looks like your problem:

Undeclared dependencies with linkage:

  luajit

You've modified your local neovim.rb which seems to have broken your build.

Can you try installing from the bottle?

madis · 2022-04-19T13:20:55Z

Can you try nvim -u NONE --version (which should skip bundled plugins as well)?

Same result

$ /home/linuxbrew/.linuxbrew/bin/nvim -u NONE --version
vim/_init_packages.lua: cannot load incompatible bytecode
stack traceback:
	[C]: at 0x004f11c0
	[C]: at 0x7fa06be58880
E970: Failed to initialize builtin lua modules

Also, what's the LuaJIT version here? Shouldn't Neovim link again against luajit-openresty?

Unfortunately I don't know how to answer that.

madis · 2022-04-19T13:28:17Z

This looks like your problem:
Undeclared dependencies with linkage:

  luajit
You've modified your local neovim.rb which seems to have broken your build.

I'm not sure how you deduced that I've modified my local neovim.rb. Maybe it's a side effect of something else. I've never edited the local neovim.rb (brew formula I assume)

Can you try installing from the bottle?
I'm not completely sure if I did it right. Followed the instructions from https://github.com/mapbox/homebrew/blob/master/share/doc/homebrew/Bottles.md#bottle-usage

Ran:

$ brew install --build-bottle neovim
$ brew bottle neovim
$ brew uninstall neovim
$ brew reinstall ./neovim--0.7.0.x86_64_linux.bottle.1.tar.gz

$ /home/linuxbrew/.linuxbrew/bin/nvim
vim/_init_packages.lua: cannot load incompatible bytecode
stack traceback:
	[C]: at 0x004f11c0
	[C]: at 0x7f708bc3a880
E970: Failed to initialize builtin lua modules

madis · 2022-04-19T13:33:01Z

Someone from neovim/neovim devs posted the following (maybe useful for solving this?)

Cannot reproduce this (at least on macOS). Neovim should not be built against PUC Lua, and certainly not Lua 5.4 (which is incompatible with Lua 5.1, which Neovim targets). Please open an issue at linuxbrew.

(You can try temporarily uninstalling -- or unlinking -- lua and then reinstalling neovim.)

neovim/neovim#18169 (comment)

gromgit · 2022-04-19T13:46:21Z

brew install --build-bottle neovim

This builds a brand-new bottle on your system, which would potentially pick up locally-installed stuff like luajit that aren't linked in a "clean" build. That's almost certainly the root of your problem.

You want to do this instead:

brew install --force-bottle neovim

or better yet:

brew rm neovim
brew autoremove
brew install neovim

then brew linkage neovim should print:

$ brew linkage neovim
System libraries:
  /lib/x86_64-linux-gnu/libc.so.6
  /lib/x86_64-linux-gnu/libm.so.6
  /lib/x86_64-linux-gnu/libpthread.so.0
  /lib/x86_64-linux-gnu/libutil.so.1
Homebrew libraries:
  /home/linuxbrew/.linuxbrew/lib/libtermkey.so.1 (libtermkey)
  /home/linuxbrew/.linuxbrew/lib/libuv.so.1 (libuv)
  /home/linuxbrew/.linuxbrew/opt/luajit-openresty/lib/libluajit-5.1.so.2 (luajit-openresty)
  /home/linuxbrew/.linuxbrew/lib/libluv.so.1 (luv)
  /home/linuxbrew/.linuxbrew/lib/libmsgpackc.so.2 (msgpack)
  /home/linuxbrew/.linuxbrew/lib/libtree-sitter.so.0 (tree-sitter)
  /home/linuxbrew/.linuxbrew/lib/libunibilium.so.4 (unibilium)
Dependencies with no linkage:
  libnsl

carlocab · 2022-04-19T13:47:44Z

I'm not sure how you deduced that I've modified my local neovim.rb. Maybe it's a side effect of something else. I've never edited the local neovim.rb (brew formula I assume)

That was my conclusion based on the output of brew linkage. Editing the local formula is the likeliest explanation for the output you're getting.

Ran:


$ brew install --build-bottle neovim

$ brew bottle neovim

$ brew uninstall neovim

$ brew reinstall ./neovim--0.7.0.x86_64_linux.bottle.1.tar.gz



$ /home/linuxbrew/.linuxbrew/bin/nvim

vim/_init_packages.lua: cannot load incompatible bytecode

stack traceback:

	[C]: at 0x004f11c0

	[C]: at 0x7f708bc3a880

E970: Failed to initialize builtin lua modules

No, I don't mean building your own bottle locally. Doing a source build on your machine seems to be what's causing your problem, so building your own bottle won't get around it (as that still involves a source build on your machine). I just meant a plain brew install neovim.

carlocab · 2022-04-19T14:04:25Z

One other possibility is that nvim is mistakenly picking up your

/home/linuxbrew/.linuxbrew/lib/libluajit-5.1.so.2

when it should be using

/home/linuxbrew/.linuxbrew/opt/luajit-openresty/lib/libluajit-5.1.so.2

Can you try doing

brew unlink luajit && brew reinstall neovim

?

carlocab · 2022-04-19T14:10:49Z

Yes, I think this is your problem:

linuxbrew@8527cd738e0c:~$ objdump -p $(which nvim) | grep RPATH | sed 's/ RPATH \+//' | tr ':' '\n'
 /home/linuxbrew/.linuxbrew/Cellar/neovim/0.7.0/lib
/home/linuxbrew/.linuxbrew/lib
/home/linuxbrew/.linuxbrew/opt/ncurses/lib
/home/linuxbrew/.linuxbrew/opt/readline/lib
/home/linuxbrew/.linuxbrew/opt/zlib/lib
/home/linuxbrew/.linuxbrew/opt/libxml2/lib
/home/linuxbrew/.linuxbrew/opt/gettext/lib
/home/linuxbrew/.linuxbrew/opt/unibilium/lib
/home/linuxbrew/.linuxbrew/opt/libtermkey/lib
/home/linuxbrew/.linuxbrew/opt/libuv/lib
/home/linuxbrew/.linuxbrew/opt/luajit-openresty/lib
/home/linuxbrew/.linuxbrew/opt/msgpack/lib
/home/linuxbrew/.linuxbrew/opt/tree-sitter/lib
/home/linuxbrew/.linuxbrew/opt/openssl@1.1/lib
/home/linuxbrew/.linuxbrew/opt/bison/lib
/home/linuxbrew/.linuxbrew/opt/krb5/lib
/home/linuxbrew/.linuxbrew/opt/libtirpc/lib
/home/linuxbrew/.linuxbrew/opt/libnsl/lib

Here we see that

/home/linuxbrew/.linuxbrew/lib

comes before

/home/linuxbrew/.linuxbrew/opt/luajit-openresty/lib

in nvim's RPATH, when it should be the other way around.

This needs fixing in brew. In the meantime you can try unlinking luajit to work around the problem. Another hacky workaround is to do

mkdir -p "$(brew --prefix neovim)/lib"
ln -s "$(brew --prefix luajit-openresty)/lib/libluajit-5.1.so.2" "$(brew --prefix neovim)/lib"

if you don't want to do brew unlink luajit.

CC @Homebrew/linux

cho-m · 2022-04-19T17:17:15Z

in nvim's RPATH, when it should be the other way around.

This needs fixing in brew.

We've been seeing similar linkage issues in Homebrew CI for a while (particularly with libpq dependents when postgresql is also installed, though still functional here).

May be indirectly fixed for new users (not sure about existing) if we decide to swap luajit symlinks #99580

madis · 2022-04-20T06:13:42Z

You want to do this instead:

brew install --force-bottle neovim

Unfortunately same result (crash due to incompatible bytecode)

or better yet:

brew rm neovim
brew autoremove
brew install neovim

Same as above (crash)

brew linkage (after the latter install method) prints the following:

$ brew linkage neovim
System libraries:
  /lib/x86_64-linux-gnu/libc.so.6
  /lib/x86_64-linux-gnu/libm.so.6
  /lib/x86_64-linux-gnu/libpthread.so.0
  /lib/x86_64-linux-gnu/libutil.so.1
Homebrew libraries:
  /home/linuxbrew/.linuxbrew/lib/libtermkey.so.1 (libtermkey)
  /home/linuxbrew/.linuxbrew/lib/libuv.so.1 (libuv)
  /home/linuxbrew/.linuxbrew/lib/libluajit-5.1.so.2 (luajit)
  /home/linuxbrew/.linuxbrew/lib/libluv.so.1 (luv)
  /home/linuxbrew/.linuxbrew/lib/libmsgpackc.so.2 (msgpack)
  /home/linuxbrew/.linuxbrew/lib/libtree-sitter.so.0 (tree-sitter)
  /home/linuxbrew/.linuxbrew/lib/libunibilium.so.4 (unibilium)
Undeclared dependencies with linkage:
  luajit
Dependencies with no linkage:
  libnsl

madis · 2022-04-20T06:19:46Z

removed earlier text

This needs fixing in brew. In the meantime you can try unlinking luajit to work around the problem. Another hacky workaround is to do
mkdir -p "$(brew --prefix neovim)/lib"
ln -s "$(brew --prefix luajit-openresty)/lib/libluajit-5.1.so.2" "$(brew --prefix neovim)/lib"

☝️ this (the 2 commands) made Neovim (installed via homebrew) start successfully 🥳

Also may be worth mentioning, that downloading the Neovim compiled binary (nvim-linux64.tar.gz in my case) from their Github releases page (https://github.com/neovim/neovim/releases/tag/v0.7.0) works also without issues.

if you don't want to do brew unlink luajit.

CC @Homebrew/linux

carlocab · 2022-04-20T07:31:49Z

Also may be worth mentioning, that downloading the Neovim compiled binary (nvim-linux64.tar.gz in my case) from their Github releases page (https://github.com/neovim/neovim/releases/tag/v0.7.0) works also without issues.

This is because the GitHub release is a statically linked executable. It's nice to do to make something portable but generally frowned upon by package managers (primarily for security reasons).

ghost · 2022-04-20T10:56:31Z

I have the same problem on arch linux.

gromgit · 2022-04-20T11:27:38Z

Yes, this issue affects all Linux Homebrew users who have both neovim and luajit installed. See #99630 (comment) for a couple of workarounds, as the official solution is being worked on.

danielnachun · 2022-04-20T17:49:18Z

The root cause of this problem is probably the ordering of the array here: https://github.com/Homebrew/brew/blob/fa4f239cd6e7b96de54825d779ca2a8ac3ff7ec2/Library/Homebrew/extend/os/linux/extend/ENV/super.rb#L40-L46

  def determine_rpath_paths(formula)
    PATH.new(
      *formula&.lib,
      "#{HOMEBREW_PREFIX}/lib",
      PATH.new(run_time_deps.map { |dep| dep.opt_lib.to_s }).existing,
    )
  end

should probably be changed to

  def determine_rpath_paths(formula)
    PATH.new(
      *formula&.lib,
      PATH.new(run_time_deps.map { |dep| dep.opt_lib.to_s }).existing,
      "#{HOMEBREW_PREFIX}/lib",
    )
  end

This would make sure that the opt directories for the dependencies always pre-empt whatever is in HOMEBREW_PREFIX/lib.

Interestingly I wonder if after we make this change, we should start to audit for linkage through HOMEBREW_PREFIX/lib rather than opt directories. Technically we should only be linking to brewed GCC 5 (soon to be 7) through HOMEBREW_PREFIX/lib, and that is only on platforms whose host GCC is too old. In CI, all brewed dependencies should be linked through their opt directories, not HOMEBREW_PREFIX/lib. I believe that would resolve the other linkage issues @cho-m mentioned with libpq and postgresql and probably others.

github-actions · 2022-05-12T00:20:47Z

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

hardfau1t · 2022-06-15T15:50:44Z

Just for reference, i was getting the same issue and i was using neovim on aws-arch instsance, turns out by using luajit from community/luajit solved, instead of ec2/luajit

madis added the bug Reproducible Homebrew/homebrew-core bug label Apr 19, 2022

madis mentioned this issue Apr 19, 2022

Neovim 0.7 crashes with "vim/_init_packages.lua: cannot load incompatible bytecode" neovim/neovim#18169

Closed

phmccarty mentioned this issue Apr 30, 2022

neovim will not run after 36210 update clearlinux/distribution#2626

Open

cho-m mentioned this issue May 4, 2022

superenv: prioritize dependencies' opt_lib in Linux rpath Homebrew/brew#13240

Merged

7 tasks

github-actions bot added the stale No recent activity label May 12, 2022

github-actions bot closed this as completed May 19, 2022

github-actions bot added the outdated PR was locked due to age label Jul 16, 2022

github-actions bot locked as resolved and limited conversation to collaborators Jul 16, 2022

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Neovim 0.7 crashes with "vim/_init_packages.lua: cannot load incompatible bytecode" #99630

Neovim 0.7 crashes with "vim/_init_packages.lua: cannot load incompatible bytecode" #99630

madis commented Apr 19, 2022 •

edited

clason commented Apr 19, 2022 •

edited

clason commented Apr 19, 2022

carlocab commented Apr 19, 2022

madis commented Apr 19, 2022

clason commented Apr 19, 2022 •

edited

carlocab commented Apr 19, 2022

madis commented Apr 19, 2022

madis commented Apr 19, 2022 •

edited

madis commented Apr 19, 2022

gromgit commented Apr 19, 2022 •

edited

carlocab commented Apr 19, 2022

carlocab commented Apr 19, 2022

carlocab commented Apr 19, 2022 •

edited

cho-m commented Apr 19, 2022 •

edited

madis commented Apr 20, 2022

madis commented Apr 20, 2022 •

edited

carlocab commented Apr 20, 2022

ghost commented Apr 20, 2022

gromgit commented Apr 20, 2022

danielnachun commented Apr 20, 2022

github-actions bot commented May 12, 2022

hardfau1t commented Jun 15, 2022

Neovim 0.7 crashes with "vim/_init_packages.lua: cannot load incompatible bytecode" #99630

Neovim 0.7 crashes with "vim/_init_packages.lua: cannot load incompatible bytecode" #99630

Comments

madis commented Apr 19, 2022 • edited

brew gist-logs <formula> link OR brew config AND brew doctor output

Brew doctor

Verification

What were you trying to do (and why)?

What happened (include all command output)?

What did you expect to happen?

Step-by-step reproduction instructions (by running brew commands)

clason commented Apr 19, 2022 • edited

clason commented Apr 19, 2022

carlocab commented Apr 19, 2022

madis commented Apr 19, 2022

clason commented Apr 19, 2022 • edited

carlocab commented Apr 19, 2022

madis commented Apr 19, 2022

madis commented Apr 19, 2022 • edited

madis commented Apr 19, 2022

gromgit commented Apr 19, 2022 • edited

carlocab commented Apr 19, 2022

carlocab commented Apr 19, 2022

carlocab commented Apr 19, 2022 • edited

cho-m commented Apr 19, 2022 • edited

madis commented Apr 20, 2022

madis commented Apr 20, 2022 • edited

carlocab commented Apr 20, 2022

ghost commented Apr 20, 2022

gromgit commented Apr 20, 2022

danielnachun commented Apr 20, 2022

github-actions bot commented May 12, 2022

hardfau1t commented Jun 15, 2022

madis commented Apr 19, 2022 •

edited

`brew gist-logs <formula>` link OR `brew config` AND `brew doctor` output

Step-by-step reproduction instructions (by running `brew` commands)

clason commented Apr 19, 2022 •

edited

clason commented Apr 19, 2022 •

edited

madis commented Apr 19, 2022 •

edited

gromgit commented Apr 19, 2022 •

edited

carlocab commented Apr 19, 2022 •

edited

cho-m commented Apr 19, 2022 •

edited

madis commented Apr 20, 2022 •

edited