Pkg.jl: Segfault when installing or updating packages

[prosoitos]

Trying to update my packages caused a segfault and Julia crash. Restarting Julia and rebooting my system had no effect.

I uninstalled all my packages one by one, hoping that the problem would come from one of them and that reinstalling that package would solve things, but I still have the problem without any installed package.

As adding packages causes the same crash, I cannot reinstall them either :stuck_out_tongue:

---

System info:

Julia Version 1.3.1
Commit 2d5741174c (2019-12-30 21:36 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i7-5600U CPU @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, broadwell)

---

Error I get after crash:

signal (11): Segmentation fault
in expression starting at none:0
unknown function (ip: 0x7f1f57fd3e73)
http_parser_execute at /usr/bin/../lib/libhttp_parser.so.2.9 (unknown line)
unknown function (ip: 0x7f1f57fd5390)
unknown function (ip: 0x7f1f57fd7770)
unknown function (ip: 0x7f1f57fd9b58)
unknown function (ip: 0x7f1f57fd7f91)
git_remote_fetch at /usr/bin/../lib/libgit2.so (unknown line)
unknown function (ip: 0x7f1f6a8e8cb2)
unknown function (ip: 0x7f1f6a8ea0d8)
unknown function (ip: 0x7f1f6a8f3000)
unknown function (ip: 0x7f1f6a9124de)
unknown function (ip: 0x7f1f6a914101)
unknown function (ip: 0x7f1f6a9928df)
unknown function (ip: 0x7f1f6a992c1a)
unknown function (ip: 0x7f1f6a90caeb)
do_add! at /build/julia/src/julia-1.3.1/usr/share/julia/stdlib/v1.3/Pkg/src/REPLMode.jl:505
jl_f__apply at /usr/bin/../lib/libjulia.so.1 (unknown line)
jl_f__apply_latest at /usr/bin/../lib/libjulia.so.1 (unknown line)
unknown function (ip: 0x7f1f6a8a682b)
jl_f__apply at /usr/bin/../lib/libjulia.so.1 (unknown line)
unknown function (ip: 0x7f1f6aa1e522)
unknown function (ip: 0x7f1f6a9c4104)
unknown function (ip: 0x7f1f6a9c452d)
unknown function (ip: 0x7f1f6a9c82e8)
unknown function (ip: 0x7f1f6a9c8416)
jl_f__apply at /usr/bin/../lib/libjulia.so.1 (unknown line)
jl_f__apply_latest at /usr/bin/../lib/libjulia.so.1 (unknown line)
unknown function (ip: 0x7f1f6aaa6ce1)
unknown function (ip: 0x7f1f6aab9d9e)
unknown function (ip: 0x7f1f6aabacd1)
unknown function (ip: 0x7f1f6a8ccd9c)
unknown function (ip: 0x7f1f6a8cd358)
jl_f__apply at /usr/bin/../lib/libjulia.so.1 (unknown line)
jl_f__apply_latest at /usr/bin/../lib/libjulia.so.1 (unknown line)
unknown function (ip: 0x7f1f6a7e0717)
unknown function (ip: 0x7f1f6a7e6ff2)
unknown function (ip: 0x7f1f6a7e7512)
unknown function (ip: 0x7f1f6a7e7655)
unknown function (ip: 0x5604883f34fe)
unknown function (ip: 0x5604883f30a7)
__libc_start_main at /usr/bin/../lib/libc.so.6 (unknown line)
unknown function (ip: 0x5604883f315d)
Allocations: 945982 (Pool: 945715; Big: 267); GC: 1
[1]    3241 segmentation fault (core dumped)  julia

[johnnychen94]

Can you verify if this issue happens when you use a new package location?

For example, try to install packages with JULIA_DEPOT_PATH=~/tmp/julia julia. If that works normally, it means your previous package folder(e.g., ~/.julia if you didn't set it manually) is broken, you can then rebuild it. If not, then can you report what package causes the segfault?

[prosoitos]

Same problem.

And as for the package: it does not seem to be linked to any package. The same thing happens whatever package I am trying to add.

[prosoitos]

I can try to re-install Julia maybe.

[prosoitos]

Uninstalling Julia, removing the ~/.julia, rebooting, and re-installing did not help.

[prosoitos]

Arch upgraded from julia 1.3.0 to 1.3.1 at the beginning of January and I don't think that I tried to add or upgrade packages after that. So maybe there is something up with 1.3.1??

I could try to downgrade and try again...

[prosoitos]

Same problem with 1.3.0 :slightly_frowning_face:

Not sure what else to try :slightly_frowning_face:

[DilumAluthge]

Are you using the official binaries from julialang.org?

[prosoitos]

Yes.

I am on Arch Linux and I installed Julia through the community repository: https://www.archlinux.org/packages/community/x86_64/julia/

So I didn't install directly from source, but I would imagine that the Arch Julia package is using the official binaries.

[DilumAluthge]

I am not sure if Arch Linux uses the official julialang.org binaries.

Can you download the binaries from https://julialang.org/downloads/ and see if you can still reproduce the bug?

[KristofferC]

That distro release is known to be bugged. The supported way of installing julia is through the binaries on the download page that has been linked already.

[prosoitos]

I just tried using the binaries directly and indeed, this fixed the problem. I reported the problem to the Arch package manager.

Thank you for the help.

[prosoitos]

Now that I am aware of this question of official binaries vs packages provided by distro managers, I realized that there is a package in the AUR which downloads and installs the official binaries.

This allows to have Julia managed by pacman (with the nicer integration in the system and easy updating) while using the official binaries, so I am posting it here in case it helps other Arch users.

https://aur.archlinux.org/packages/julia-bin/

[johnnychen94]

emmm... I seem to over-advertise it but I would say https://github.com/johnnychen94/jill.py makes such thing much easier (supports all platforms)

[cauachagas]

The arch-linux upgrade the http-parser 2.9.2 -> 2.9.3, that is incompatible with julia

So, let's downgrade to the 2.9.2

sudo pacman -S downgrade 
sudo downgrade http-parser # ignore update for http-parse
wget http://archlinux.arkena.net/archive/packages/h/http-parser/http-parser-2.9.2-1-x86_64.pkg.tar.xz
sudo pacman -U http-parser-2.9.2-1-x86_64.pkg.tar.xz

Please, report the solution to the Arch package manager.

[prosoitos]

Thanks. Apparently it has already been fixed.