Solved: ruby installating hangs in configure step: checking for broken backtrace

saskia · September 22, 2018

Hello,

first of all thank you everyone for all the effort you have put into funtoo/gentoo the wiki, the forum and everything not so obvious.

As for the problem... I've installed funtoo and gentoo several times and everytime it went more or less smoothly. So I decided I want to switch my NUC to funtoo, too, and ran into some weird issues. Please note that this is an offline installation.

I started the way I usually set this up. Use the installation wiki as a check list. ..., then emerge @world -uND and all went smooth so far.

Then I rebooted and ran into several blockers which I have no idea how to debug [and which I'm unsure whether or not I shall mention them all here or in separate posts].

First thing after reboot I wanted to install neovim [which hangs at some other point [scanning dependencies of target helptags] when I tried to rebuild without ruby use flags].

After waiting for several hours I decided to abort and build ruby by itself and during the prepare phase it keeps hanging at the line:



checking for broken backtrace

the log files tell me exactly the same as the console output.

I repeated this step a few times, same result every time.

So what's going on? How can I check if my system is missing something? How can I debug this hang?

palica · September 23, 2018

what exact package(s) (with version number and maybe emerge -av <package> output) are you trying to emerge and fail? what is the output that you are getting? what other blockers did you encounter?

please read also

saskia · September 23, 2018

1 hour ago, palica said:

what exact package(s) (with version number and maybe emerge -av <package> output) are you trying to emerge and fail? what is the output that you are getting? what other blockers did you encounter?

please read also

Hello palica, thanks for your reply.

Technically these packages [neovim and ruby] don't fail, they hang infinitely [as in a couple hours - then I killed the emerge].

The ruby versions are 2.4.3 and 2.3.6 neovim is 0.3.1.


emerge -pv ruby

These are the packages that would be merged, in order:

Calculating dependencies  ... done!
[ebuild  N     ] dev-lang/ruby-2.4.3:2.4::ruby-kit  USE="gdbm jemalloc libressl rdoc ssl -berkdb -debug -doc -examples -ipv6 -rubytests -socks5 -static-libs -tk -xemacs" 0 KiB
[ebuild  N     ] dev-lang/ruby-2.3.6:2.3::ruby-kit  USE="gdbm jemalloc libressl ncurses rdoc readline ssl -berkdb -debug -doc -examples -ipv6 -rubytests -socks5 -tk -xemacs" 0 KiB
[ebuild  N     ] dev-ruby/rubygems-2.7.4::ruby-kit  USE="-server -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] virtual/rubygems-14::ruby-kit  RUBY_TARGETS="ruby23 ruby24 (-rbx) -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/rake-12.3.0::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/xmlrpc-0.3.0::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/power_assert-1.1.1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
ebuild  N     ] dev-ruby/test-unit-3.2.7:2::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/json-2.1.0:2::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/minitest-5.11.1:5::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/did_you_mean-1.1.2:2.4::ruby-kit  USE="-test" RUBY_TARGETS="ruby24" 0 KiB
[ebuild  N     ] dev-ruby/net-telnet-0.1.1-r1:1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/did_you_mean-1.0.2:1::ruby-kit  USE="-test" RUBY_TARGETS="ruby23" 0 KiB
[ebuild  N     ] dev-ruby/racc-1.4.14::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/kpeg-1.1.0:1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/rdoc-6.0.1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB

Total: 16 packages (16 new), Size of downloads: 0 KiB

and


emerge -pv neovim

These are the packages that would be merged, in order:

Calculating dependencies  . ... done!

[ebuild  N     ] dev-lang/ruby-2.3.6:2.3::ruby-kit  USE="gdbm jemalloc libressl ncurses rdoc readline ssl -berkdb -debug -doc -examples -ipv6 -rubytests -socks5 -tk -xemacs" 0 KiB
[ebuild  N     ] dev-lang/ruby-2.4.3:2.4::ruby-kit  USE="gdbm jemalloc libressl rdoc ssl -berkdb -debug -doc -examples -ipv6 -rubytests -socks5 -static-libs -tk -xemacs" 0 KiB
[ebuild  N     ] dev-ruby/rubygems-2.7.4::ruby-kit  USE="-server -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] virtual/rubygems-14::ruby-kit  RUBY_TARGETS="ruby23 ruby24 (-rbx) -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/rake-12.3.0::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/power_assert-1.1.1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/net-telnet-0.1.1-r1:1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/test-unit-3.2.7:2::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/json-2.1.0:2::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/minitest-5.11.1:5::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/did_you_mean-1.0.2:1::ruby-kit  USE="-test" RUBY_TARGETS="ruby23" 0 KiB
[ebuild  N     ] dev-ruby/xmlrpc-0.3.0::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/did_you_mean-1.1.2:2.4::ruby-kit  USE="-test" RUBY_TARGETS="ruby24" 0 KiB
[ebuild  N     ] dev-ruby/racc-1.4.14::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/kpeg-1.1.0:1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/rdoc-6.0.1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/msgpack-1.2.2::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24" 0 KiB
[ebuild  N     ] dev-ruby/neovim-ruby-client-0.5.1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24" 0 KiB
[ebuild  N     ] app-editors/neovim-0.3.1::editors-kit  USE="clipboard jemalloc luajit nvimpager python ruby tui -remote" 0 KiB

Total: 19 packages (19 new), Size of downloads: 0 KiB

This is with the ruby use flag, without neovim builds fine but hangs later.

Attached are the build logs.

I just noticed in the output that ruby has the libressl use flag. I encountered other issues regarding that when I tried to emerge gparted and lighttpd.

Lighttpd didn't compile with libressl and gparted has a dependency: sys-fs/diskdev_cmds-332.14_p1:0/0::core-kit which pulls in openssl and is a blocker.

I will investigate if ruby builds without libressl. EDIT: same result


emerge -pv ruby

These are the packages that would be merged, in order:

Calculating dependencies  .... done!
[ebuild  N     ] dev-lang/ruby-2.4.3:2.4::ruby-kit  USE="gdbm jemalloc rdoc -berkdb -debug -doc -examples -ipv6 -libressl -rubytests -socks5 -ssl -static-libs -tk -xemacs" 0 KiB
[ebuild  N     ] dev-lang/ruby-2.3.6:2.3::ruby-kit  USE="gdbm jemalloc ncurses rdoc readline -berkdb -debug -doc -examples -ipv6 -libressl -rubytests -socks5 -ssl -tk -xemacs" 0 KiB
[ebuild  N     ] dev-ruby/rubygems-2.7.4::ruby-kit  USE="-server -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] virtual/rubygems-14::ruby-kit  RUBY_TARGETS="ruby23 ruby24 (-rbx) -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/rake-12.3.0::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/xmlrpc-0.3.0::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/power_assert-1.1.1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/test-unit-3.2.7:2::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/json-2.1.0:2::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/minitest-5.11.1:5::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/did_you_mean-1.1.2:2.4::ruby-kit  USE="-test" RUBY_TARGETS="ruby24" 0 KiB
[ebuild  N     ] dev-ruby/net-telnet-0.1.1-r1:1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/did_you_mean-1.0.2:1::ruby-kit  USE="-test" RUBY_TARGETS="ruby23" 0 KiB
[ebuild  N     ] dev-ruby/racc-1.4.14::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/kpeg-1.1.0:1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB
[ebuild  N     ] dev-ruby/rdoc-6.0.1::ruby-kit  USE="-doc -test" RUBY_TARGETS="ruby23 ruby24 -ruby25" 0 KiB

Total: 16 packages (16 new), Size of downloads: 0 KiB

neovim-0.3.1.log

ruby-2.3.6.log

ruby-2.4.3.log

ruby-2.4.3-sans_ssl.log

Edited September 23, 2018 by saskia
updated logs for ruby sans ssl

saskia · September 25, 2018

The issue was related to jemalloc.

palica · September 25, 2018

hi saskia!

unfortunately I am unable to reproduce this on my setup. both packages emerge fine (ruby and neovim).

saskia · September 26, 2018

Hello palica,

Thanks a lot for your effort.

It is kind of a weird issue and I never ran into something like that before.

All I know is that ruby as well as neovim emerge fine without jemalloc, i.e. USE=-jemalloc. Rust, which happens to have a jemalloc use flag, too, emerged without issues.

It happens on pure64 as well as on multilib.

The hardware is a NUC6i5-SYK. I haven't experience any issues at all with this thing when it ran Arch Linux, however an internet search revealed that there are bugs and that linux support is not so awesome.

If it happened only in my custom kernel I would blame that but the debian kernel [4.14.12], which is what I used initially, doesn't solve the issue either.

jemalloc-5.0.1:0/2::dev-kit USE=hardned hugepages lazy-lock xmalloc -debug -static-libs -stats

Emerging jemalloc with USE=-hugepages didn't solve the issue. There are a few options left...

EDIT: sorry for lack of markup but it seems I didn't have a JS powered editor

palica · September 27, 2018

Still no luck reproducing your issue even with libressl and jemalloc it compiles fine. Recompiling world with libressl and will try again, but looks like hw related failure. Give more info as what image did you use to install funtoo. I would probably try with generic_64bit image and expand from there, as some of intel cpu don't have all the cpu capabilities they should have according to their family specs. My NUC also doesn't support aes and rdrnd although ivybridge :) (Intel(R) Core(TM) i3-3217U CPU @ 1.80GHz)

saskia · September 27, 2018

Hi,

Thanks for your ongoing effort!

I was using the stage3-intel64-skylake-funtoo-current-2018-08-21.tar.xz both, the multilib and the pure64 one.

Both fail the same way.

When I run nvim in the build directory directly

cd /var/tmp/portage/app-editors/neovim-0.3.1/work/neovim-0.3.1_build/runtime && /var/tmp/portage/app-editors/neovim-0.3.1/work/neovim-0.3.1_build/bin/nvim

this is the result

<jemalloc>: Error in dlsym(RTLD_NEXT, "pthread_create"
  Aborted.

With USE=-jemalloc both ruby as well as neovim built successfully.

Rust build successfully with jemalloc enabled.

I cannot relate the issue between Ruby and neovim as ruby hangs in the configure phase and I have no clue how to debug that.

P.S. Lighttpd also built successfully with libressl on the pure64 stage3.

palica · September 27, 2018

seems a bit like this

https://bugs.archlinux.org/task/54447

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Solved: ruby installating hangs in configure step: checking for broken backtrace

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Hello palica, thanks for your reply.

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