gem installation completes without errors but does not compile native extensions #545

Watita · 2024-06-30T17:26:32Z

Watita
Jun 30, 2024

Hi everyone,
I am using debian testing with Ruby installed via apt (Ruby 3.1 and gem 3.4.20) and, since last update, the sqlite3 gem installs with no errors but the native extensions are not compiled and the require 'sqlite3' instruction fails with the following error:

irb(main):001:0> require 'sqlite3'
internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:86:in 'require': cannot load such file -- sqlite3/sqlite3_native (LoadError)
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:86:in 'require'
from /var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3.rb:6:in 'rescue in < top (required) >'
from /var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3.rb:2:in `< top (required) >'
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:160:in 'require'
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:160:in 'rescue in require'
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:40:in 'require'
from (irb):1:in '< main >'
from /usr/lib/ruby/gems/3.1.0/gems/irb-1.4.1/exe/irb:11:in '< top (required) >'
from /usr/local/bin/irb:25:in 'load'
from /usr/local/bin/irb:25:in '< main >'
internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:86:in 'require': /lib/x86_64-linux-gnu/libc.so: invalid ELF header - /var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.1/sqlite3_native.so (LoadError)
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:86:in 'require'
from /var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3.rb:4:in '<top (required)>'
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:160:in 'require'
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:160:in 'rescue in require'
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:40:in 'require'
from (irb):1:in '< main >'
from /usr/lib/ruby/gems/3.1.0/gems/irb-1.4.1/exe/irb:11:in '< top (required) >'
from /usr/local/bin/irb:25:in 'load'
from /usr/local/bin/irb:25:in '< main >'
internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:86:in 'require': cannot load such file -- sqlite3 (LoadError)
from internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:86:in 'require'
from (irb):1:in '< main >'
from /usr/lib/ruby/gems/3.1.0/gems/irb-1.4.1/exe/irb:11:in '< top (required) >'
from /usr/local/bin/irb:25:in 'load'
from /usr/local/bin/irb:25:in '< main >'

I also attach here the output of 'gem install sqlite3 --verbose':

sergio@debian:~$ sudo gem install sqlite3 --verbose
HEAD https://index.rubygems.org/
200 OK
GET https://index.rubygems.org/info/sqlite3
200 OK
GET https://index.rubygems.org/quick/Marshal.4.8/sqlite3-2.0.2-x86_64-linux.gemspec.rz
403 Forbidden
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/.gemtest
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/CHANGELOG.md
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/CONTRIBUTING.md
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/FAQ.md
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/INSTALLATION.md
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/LICENSE
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/README.md
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/dependencies.yml
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/aggregator.c
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/aggregator.h
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/backup.c
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/backup.h
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/database.c
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/database.h
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/exception.c
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/exception.h
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/extconf.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/sqlite3.c
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/sqlite3_ruby.h
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/statement.c
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/statement.h
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/ext/sqlite3/timespec.h
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.0/sqlite3_native.so
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.1/sqlite3_native.so
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.2/sqlite3_native.so
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.3/sqlite3_native.so
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/constants.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/database.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/errors.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/pragmas.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/resultset.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/statement.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/value.rb
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/version.rb
Successfully installed sqlite3-2.0.2-x86_64-linux
1 gem installed

Thank you very much for your help

flavorjones · 2024-07-03T01:54:16Z

flavorjones
Jul 3, 2024
Maintainer

Hi, I'll try to help.

the native extensions are not compiled

Well, you're installing the precompiled version, so you're not compiling, but the compiled extension is present. In your output, you can see:

/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.0/sqlite3_native.so
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.1/sqlite3_native.so
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.2/sqlite3_native.so
/var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.3/sqlite3_native.so

However, this error message is buried in your output:

internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb:86:in 'require': /lib/x86_64-linux-gnu/libc.so: invalid ELF header - /var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.1/sqlite3_native.so (LoadError)

This tells me that you're perhaps not on an x86_64-linux system, can you tell us more about your system? What version of rubygems are you running? Did you install this gem via bundler, or via gem install?

7 replies

flavorjones Jul 8, 2024
Maintainer

What is the output of gem env and/or bundle env?

flavorjones Jul 8, 2024
Maintainer

There are a few variables that I'm trying to isolate:

did something change in debian/testing
did something change in the version of rubygems that you're running
what was the previous state? did it use the "ruby" platform gem and compile it before, or was it using the precompiled gem before?
does this reproduce if you build your own ruby (e.g. with ruby-build or ruby-install or rvm) and are on the latest rubygems?

flavorjones Jul 8, 2024
Maintainer

When I run this in the docker:testing docker file, I have issues requiring the gem but I don't get the same error as you do, I get:

<internal:/usr/lib/ruby/vendor_ruby/rubygems/core_ext/kernel_require.rb>:86:in `require': libc.so: cannot open shared
 object file: No such file or directory - /var/lib/gems/3.1.0/gems/sqlite3-2.0.2-x86_64-linux/lib/sqlite3/3.1/sqlite3
_native.so (LoadError)

and I can't figure out what's going on, but it's a different problem than you.

Watita Jul 9, 2024
Author

This is the output of gem env:

RubyGems Environment:
  - RUBYGEMS VERSION: 3.4.20
  - RUBY VERSION: 3.1.2 (2022-04-12 patchlevel 20) [x86_64-linux-gnu]
  - INSTALLATION DIRECTORY: /var/lib/gems/3.1.0
  - USER INSTALLATION DIRECTORY: /home/sergio/.gem/ruby/3.1.0
  - RUBY EXECUTABLE: /usr/bin/ruby3.1
  - GIT EXECUTABLE: /usr/bin/git
  - EXECUTABLE DIRECTORY: /usr/local/bin
  - SPEC CACHE DIRECTORY: /home/sergio/.gem/specs
  - SYSTEM CONFIGURATION DIRECTORY: /etc
  - RUBYGEMS PLATFORMS:
     - ruby
     - x86_64-linux
  - GEM PATHS:
     - /var/lib/gems/3.1.0
     - /home/sergio/.gem/ruby/3.1.0
     - /usr/local/lib/ruby/gems/3.1.0
     - /usr/lib/ruby/gems/3.1.0
     - /usr/lib/x86_64-linux-gnu/ruby/gems/3.1.0
     - /usr/share/rubygems-integration/3.1.0
     - /usr/share/rubygems-integration/all
     - /usr/lib/x86_64-linux-gnu/rubygems-integration/3.1.0
  - GEM CONFIGURATION:
     - :update_sources => true
     - :verbose => true
     - :backtrace => true
     - :bulk_threshold => 1000
     - "gem" => "--no-document"
  - REMOTE SOURCES:
     - https://rubygems.org/
  - SHELL PATH:
     - /usr/local/bin
     - /usr/bin
     - /bin
     - /usr/local/games
     - /usr/games

I am pretty sure that before the update the installation of sqlite3 was building the native extentions.

I also used rvm to install version 3.3.4 (the latest) and 3.3.1 again (that's the same I was using with the issue). But after the installation of 3.3.4 version, rubygems was updated to 3.5.9 and this time sqlite3 installs correctly without compiling native extentions, as you can see here:

sergio@debian:~$ rvm use 3.3.4
Using /home/sergio/.rvm/gems/ruby-3.3.4
sergio@debian:~$ gem install sqlite3
Successfully installed sqlite3-2.0.2-x86_64-linux-gnu
1 gem installed
sergio@debian:~$ irb
3.3.4 :001 > require 'sqlite3'
 => true

and:

sergio@debian:~$ gem env
RubyGems Environment:
  - RUBYGEMS VERSION: 3.5.11
  - RUBY VERSION: 3.3.4 (2024-07-09 patchlevel 94) [x86_64-linux]
  - INSTALLATION DIRECTORY: /home/sergio/.rvm/gems/ruby-3.3.4
  - USER INSTALLATION DIRECTORY: /home/sergio/.gem/ruby/3.3.0
  - RUBY EXECUTABLE: /home/sergio/.rvm/rubies/ruby-3.3.4/bin/ruby
  - GIT EXECUTABLE: /usr/bin/git
  - EXECUTABLE DIRECTORY: /home/sergio/.rvm/gems/ruby-3.3.4/bin
  - SPEC CACHE DIRECTORY: /home/sergio/.gem/specs
  - SYSTEM CONFIGURATION DIRECTORY: /home/sergio/.rvm/rubies/ruby-3.3.4/etc
  - RUBYGEMS PLATFORMS:
     - ruby
     - x86_64-linux
  - GEM PATHS:
     - /home/sergio/.rvm/gems/ruby-3.3.4
     - /home/sergio/.rvm/rubies/ruby-3.3.4/lib/ruby/gems/3.3.0
  - GEM CONFIGURATION:
     - :update_sources => true
     - :verbose => true
     - :backtrace => true
     - :bulk_threshold => 1000
     - "gem" => "--no-document"
  - REMOTE SOURCES:
     - https://rubygems.org/
  - SHELL PATH:
     - /home/sergio/.rvm/gems/ruby-3.3.4/bin
     - /home/sergio/.rvm/gems/ruby-3.3.4@global/bin
     - /home/sergio/.rvm/rubies/ruby-3.3.4/bin
     - /home/sergio/.rvm/bin
     - /usr/local/bin
     - /usr/bin
     - /bin
     - /usr/local/games
     - /usr/games

So is it likely to be something wrong in the rubygems package that comes with apt-install /testing?

Thank you

flavorjones Jul 11, 2024
Maintainer

is it likely to be something wrong in the rubygems package that comes with apt-install /testing

This would be my guess, yes.

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gem installation completes without errors but does not compile native extensions #545

Watita Jun 30, 2024

Replies: 1 comment · 7 replies

flavorjones Jul 3, 2024 Maintainer

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Watita Jul 9, 2024 Author

flavorjones Jul 11, 2024 Maintainer

Watita
Jun 30, 2024

Replies: 1 comment 7 replies

flavorjones
Jul 3, 2024
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flavorjones Jul 8, 2024
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flavorjones Jul 8, 2024
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Watita Jul 9, 2024
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flavorjones Jul 11, 2024
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