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Troubleshooting Ruby

The following are possible solutions to problems you might encounter with Ruby and GDK.

Rebuilding gems with native extensions

There may be times when local libraries that are used to build some gems' native extensions are updated (for example, libicu), thus resulting in errors like:

rails-background-jobs.1 | /home/user/.rvm/gems/ruby-2.3.0/gems/activesupport-4.2.5.2/lib/active_support/dependencies.rb:274:in 'require': libicudata.so
cannot open shared object file: No such file or directory - /home/user/.rvm/gems/ruby-2.3.0/gems/charlock_holmes-0.7.3/lib/charlock_holmes/charlock_holmes.so (LoadError)
cd /home/user/gitlab-development-kit/gitlab && bundle exec rake gettext:compile > /home/user/gitlab-development-kit/gitlab/log/gettext.log 2>&1
make: *** [.gettext] Error 1
rake aborted!
LoadError: dlopen(/home/user/.rbenv/versions/2.6.3/lib/ruby/gems/2.5.0/gems/charlock_holmes-0.7.6/lib/charlock_holmes/charlock_holmes.bundle, 9): Library not loaded: /usr/local/opt/icu4c/lib/libicudata.63.1.dylib
  Referenced from: /home/user/.rbenv/versions/2.6.3/lib/ruby/gems/2.5.0/gems/charlock_holmes-0.7.6/lib/charlock_holmes/charlock_holmes.bundle
  Reason: image not found - /home/user/.rbenv/versions/2.6.3/lib/ruby/gems/2.5.0/gems/charlock_holmes-0.7.6/lib/charlock_holmes/charlock_holmes.bundle

In that case, find the offending gem and use pristine to rebuild its native extensions:

gem pristine charlock_holmes

Or for example re2 on MacOS:

/Users/user/gitlab-development-kit/gitlab/lib/gitlab/untrusted_regexp.rb:25:  [BUG] Segmentation fault at 0x0000000000000000
ruby 2.6.6p146 (2020-03-31 revision 67876) [x86_64-darwin19]

In which case you would run:

gem pristine re2

An error occurred while installing thin (1.7.2) on macOS

[SNIPPED]

thin.c:338:8: error: implicit declaration of function 'thin_http_parser_has_error' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
    if(thin_http_parser_has_error(http)) {
       ^
thin.c:338:8: note: did you mean 'http_parser_has_error'?
./parser.h:44:5: note: 'http_parser_has_error' declared here
int http_parser_has_error(http_parser *parser);
    ^
thin.c:359:10: error: implicit declaration of function 'thin_http_parser_has_error' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
  return thin_http_parser_has_error(http) ? Qtrue : Qfalse;
         ^
thin.c:374:10: error: implicit declaration of function 'thin_http_parser_is_finished' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
  return thin_http_parser_is_finished(http) ? Qtrue : Qfalse;
         ^
9 errors generated.
make: *** [thin.o] Error 1

make failed, exit code 2

Gem files will remain installed in /Users/tkuah/.rbenv/versions/2.7.2/lib/ruby/gems/2.7.0/gems/thin-1.7.2 for inspection.
Results logged to /Users/tkuah/.rbenv/versions/2.7.2/lib/ruby/gems/2.7.0/extensions/x86_64-darwin-19/2.7.0/thin-1.7.2/gem_make.out

An error occurred while installing thin (1.7.2), and Bundler cannot continue.
Make sure that `gem install thin -v '1.7.2' --source 'https://rubygems.org/'` succeeds before bundling.

To fix this, you can run the following in the gitlab directory:

bundle config build.thin --with-cflags="-Wno-error=implicit-function-declaration"
bundle install

See this issue for more details.

An error occurred while installing thrift (0.14.0)

The installation of the thrift v0.14.0 gem during bundle install can fail with the following error due to a known bug.

[SNIPPED]

current directory: /wrkdirs/usr/ports/devel/rubygem-thrift/work/stage/usr/local/lib/ruby/gems/2.7/gems/thrift-0.14.0/ext
make "DESTDIR="
compiling binary_protocol_accelerated.c
binary_protocol_accelerated.c:404:68: error: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Werror,-Wcompound-token-split-by-macro]
  VALUE thrift_binary_protocol_class = rb_const_get(thrift_module, rb_intern("BinaryProtocol"));
                                                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/include/ruby-2.7/ruby/ruby.h:1847:23: note: expanded from macro 'rb_intern'
        __extension__ (RUBY_CONST_ID_CACHE((ID), (str))) : \
                      ^
binary_protocol_accelerated.c:404:68: note: '{' token is here
  VALUE thrift_binary_protocol_class = rb_const_get(thrift_module, rb_intern("BinaryProtocol"));
                                                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/include/ruby-2.7/ruby/ruby.h:1847:24: note: expanded from macro 'rb_intern'
        __extension__ (RUBY_CONST_ID_CACHE((ID), (str))) : \
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/include/ruby-2.7/ruby/ruby.h:1832:5: note: expanded from macro 'RUBY_CONST_ID_CACHE'
    {                                                   \
    ^

As a workaround, you can set the following Bundler config:

bundle config build.thrift --with-cppflags="-Wno-error=compound-token-split-by-macro"
bundle install

Running gem install thrift -v '0.14.0' --source 'https://rubygems.org' won't work because gem bypasses the Bundler config.

An error occurred while installing gpgme on macOS

Check if you have gawk installed >= 5.0.0 and uninstall it.

Re-run the gdk install again and follow any on-screen instructions related to installing gpgme.

undefined symbol: SSLv2_method

This happens if your local OpenSSL library is updated and your Ruby binary is built against an older version.

If you are using rvm, you should reinstall the Ruby binary. The following command fetches Ruby 2.3 and installs it from source:

rvm reinstall --disable-binary 2.3

gem install gpgme 2.0.x fails to compile native extension on macOS Mojave

If building gpgme gem fails with an Undefined symbols for architecture x86_64 error on macOS Mojave, build gpgme using system libraries instead.

  1. Ensure necessary dependencies are installed:

    brew install gpgme

  2. (optional) Try building the gpgme gem manually to ensure it compiles. If it fails, debug the failure with the error messages. To compile the gpgme gem manually run:

    gem install gpgme -- --use-system-libraries

  3. Configure Bundler to use system libraries for the gpgme gem:

    bundle config build.gpgme --use-system-libraries

You can now run gdk install or bundle again.

FFI gem issues

The following are problems you might encounter when installing the FFI gem with possible solutions.

gem install ffi fails with 'ffi.h file not found'

If you see the following error installing the ffi gem via gdk install:

Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
...
sed: 1: "s?\@XML_LIBDIR\@?-L/Use ...": bad flag in substitute command: '/'
...
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.
...
An error occurred while installing nokogiri (1.10.4), and Bundler cannot continue.
Make sure that `gem install nokogiri -v '1.10.4' --source 'https://rubygems.org/'` succeeds before bundling.
...
compiling AbstractMemory.c
In file included from AbstractMemory.c:47:
In file included from ./AbstractMemory.h:42:
./Types.h:78:10: fatal error: 'ffi.h' file not found
#include <ffi.h>
        ^~~~~~~
1 error generated.
make[1]: *** [AbstractMemory.o] Error 1
...
An error occurred while installing ffi (1.11.1), and Bundler cannot continue.
Make sure that `gem install ffi -v '1.11.1' --source 'https://rubygems.org/'` succeeds before bundling.

A solution on macOS is to:

  1. Ensure the PKG_CONFIG_PATH and LDFLAGS environment variables are correctly set:

    export PKG_CONFIG_PATH="$PKG_CONFIG_PATH:$(brew --prefix)/opt/libffi/lib/pkgconfig"
export LDFLAGS="$LDFLAGS:-L$(brew --prefix)/opt/libffi/lib"

  2. Re-run gdk install

gem install ffi fails with 'error: implicit declaration of function'

Installing ffi 1.13.1 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

current directory:
/Users/gdk/.rbenv/versions/2.6.6/lib/ruby/gems/2.6.0/gems/ffi-1.13.1/ext/ffi_c
-- snip --
compiling Function.c
Function.c:852:17: error: implicit declaration of function
'ffi_prep_closure_loc' is invalid in C99
[-Werror,-Wimplicit-function-declaration]
ffiStatus = ffi_prep_closure_loc(code, &fnInfo->ffi_cif, callback_invoke,
closure, code);
                ^
Function.c:852:17: note: did you mean 'ffi_prep_closure'?
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/ffi/ffi.h:269:1:
note: 'ffi_prep_closure' declared here
ffi_prep_closure(
^
1 error generated.
make[2]: *** [Function.o] Error 1

make failed, exit code 2

Gem files will remain installed in
/Users/gdk/.rbenv/versions/2.6.6/lib/ruby/gems/2.6.0/gems/ffi-1.13.1 for
inspection.
Results logged to
/Users/gdk/.rbenv/versions/2.6.6/lib/ruby/gems/2.6.0/extensions/x86_64-darwin-18/2.6.0/ffi-1.13.1/gem_make.out

An error occurred while installing ffi (1.13.1), and Bundler cannot continue.
Make sure that `gem install ffi -v '1.13.1' --source 'https://rubygems.org/'`
succeeds before bundling.

In Gemfile:
  rbtrace was resolved to 0.4.14, which depends on
    ffi
make[1]: *** [/Users/gdk/code/ee-gdk/gitaly/.ruby-bundle] Error 5
make: *** [gitaly/bin/gitaly] Error 2

A solution on macOS is to re-install Xcode Command Line Tools.

LoadError due to readline

On macOS, GitLab may fail to start and fail with an error message about libreadline:

LoadError:
    dlopen(/Users/gdk/.rbenv/versions/2.6.3/lib/ruby/2.5.0/x86_64-darwin15/readline.bundle, 9): Library not loaded: /usr/local/opt/readline/lib/libreadline.7.dylib
        Referenced from: /Users/gdk/.rbenv/versions/2.6.3/lib/ruby/2.5.0/x86_64-darwin15/readline.bundle
        Reason: image not found - /Users/gdk/.rbenv/versions/2.6.3/lib/ruby/2.5.0/x86_64-darwin15/readline.bundle

This happens because the Ruby interpreter was linked with a version of the readline library that may have been updated on your system. To fix the error, reinstall the Ruby interpreter. For example, for environments managed with:

  • rbenv, run rbenv install 2.7.2.
  • RVM, run rvm reinstall ruby-2.7.2.

'LoadError: dlopen' when starting Ruby apps

This can happen when you try to load a Ruby gem with native extensions that were linked against a system library that is no longer there. A typical culprit is Homebrew on macOS, which encourages frequent updates (brew update && brew upgrade) which may break binary compatibility.

bundle exec rake db:create dev:setup
rake aborted!
LoadError: dlopen(/Users/gdk/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/extensions/x86_64-darwin-13/2.1.0-static/charlock_holmes-0.6.9.4/charlock_holmes/charlock_holmes.bundle, 9): Library not loaded: /usr/local/opt/icu4c/lib/libicui18n.52.1.dylib
  Referenced from: /Users/gdk/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/extensions/x86_64-darwin-13/2.1.0-static/charlock_holmes-0.6.9.4/charlock_holmes/charlock_holmes.bundle
  Reason: image not found - /Users/gdk/.rbenv/versions/2.1.2/lib/ruby/gems/2.1.0/extensions/x86_64-darwin-13/2.1.0-static/charlock_holmes-0.6.9.4/charlock_holmes/charlock_holmes.bundle
/Users/gdk/gitlab-development-kit/gitlab/config/application.rb:6:in `<top (required)>'
/Users/gdk/gitlab-development-kit/gitlab/Rakefile:5:in `require'
/Users/gdk/gitlab-development-kit/gitlab/Rakefile:5:in `<top (required)>'
(See full trace by running task with --trace)

In the above example, you see that the charlock_holmes gem fails to load libicui18n.52.1.dylib. You can try fixing this by re-installing charlock_holmes.

'bundle install' fails due to permission problems

This can happen if you are using a system-wide Ruby installation. You can override the Ruby gem install path with BUNDLE_PATH:

# Install gems in (current directory)/vendor/bundle
make BUNDLE_PATH=$(pwd)/vendor/bundle

'bundle install' fails while compiling eventmachine gem

On OS X El Capitan, the eventmachine gem compilation might fail with:

Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
<snip>
make "DESTDIR=" clean

make "DESTDIR="
compiling binder.cpp
In file included from binder.cpp:20:
./project.h:116:10: fatal error: 'openssl/ssl.h' file not found
#include <openssl/ssl.h>
        ^
1 error generated.
make: *** [binder.o] Error 1

make failed, exit code 2

To fix it:

bundle config build.eventmachine --with-cppflags=-I/usr/local/opt/openssl/include

and then do bundle install once again.

Bootsnap-related problems

If your local instance does not start up and you see bootsnap errors like this:

2020-07-09_07:29:27.20103 rails-web             : .rvm/gems/ruby-2.6.6/gems/bootsnap-1.4.6/lib/bootsnap/load_path_cache/core_ext/active_support.rb:61:in `block in load_missing_constant': uninitialized constant EE::OperationsHelper (NameError)
2020-07-09_07:29:27.20104 rails-web             : .rvm/gems/ruby-2.6.6/gems/bootsnap-1.4.6/lib/bootsnap/load_path_cache/core_ext/active_support.rb:17:in `allow_bootsnap_retry'

You should remove the bootsnap cache:

gdk stop
rm -rf gitlab/tmp/cache/bootsnap-*
gdk start

Truncate Rails logs

The logs in gitlab/log keep growing forever as you use the GDK.

You can truncate them either manually with the provided Rake task:

rake gitlab:truncate_logs

Or add a GDK hook to your gdk.yml with the following to truncate them before every gdk update:

gdk:
  update_hooks:
    before:
      - rake gitlab:truncate_logs

OpenSSL 3 breaks Ruby builds

Ubuntu 22.04 and Fedora 36 ship with OpenSSL 3.0, which causes Ruby builds and gem failures. Ruby 2.7.x and 3.0.x don't support OpenSSL 3.

As a workaround, you must compile and install OpenSSL 1.1.1:

  1. Install the dependencies:

    ## Ubuntu 22.04
sudo apt install build-essential checkinstall zlib1g-dev

## Fedora 36
sudo dnf groupinstall "Development Tools"
sudo dnf install perl-core zlib-devel

  2. Download OpenSSL 1.1.1:

    cd ~/Downloads
wget https://www.openssl.org/source/openssl-1.1.1o.tar.gz
tar xf openssl-1.1.1o.tar.gz

  3. Compile OpenSSL 1.1.1:

    cd ~/Downloads/openssl-1.1.1o
./config --prefix=/opt/openssl-1.1.1o --openssldir=/opt/openssl-1.1.1o shared zlib
make
make test
sudo make install

  4. Link the system's certs to OpenSSL's 1.1.1 directory:

    sudo rm -rf /opt/openssl-1.1.1o/certs
sudo ln -s /etc/ssl/certs /opt/openssl-1.1.1o

  5. Add the following line to your .bashrc or .zshrc:

    export RUBY_CONFIGURE_OPTS="--with-openssl-dir=/opt/openssl-1.1.1o/"

  6. Start a new shell for the environment variable to apply, or source your .bashrc or .zshrc:

    source ~/.bashrc
source ~/.zshrc

  7. Remove Ruby 2.7.5 with asdf:

    asdf uninstall ruby 2.7.5

  8. Bootstrap GDK:

    rm <path/to/gdk>/.cache/.gdk_platform_setup
rm <path/to/gdk>/.cache/.gdk_bootstrapped
make bootstrap

  9. Update GDK:

    gdk update