Trouble moving from 1.16.8 to 1.18.3 #3451

AlbertGrimley · 2025-02-27T14:52:29Z

AlbertGrimley
Feb 27, 2025

Hello. dependabot identified a vulnerability in my ruby project and wants to move nokogiri from 1.16.8 to 1.18.3. I'm not able to build:

Any help would be much appreciated. Thank you!

AlbertGrimley · 2025-02-27T15:02:03Z

AlbertGrimley
Feb 27, 2025
Author

When I run a bundle update, I get the following:

Installing nokogiri 1.18.3 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

current directory: /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/nokogiri-1.18.3/ext/nokogiri

/Users/AlbertGrimley/.rbenv/versions/3.1.2/bin/ruby -I /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0 -r
./siteconf20250227-64987-862xns.rb extconf.rb
checking for whether -std=c99 is accepted as CFLAGS... yes
checking for whether -Wno-declaration-after-statement is accepted as CFLAGS... yes
checking for whether -O2 is accepted as CFLAGS... yes
checking for whether -g is accepted as CFLAGS... yes
checking for whether -Winline is accepted as CFLAGS... yes
checking for whether -Wmissing-noreturn is accepted as CFLAGS... yes
checking for whether -Wconversion is accepted as CFLAGS... no
checking for whether -Wno-error=unused-command-line-argument-hard-error-in-future is accepted as CFLAGS... no
checking for whether -Wno-unknown-warning-option is accepted as CFLAGS... yes
Building nokogiri using packaged libraries.
Static linking is enabled.
Cross build is disabled.
checking for iconv.h... yes
Using mini_portile version 2.8.8
checking for iconv... yes
---------- IMPORTANT NOTICE ----------
Building Nokogiri with a packaged version of libxml2-2.13.6.
Configuration options: --host=arm64-apple-darwin23 --enable-static --disable-shared
--libdir=/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/nokogiri-1.18.3/ports/arm64-darwin23/libxml2/2.13.6/lib
--with-legacy --with-iconv=yes --disable-dependency-tracking --without-python --without-readline --with-c14n
--with-debug --with-threads --disable-shared --enable-static RANLIB=/usr/bin/ranlib CPPFLAGS= CFLAGS=-O2\ -g\ -fPIC
The following patches are being applied:

0001-Remove-script-macro-support.patch
0002-Update-entities-to-remove-handling-of-ssi.patch
0009-allow-wildcard-namespaces.patch
0010-update-config.guess-and-config.sub-for-libxml2.patch
0011-rip-out-libxml2-s-libc_single_threaded-support.patch
0019-xpath-Use-separate-static-hash-table-for-standard-fu.patch

The Nokogiri maintainers intend to provide timely security updates, but if
this is a concern for you and want to use your OS/distro system library
instead, then abort this installation process and install nokogiri as
instructed at:

https://nokogiri.org/tutorials/installing_nokogiri.html#installing-using-standard-system-libraries

Note, however, that nokogiri cannot guarantee compatibility with every
version of libxml2 that may be provided by OS/package vendors.

Extracting libxml2-2.13.6.tar.xz into tmp/arm64-apple-darwin23/ports/libxml2/2.13.6... *** 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.

Provided configuration options:
--with-opt-dir
--without-opt-dir
--with-opt-include
--without-opt-include=${opt-dir}/include
--with-opt-lib
--without-opt-lib=${opt-dir}/lib
--with-make-prog
--without-make-prog
--srcdir=.
--curdir
--ruby=/Users/AlbertGrimley/.rbenv/versions/3.1.2/bin/$(RUBY_BASE_NAME)
--help
--clean
--prevent-strip
--enable-system-libraries
--disable-system-libraries
--use-system-libraries
--enable-system-libraries
--disable-system-libraries
--use-system-libraries
--enable-static
--disable-static
--enable-cross-build
--disable-cross-build
--enable-cross-build
--disable-cross-build
--enable-xml2-legacy
--disable-xml2-legacy
--with-zlib-dir
--without-zlib-dir
--with-zlib-include
--without-zlib-include=${zlib-dir}/include
--with-zlib-lib
--without-zlib-lib=${zlib-dir}/lib
--with-iconv-dir
--without-iconv-dir
--with-iconv-include
--without-iconv-include=${iconv-dir}/include
--with-iconv-lib
--without-iconv-lib=${iconv-dir}/lib
--with-xml2-source-dir
--enable-xml2-legacy
--disable-xml2-legacy
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/mini_portile2-2.8.8/lib/mini_portile2/mini_portile.rb:557:in
xzcat_exe': xzcat not found (RuntimeError) from /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/mini_portile2-2.8.8/lib/mini_portile2/mini_portile.rb:568:in tar_command'
from
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/mini_portile2-2.8.8/lib/mini_portile2/mini_portile.rb:579:in
extract_file' from /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/mini_portile2-2.8.8/lib/mini_portile2/mini_portile.rb:140:in block in extract'
from
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/mini_portile2-2.8.8/lib/mini_portile2/mini_portile.rb:138:in
each' from /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/mini_portile2-2.8.8/lib/mini_portile2/mini_portile.rb:138:in extract'
from
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/mini_portile2-2.8.8/lib/mini_portile2/mini_portile.rb:233:in
cook' from extconf.rb:558:in block (2 levels) in process_recipe'
from extconf.rb:337:in chdir' from extconf.rb:337:in chdir_for_build'
from extconf.rb:558:in block in process_recipe' from <internal:kernel>:90:in tap'
from extconf.rb:456:in process_recipe' from extconf.rb:900:in

'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/extensions/arm64-darwin-23/3.1.0/nokogiri-1.18.3/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/nokogiri-1.18.3 for
inspection.
Results logged to
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/extensions/arm64-darwin-23/3.1.0/nokogiri-1.18.3/gem_make.out

/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/rubygems/ext/builder.rb:95:in run' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/rubygems/ext/ext_conf_builder.rb:47:in block in build'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/tempfile.rb:317:in open' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/rubygems/ext/ext_conf_builder.rb:26:in build'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/rubygems/ext/builder.rb:161:in build_extension' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/rubygems/ext/builder.rb:195:in block in build_extensions'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/rubygems/ext/builder.rb:192:in each' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/rubygems/ext/builder.rb:192:in build_extensions'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/3.1.0/rubygems/installer.rb:853:in build_extensions' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/rubygems_gem_installer.rb:71:in build_extensions'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/rubygems_gem_installer.rb:28:in
install' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/source/rubygems.rb:204:in install'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/installer/gem_installer.rb:54:in
install' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/installer/gem_installer.rb:16:in install_from_spec'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/installer/parallel_installer.rb:186:in
do_install' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/installer/parallel_installer.rb:177:in block in worker_pool'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/worker.rb:62:in apply_func' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/worker.rb:57:in block in
process_queue'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/worker.rb:54:in loop' /Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/worker.rb:54:in process_queue'
/Users/AlbertGrimley/.rbenv/versions/3.1.2/lib/ruby/gems/3.1.0/gems/bundler-2.3.13/lib/bundler/worker.rb:91:in `block (2
levels) in create_threads'

An error occurred while installing nokogiri (1.18.3), and Bundler cannot continue.

In Gemfile:
rails was resolved to 7.2.2.1, which depends on
actioncable was resolved to 7.2.2.1, which depends on
actionpack was resolved to 7.2.2.1, which depends on
actionview was resolved to 7.2.2.1, which depends on
rails-dom-testing was resolved to 2.2.0, which depends on
nokogiri

0 replies

stevecheckoway · 2025-02-28T01:18:59Z

stevecheckoway
Feb 28, 2025
Maintainer

From a quick glance, this looks like it might be due to flavorjones/mini_portile@422f194.

xzcat isn't available on macOS by default but /usr/bin/tar supports xz compression.

% /usr/bin/tar -Jcf a.tar.xz a.hs
% file a.tar.xz
a.tar.xz: XZ compressed data, checksum CRC64
% /usr/bin/tar -Jxvf a.tar.xz
x a.hs

0 replies

flavorjones · 2025-02-28T03:34:33Z

flavorjones
Feb 28, 2025
Maintainer

Your original problem, encountered while trying to install the precompiled native gems, can be solved by adding the platform x86_64-linux-gnu and/or x86_64-linux-musl to your Gemfile.lock, see the release notes for v1.18.0. You can do this with a command like

bundle lock --add-platform x86_64-linux-gnu

The problem in your second post, encountered while trying to compile from source, is correctly diagnosed by Steve in his comment above.

1 reply

AlbertGrimley Feb 28, 2025
Author

I had read the release notes and tried running the exact command you mentioned. It says it wrote the lock file but there are no changes in the lock file.

AlbertGrimley · 2025-02-28T14:44:15Z

AlbertGrimley
Feb 28, 2025
Author

Updating to bundler 2.6.2 and running a bundle update fixes my bundle install on my mac. However, my Heroku deploy is now failing. Looking into that now :)

0 replies

AlbertGrimley · 2025-02-28T15:00:08Z

AlbertGrimley
Feb 28, 2025
Author

remote: -----> Using Ruby version: ruby-3.1.2
remote: -----> Installing dependencies using bundler 2.6.2
remote: Running: BUNDLE_WITHOUT='development:test' BUNDLE_PATH=vendor/bundle BUNDLE_BIN=vendor/bundle/bin BUNDLE_DEPLOYMENT=1 bundle install -j4
remote: Fetching gem metadata from https://rubygems.org/.........
remote: The following platform specific gems are getting installed, yet the lockfile includes only their generic ruby version:
remote: * nokogiri-1.18.3-x86_64-linux
remote: Please run bundle lock --normalize-platforms and commit the resulting lockfile.
remote: Alternatively, you may run bundle lock --add-platform <list-of-platforms-that-you-want-to-support>
remote: nokogiri-1.18.3-x86_64-linux requires rubygems version >= 3.3.22, which is
remote: incompatible with the current version, 3.3.7
remote: Bundler Output: Fetching gem metadata from https://rubygems.org/.........
remote: The following platform specific gems are getting installed, yet the lockfile includes only their generic ruby version:
remote: * nokogiri-1.18.3-x86_64-linux
remote: Please run bundle lock --normalize-platforms and commit the resulting lockfile.
remote: Alternatively, you may run bundle lock --add-platform <list-of-platforms-that-you-want-to-support>
remote: nokogiri-1.18.3-x86_64-linux requires rubygems version >= 3.3.22, which is
remote: incompatible with the current version, 3.3.7

I tried running normalize-platforms and that didn't yelp. Same message.

5 replies

AlbertGrimley Feb 28, 2025
Author

Gemfile.lock attached for reference.
Gemfile.lock.txt

flavorjones Mar 2, 2025
Maintainer

The error message is right there in the log you posted:

remote: nokogiri-1.18.3-x86_64-linux requires rubygems version >= 3.3.22, which is
remote: incompatible with the current version, 3.3.7

AlbertGrimley Mar 3, 2025
Author

Yes. I tried adding
gem "rubygems-update", ">= 3.3.22"
to the gemfile and that didn't help. Same error.

flavorjones Mar 3, 2025
Maintainer

I have no idea how to upgrade rubygems in a Heroku build. I imagine Heroku may have documentation on how to do this, or a support team who can answer your questions.

AlbertGrimley Mar 3, 2025
Author

After a lot of fighting with heroku, my deploy is now successful and working. Thanks, all!

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Trouble moving from 1.16.8 to 1.18.3 #3451

AlbertGrimley Feb 27, 2025

Replies: 5 comments · 6 replies

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