Mac user and getting WARNING: Nokogiri was built against LibXML version 2.7.8, but has dynamically loaded 2.7.3

I have done all kinds of research and tried many different things. I know this question has been answered many times, but none of the suggested solutions are working for me.

After upgrading to Lion I am getting segmentation faults in Ruby. I'm fairly confident it's Nokogiri. So I installed libxml2 via Homebrew. I ran brew link libxml2. Then I reinstalled Nokogiri using that version of the library.

For proof:

$ nokogiri -v
# Nokogiri (1.5.0)
---
warnings: []
nokogiri: 1.5.0
ruby:
version: 1.9.2
platform: x86_64-darwin11.0.0
description: ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-darwin11.0.0]
engine: ruby
libxml:
binding: extension
compiled: 2.7.8
loaded: 2.7.8

I've already included Nokogiri at the top of my gemfile and I've also required it in my environment file. I have no idea why I am still getting that warning.

Any suggestions or ideas to make sure it's loading the right version libxml2?

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I had similar problem and just solved this way:

In my case, I have RVM installed, and I had @global and @project gem sets. Both of them had nokogiri installed and one of them had built with with different libxml.

Rebuilding both of them (I have reason to do this) solved the problem.

Hope this helps..

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Bundler has options to set the default build locations. So for instance, with libxml2 installed via macports:

$ bundle config build.nokogiri --with-xml2-include=/opt/local/include/libxml2 --with-xml2-lib=/opt/local/lib --with-xslt-dir=/opt/local

After doing this and bundle install, the warning went away.

There's also some helpful examples for setting build options on the nokogiri wiki.

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最佳答案

I just spent the better part of the morning working through this warning. This fix is for people using Mac OS Lion. The fix above using 

bundle config build.nokogiri --with-xml2-include=/opt/local/include/libxml2 --with-xml2-lib=/opt/local/lib --with-xslt-dir=/opt/local

is for Snow Leopard with libxml2 installed via MacPorts.

With Lion, libxml2 is loaded as part of the bootstrap process. Regardless of which libxml2 Nokogiri is pointing to, the Lion system default library for libxml2 will be used at runtime. Lion uses libxml2.2.7.3 found in /usr (not /usr/local).

As mentioned many other places, one can just ignore the warning. If, like me, the warning drives you crazy, you can do this:

bundle config build.nokogiri --with-xml2-dir=/usr --with-xslt-dir=/opt/local --with-iconv-dir=/opt/local

Interestingly, if you type nokogiri -v at the command line you will get the opposite warning:

WARNING: Nokogiri was built against LibXML version 2.7.3, but has dynamically loaded 2.7.8

This suggests there is more to how libxml2 is being loaded, with Ruby and Rails using the system loaded libxml2 and the command line using libxml2 from the environment path. Anyway, this silences the error for me.

I’ll say it again – this is only for Lion. The previous fix will work for Snow Leopard.

This is the end of the answer. Stop reading here.

OK, you didn’t stop reading... well...

NOT RECOMMENDED!!!!!!

You have been warned. You can verify that Mac OSX is loading the libxml2 library in its bootstrap by disabling libxml2 found in /usr/lib. Do something like copying all versions of libxml2*.dylib to libxml2*.dylib.old (on my machine this was libxml2.2.7.3, libxml2.2 and libxml2).

After you have done this, running Nokogiri will not produce any errors. That is because it can’t find the loaded libxml2 and will now follow the environment path, eventually finding libxml2.2.7.8 in /opt/local.

BUT you won’t be able to copy the old libxml files back. This is because the OS needs the libxml2 that was loaded in the bootstrap.

Powering off and powering on again will brick your machine. The login screen will hang and hang and hang. Power off and power on again in single-user mode (hold Command-S while rebooting). You can watch the bootstrap occur. Low and behold, it throws an error that it can’t load libxml2 and then stops working.

Power off and power on again. This time boot into recovery mode (either hold Command-R or hold Option and then select the recovery disk). In recovery mode open the terminal (utilities/terminal). Mount /usr/lib on your HD (try /Volumes/Macintosh\ HD/usr/lib) and copy the libxml2 files back. Reboot and all will be fine.

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None of this worked for me.

I had libxml2 installed at a later version (2.7.8) with brew. This caused nokogiri to compile against it and the later problems. Solution, remove it, then build, then install if desired.

Here's what worked:

  • brew uninstall libxml2 (if previously installed)
  • gem uninstall nokogiri
  • gem install nokogiri
  • brew install libxml2 (optional)
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To fix this if you're using homebrew and bundler, add gem 'nokogiri' to the top of your Gemfile, then run these commands:

gem uninstall nokogiri libxml-ruby
brew update
brew uninstall libxml2
brew install libxml2 --with-xml2-config
brew install libxslt
bundle config build.nokogiri --with-xml2-include=/usr/local/Cellar/libxml2/2.9.1/include/libxml2 --with-xml2-lib=/usr/local/Cellar/libxml2/2.9.1/lib --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26/
bundle install

If you don't use bundler, run these commands instead:

gem uninstall nokogiri libxml-ruby
brew update
brew uninstall libxml2
brew install libxml2 --with-xml2-config
brew install libxslt
gem install nokogiri -- --with-xml2-include=/usr/local/Cellar/libxml2/2.9.1/include/libxml2 --with-xml2-lib=/usr/local/Cellar/libxml2/2.9.1/lib --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26/

In your app, you should require nokogiri first, to force the app to load the dynamic libxml2 library instead of the older system version of libxml2 loaded by gems that failed to specify which library to load.

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The solution (for me) after updating to Mountain Lion was much simplier:

gem uninstall nokogiri
# (and ignore the warnings about dependencies)
gem install nokogiri
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gem uninstall nokogiri
bundle  #install nokogiri again

If that fails with "libxml2 is missing." and you see gems/nokogiri-1.5.0/ext/nokogiri/mkmf.log trying to use "/usr/bin/gcc-4.2 ...", then you're missing /usr/bin/gcc-4.2

Solution: 

sudo ln -s /usr/bin/gcc /usr/bin/gcc-4.2

Before:

$ ll /usr/bin/gcc*
lrwxr-xr-x  1 root  wheel  12 Jan 15 00:16 /usr/bin/gcc -> llvm-gcc-4.2

After:

$ ll /usr/bin/gcc*
lrwxr-xr-x  1 root  wheel  12 Jan 15 00:16 /usr/bin/gcc -> llvm-gcc-4.2
lrwxr-xr-x  1 root  wheel  12 Jan 15 21:07 /usr/bin/gcc-4.2 -> /usr/bin/gcc

If you're really missing libxml2 libxslt, then

brew update
brew install libxml2 libxslt
brew link libxml2 libxslt
bundle config build.nokogiri --with-xml2-include=/usr/local/Cellar/libxml2/2.8.0/include/libxml2/ --with-xml2-lib=/usr/local/Cellar/libxml2/2.8.0/lib/ --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26/
bundle

FYI: I'm running Mountain Lion with brew, and bundler.

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If you installed Nokogiri with gem install nokogiri, you can resolve this warning by running gem pristine nokogiri to recompile the gem's C extension.

If you installed Nokogiri with bundle install, you can resolve this warning by running bundle exec gem pristine nokogiri to recompile the C extension of the gem wherever Bundler installed it.

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gem install libxml-ruby helps me

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As per the comment from patrickmcgraw above, simply putting nokogiri as the first entry in my Gemfile worked for me. I'm putting it as a separate answer because the original comment has been buried.

source 'http://rubygems.org'
gem 'nokogiri'
gem 'rails', '3.0.20'
etc...
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I actually had 2 versions of libxml installed, one from source, one from an RPM.

The following is my complete solution

I uninstalled source (from the source directory) 

sudo make uninstall

Remove bundles

rm -rf ~/.bundle ~/.bundler

Updated LD (might have to do this as root, not sudo)

sudo ldconfig

Then reinstalled the bundle

bundle install
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Just ran into this myself (OS X Lion 10.7.5). My exact message was: Nokogiri was built against LibXML version 2.8.0, but has dynamically loaded 2.7.3

I tried a few suggestions mentioned here, none worked, but this did: 

gem install nokogiri -- --with-xml2-dir=/usr --with-xslt-dir=/opt/local --with-iconv-dir=/opt/local

The explanation is: "This happens because the Lion system default libxml2 (loaded at bootstrap) is used, regardless of which libxml2 Nokogiri was built against."

Credits to: https://coderwall.com/p/o5ewia

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OS : Maverick 10.9.3

Ruby 1.9.3

WARNING: Nokogiri was built against LibXML version 2.9.1, but has dynamically loaded 2.9.0

My solution:

gem uninstall nokogiri
brew update
cd /usr/local
brew versions libxml2
git checkout 5dd45d7 /usr/local/Library/Formula/libxml2.rb # libxml version 2.9.0
brew install libxml2
bundle install or gem install nokogiri -v "1.5.11"

Hope this help

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Looks like you have updated your system libraries after installing the gem, so you have to update Nokogiri. To use the current lib version:

 gem install nokogiri -- --use-system-libraries
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If you have this message and your nokogiri is out-of-date with the version available from the gem source, simply run bundle update nokogiri to get the new code and recompile. Your error should go away.

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OS: Catalina

Warning: warning nokogiri was built against libxml version 2.9.10 but has dynamically loaded 2.9.4

I followed Michiel de Mare steps, but brew install libxml2 --with-xml2-config failed with invalid option error. So I installed libxml2 and libxslt and took note of the output from both commands.

 brew install libxml2
==> Downloading https://homebrew.bintray.com/bottles/libxml2-2.9.10_2.catalina.bottle.tar.gz
Already downloaded: /Users/alberto/Library/Caches/Homebrew/downloads/9ddf5cb90fd16a7eb531e37bb748fd392f30214d9fe1568b2b70d28cc368c8f7--libxml2-2.9.10_2.catalina.bottle.tar.gz
==> Pouring libxml2-2.9.10_2.catalina.bottle.tar.gz
==> Caveats
libxml2 is keg-only, which means it was not symlinked into /usr/local,
because macOS already provides this software and installing another version in
parallel can cause all kinds of trouble.


If you need to have libxml2 first in your PATH run:
echo 'export PATH="/usr/local/opt/libxml2/bin:$PATH"' >> ~/.zshrc


For compilers to find libxml2 you may need to set:
export LDFLAGS="-L/usr/local/opt/libxml2/lib"
export CPPFLAGS="-I/usr/local/opt/libxml2/include"


For pkg-config to find libxml2 you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/libxml2/lib/pkgconfig"


==> Summary
🍺  /usr/local/Cellar/libxml2/2.9.10_2: 280 files, 10.6MB



brew install libxslt
==> Downloading https://homebrew.bintray.com/bottles/libxslt-1.1.34.catalina.bottle.tar.gz
==> Downloading from https://d29vzk4ow07wi7.cloudfront.net/cbadecf3186f45754220dff4cbdfbb576882a211d615b52249a4c9d8ba4d7c3a?response-content-disposition=attachment%3Bfil
######################################################################## 100.0%
==> Pouring libxslt-1.1.34.catalina.bottle.tar.gz
==> Caveats
To allow the nokogiri gem to link against this libxslt run:
gem install nokogiri -- --with-xslt-dir=/usr/local/opt/libxslt


libxslt is keg-only, which means it was not symlinked into /usr/local,
because macOS already provides this software and installing another version in
parallel can cause all kinds of trouble.


If you need to have libxslt first in your PATH run:
echo 'export PATH="/usr/local/opt/libxslt/bin:$PATH"' >> ~/.zshrc


For compilers to find libxslt you may need to set:
export LDFLAGS="-L/usr/local/opt/libxslt/lib"
export CPPFLAGS="-I/usr/local/opt/libxslt/include"


For pkg-config to find libxslt you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/libxslt/lib/pkgconfig"


==> Summary
🍺  /usr/local/Cellar/libxslt/1.1.34: 136 files, 2.8MB

And I used those directories when configuring bundle for nokogiri

bundle config build.nokogiri --with-xml2-include=/usr/local/opt/libxml2/include --with-xml2-lib=/usr/local/opt/libxml2/lib --with-xslt-dir=/usr/local/opt/libxslt

To summarize I executed these steps

gem uninstall nokogiri libxml-ruby
brew update
brew uninstall libxml2
brew install libxml2
brew install libxslt
bundle config build.nokogiri --with-xml2-include=/usr/local/opt/libxml2/include --with-xml2-lib=/usr/local/opt/libxml2/lib --with-xslt-dir=/usr/local/opt/libxslt
bundle install

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