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

Question

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?

Solution 1

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.

Solution 2

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.

Solution 3

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.

Solution 4

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)

Solution 5

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

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

View more solutions

Comments

[Nate Berkopec]

Nokogiri 1.6 and higher now bundles libxml2 with the gem, so you can fix this error by just removing libxml2 from Homebrew. brew remove --force libxml2 bundle config --delete build.nokogiri gem uninstall nokogiri libxml-ruby bundle

[Mario Uher]

This is the answer: [stackoverflow.com/questions/16921700/… [1]: stackoverflow.com/questions/16921700/…

[egyamado]

@NateBerkopec. Your solution worked for me while the accepted answer didn't.

[Damien Roche]

1.6.2.1 and Ubuntu 12.04 don't play nice. Dropping back to 1.6.1 fixed it after trying every other fix I could find.

[Phillip Koebbe]

heh...your instructions to split the build options between /usr and /opt/local (MacPorts) did it for me ... thanks

[Kenton]

Glad to see someone smarter than me also fell afoul of the Apple Bootstrap libxml2 nightmare :)

[M. Scott Ford]

I don't think the link and unlink commands are needed. I was able get away without using them.

[starscream_disco_party]

I just stumbled across this post randomly and had no use for it, but this detailed answer deserves many upvotes for the effort!

[asymmetric]

note that you might have to prepend the gem commands with bundle exec - for example if you're using rbenv.

[Nate Berkopec]

Is there any reason you aren't including brew uninstall libxslt?

[acoustic_north]

I might also add that I had to delete my vendor/bundle folder where I had nokogiri previously installed and rerun bundle install to make sure I got the fresh installation of nokogiri.

[patrickmcgraw]

I was able to make the warning go away just by moving nokogiri to the first gem in my Gemfile

[Alexander Presber]

Works like a charm. Thanks.

[Misery]

This fixed it for me on OS X 10.8.2 with libxml 2.7.8 / 2.8.0. Just removing the nokogiri gem and reinstalling it did not solve it, but brew uninstall libxml2 beforehand did. thanks!

[Nate Berkopec]

For those copy-pasting this answer, the lastest version of libxml2 is 2.9.0 - be sure to edit this when copy pasting!

[IAmNaN]

Thanks for the feedback, Old Pro. I encourage you to consider re-reading the SO Privileges Q&A. "Use your downvotes whenever you encounter an egregiously sloppy, no-effort-expended post, or an answer that is clearly and perhaps dangerously incorrect." This answer clearly worked for several people including the OP so I don't think it warrants a downvote.

[sberkley]

I used a variation on this solution (where my dynamically loaded version was 2.9.0): bundle config build.nokogiri --with-xml2-include=/usr/local/Cellar/libxml2/2.9.0/include/‌​libxml2/

[user569825]

Due to the recently discovered cpu consumption DOS vulnerability (vuxml.org/freebsd/843a4641-9816-11e2-9c51-080027019be0.html‌​) we updated libxml2 on FreeBSD, causing the nokogiri warning in question. Reinstalling as described, solved the issue.

[awenkhh]

perfect answer if using homebrew

[duma]

Thanks to @sberkley for the updated tip. I noticed, when I ran it, that if you do it at ~, it seems to set this value globally. So perhaps you can just do this once and never have to worry about it again.

[toxaq]

Excellent, thank you. bundle exec gem pristine nokogiri nailed it.

[Matt Sanders]

If you are using bundler, make sure to look at @indirect's answer below. bundle exec gem pristine nokogiri is probably what you're after.

[Philipp]

Thanks, that did it. For the sake of completeness: don't forget to reinstall the nokogiri gem after running the bundle config ... command above.

[Nate Cook]

+1 Perfect. The key is to NOT have any other version of libxml2 installed when you install nokogiri.

[Nate Cook]

Also, just in case anyone else is RubyMine, this is what I helped me fixed the error I was getting with bundle install from within RubyMine. You can see the same error in the command line if you type rake --tasks

[Wolfram Arnold]

It bears highlighting that the last sentence is important: require nokogiri first Do this by putting nokogiri in your Gemfile ahead of rails.

[FernandoEscher]

If you don't do brew link libxml2 libxslt --overwirte --force you might end up compiling with a newer version, but loading with the one currently linked (which might the old one).

[duma]

This was the correct solution for me. I'm running Mountain Lion and am using homebrew (and Intellij IDEA).

[richard]

Worked perfectly for me with warning about being built against 2.8.0 by dynamically loading 2.7.8 on Ubuntu 12.04

[Jared Beck]

For an explanation of why this works, see this answer by @Jarrett

[Canbey Bilgili]

I have tried brew uninstall libxml2 I got Error: No such keg: /usr/local/Cellar/libxml2 But brew install libxml2 libxslt worked for me on mac os x mavericks.

[Artem Aminov]

Yeah! Helps me with 'WARNING: Nokogiri was built against LibXML version 2.8.0, but has dynamically loaded 2.7.8'

[jpw]

to get the warning to go away on Lion and rails 3.2.16, I had to do both 'bundle exec gem pristine nokogiri' and also move 'gem nokogiri' ahead of 'gem rails'

[Austin Pray]

Another copy paste warning. If you run these commands exactly as copy-pasted you must change libxml2 2.9.0 to libxml2 2.9.1 like: gem install nokogiri -- --with-xml2-include=/usr/local/Cellar/libxml2/2.8.1/include/‌​libxml2 --with-xml2-lib=/usr/local/Cellar/libxml2/2.8.1/lib --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26/

[steakchaser]

Worked for me on OSX 10.8.5

[CBanga]

This worked for me in OS X Mavericks, accepted answer did not.

[johnsyweb]

Rather than hard-code the paths, you can query brew, e.g: XML2_PREFIX=$(brew --prefix libxml2) bundle config build.nokogiri --with-xml2-include="${XML2_PREFIX}/include/libxml2" --with-xml2-lib="${XML2_PREFIX}/lib"...

[IAmNaN]

No, @Tass. update simply checks if there is a new version of the gem, which there isn't in this case. It's been a more than two years but I seem to remember without running uninstall, update was a NOP. I suspect the version of nokogiri doesn't change but the libs need to compiled with different headers after upgrading the OS.This method, by the way, has worked after several OSX updates now.

[Katarzyna]

$ gem uninstall nokogiri libxml-ruby You have requested to uninstall the gem: nokogiri-1.6.1 capybara-2.4.4 depends on nokogiri (>= 1.3.3) chromedriver-helper-1.0.0 depends on nokogiri (~> 1.6) ... sprockets-3.2.0 depends on nokogiri (~> 1.3, development) sprockets-3.1.0 depends on nokogiri (~> 1.3, development) sprockets-3.0.3 depends on nokogiri (~> 1.3, development) tilt-1.4.1 depends on nokogiri (>= 0, development) xpath-2.0.0 depends on nokogiri (~> 1.3) If you remove this gem, these dependencies will not be met. Continue with Uninstall? [yN]

[Michiel de Mare]

@Katarzyna It's ok to uninstall, since you're going to reinstall the dependencies right after uninstalling them.

[Katarzyna]

@Michiel de Mare, thank you but I found the other solution. However I want to make sure: I had to shorten the list of dependencies. There were e.g. capybara & other gems that I had installed before I installed nokogiri. Wouldn't they just break?

[Greg Blass]

This should be the accepted answer, not something that could potentially brick your machine, let alone being extremely verbose and confusing.

[ndbroadbent]

I actually just needed to run xcode-select --install: github.com/sparklemotion/nokogiri/issues/… Just need to follow the installation instructions for Nokogiri: nokogiri.org/tutorials/installing_nokogiri.html#mac_os_x

[danielMitD]

Even "easier" using the config binaries deliviered with both libs: gem install nokogiri -- --use-system-libraries --with-xml2-config=$(brew --prefix libxml2)/bin/xml2-config --with-xslt-config=$(brew --prefix libxslt)/bin/xslt-config