Vagrant plugin and nokogiri install issue

Question

I am attempting to install the vagrant-windows plugin on Mac OSX 10.9.2. I however consistently receive the error that Bundler cannot install nokogiri 1.6.2.

Examining the gem_make.out file reveals that nokogiri cannot find libxml2, which I have installed and linked via homebrew.

Below is my gem_make.out

    /Applications/Vagrant/embedded/bin/ruby extconf.rb 
Building nokogiri using packaged libraries.
checking for iconv.h... yes
checking for iconv_open() in iconv.h... no
checking for iconv_open() in -liconv... yes
Building libxml2-2.8.0 for nokogiri with the following patches applied:
    - 0001-Fix-parser-local-buffers-size-problems.patch
    - 0002-Fix-entities-local-buffers-size-problems.patch
    - 0003-Fix-an-error-in-previous-commit.patch
    - 0004-Fix-potential-out-of-bound-access.patch
    - 0005-Detect-excessive-entities-expansion-upon-replacement.patch
    - 0006-Do-not-fetch-external-parsed-entities.patch
    - 0007-Enforce-XML_PARSER_EOF-state-handling-through-the-pa.patch
    - 0008-Improve-handling-of-xmlStopParser.patch
    - 0009-Fix-a-couple-of-return-without-value.patch
    - 0010-Keep-non-significant-blanks-node-in-HTML-parser.patch
    - 0011-Do-not-fetch-external-parameter-entities.patch
************************************************************************
IMPORTANT!  Nokogiri builds and uses a packaged version of libxml2.

If this is a concern for you and you want to use the system library
instead, abort this installation process and reinstall nokogiri as
follows:

    gem install nokogiri -- --use-system-libraries

If you are using Bundler, tell it to use the option:

    bundle config build.nokogiri --use-system-libraries
    bundle install

However, note that nokogiri does not necessarily support all versions
of libxml2.

For example, libxml2-2.9.0 and higher are currently known to be broken
and thus unsupported by nokogiri, due to compatibility problems and
XPath optimization bugs.
************************************************************************
Extracting libxml2-2.8.0.tar.gz into tmp/x86_64-apple-darwin12.5.0/ports/libxml2/2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0001-Fix-parser-local-buffers-size-problems.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0002-Fix-entities-local-buffers-size-problems.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0003-Fix-an-error-in-previous-commit.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0004-Fix-potential-out-of-bound-access.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0005-Detect-excessive-entities-expansion-upon-replacement.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0006-Do-not-fetch-external-parsed-entities.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0007-Enforce-XML_PARSER_EOF-state-handling-through-the-pa.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0008-Improve-handling-of-xmlStopParser.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0009-Fix-a-couple-of-return-without-value.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0010-Keep-non-significant-blanks-node-in-HTML-parser.patch...
Running 'patch' for libxml2 2.8.0... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxml2/0011-Do-not-fetch-external-parameter-entities.patch...
Running 'patch' for libxml2 2.8.0... OK
Running 'configure' for libxml2 2.8.0... OK
Running 'compile' for libxml2 2.8.0... OK
Running 'install' for libxml2 2.8.0... OK
Activating libxml2 2.8.0 (from /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/x86_64-apple-darwin12.5.0/libxml2/2.8.0)...
Building libxslt-1.1.28 for nokogiri with the following patches applied:
    - 0001-Adding-doc-update-related-to-1.1.28.patch
    - 0002-Fix-a-couple-of-places-where-f-printf-parameters-wer.patch
    - 0003-Initialize-pseudo-random-number-generator-with-curre.patch
    - 0004-EXSLT-function-str-replace-is-broken-as-is.patch
    - 0006-Fix-str-padding-to-work-with-UTF-8-strings.patch
    - 0007-Separate-function-for-predicate-matching-in-patterns.patch
    - 0008-Fix-direct-pattern-matching.patch
    - 0009-Fix-certain-patterns-with-predicates.patch
    - 0010-Fix-handling-of-UTF-8-strings-in-EXSLT-crypto-module.patch
    - 0013-Memory-leak-in-xsltCompileIdKeyPattern-error-path.patch
    - 0014-Fix-for-bug-436589.patch
    - 0015-Fix-mkdir-for-mingw.patch
************************************************************************
IMPORTANT!  Nokogiri builds and uses a packaged version of libxslt.

If this is a concern for you and you want to use the system library
instead, abort this installation process and reinstall nokogiri as
follows:

    gem install nokogiri -- --use-system-libraries

If you are using Bundler, tell it to use the option:

    bundle config build.nokogiri --use-system-libraries
    bundle install
************************************************************************
Extracting libxslt-1.1.28.tar.gz into tmp/x86_64-apple-darwin12.5.0/ports/libxslt/1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0001-Adding-doc-update-related-to-1.1.28.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0002-Fix-a-couple-of-places-where-f-printf-parameters-wer.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0003-Initialize-pseudo-random-number-generator-with-curre.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0004-EXSLT-function-str-replace-is-broken-as-is.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0006-Fix-str-padding-to-work-with-UTF-8-strings.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0007-Separate-function-for-predicate-matching-in-patterns.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0008-Fix-direct-pattern-matching.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0009-Fix-certain-patterns-with-predicates.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0010-Fix-handling-of-UTF-8-strings-in-EXSLT-crypto-module.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0013-Memory-leak-in-xsltCompileIdKeyPattern-error-path.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0014-Fix-for-bug-436589.patch...
Running 'patch' for libxslt 1.1.28... OK
Running git apply with /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/patches/libxslt/0015-Fix-mkdir-for-mingw.patch...
Running 'patch' for libxslt 1.1.28... OK
Running 'configure' for libxslt 1.1.28... OK
Running 'compile' for libxslt 1.1.28... OK
Running 'install' for libxslt 1.1.28... OK
Activating libxslt 1.1.28 (from /Users/jason/.vagrant.d/gems/gems/nokogiri-1.6.2/ports/x86_64-apple-darwin12.5.0/libxslt/1.1.28)...
checking for main() in -llzma... yes
checking for linker flags for static linking... NONE
checking for xmlParseDoc() in libxml/parser.h... no
checking for xmlParseDoc() in -lxml2... no
checking for xmlParseDoc() in -llibxml2... no
-----
libxml2 is missing.  please visit http://nokogiri.org/tutorials/installing_nokogiri.html for help with installing dependencies.
-----
*** 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
    --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=/Applications/Vagrant/embedded/bin/ruby
    --help
    --clean
    --use-system-libraries
    --enable-static
    --disable-static
    --with-zlib-dir
    --without-zlib-dir
    --with-zlib-include
    --without-zlib-include=${zlib-dir}/include
    --with-zlib-lib
    --without-zlib-lib=${zlib-dir}/lib
    --enable-cross-build
    --disable-cross-build
    --with-xml2lib
    --without-xml2lib
    --with-libxml2lib
    --without-libxml2lib

Answer 1

I found I needed to explicitly tell Nokogiri to use certain libraries. This wasn't obvious to me at first as Vagrant uses an embedded version of Ruby and not anything to do with what is installed via brew, or the OS itself.

NOKOGIRI_USE_SYSTEM_LIBRARIES=1 vagrant plugin install vagrant-windows

EDIT: Also just saw this exact same answer from earlier today in terms of nokogiri based plugins with Vagrant and not just vagrant-windows: https://stackoverflow.com/a/23635023/2619

Answer 2

Following @flurdy's suggestion, upgrading to the latest Vagrant, 1.6.5 in my case, fixed this after days of trying everything the internet has to throw at this problem.