ruby-on-rails - 无法在 Yosemite 上安装 Rails - 我觉得我已经尝试了一切

Question

我觉得我已经阅读了所有教程和所有 StackExchange 帖子，但在尝试安装 Rails 时仍然遇到相同的错误。这是我遇到的常见错误:

$ gem install rails --no-ri --no-rdoc
Building native extensions.  This could take a while...
ERROR:  Error installing rails:
    ERROR: Failed to build gem native extension.

    /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/bin/ruby -r ./siteconf20150409-59802-iosiis.rb extconf.rb
checking if the C compiler accepts ... yes
checking if the C compiler accepts -Wno-error=unused-command-line-argument-hard-error-in-future... no
Building nokogiri using packaged libraries.
checking for gzdopen() in -lz... yes
checking for iconv... yes
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxml2-2.9.2
with the following patches applied:
    - 0001-Revert-Missing-initialization-for-the-catalog-module.patch
    - 0002-Fix-missing-entities-after-CVE-2014-3660-fix.patch

Team Nokogiri will keep on doing their best to provide security
updates in a timely manner, but if this is a concern for you and want
to use the system library instead; abort this installation process and
reinstall nokogiri as follows:

    gem install nokogiri -- --use-system-libraries
        [--with-xml2-config=/path/to/xml2-config]
        [--with-xslt-config=/path/to/xslt-config]

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

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

Note, however, that nokogiri is not fully compatible with arbitrary
versions of libxml2 provided by OS/package vendors.
************************************************************************
Extracting libxml2-2.9.2.tar.gz into tmp/x86_64-apple-darwin14.1.0/ports/libxml2/2.9.2... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxml2/0001-Revert-Missing-initialization-for-the-catalog-module.patch...
Running 'patch' for libxml2 2.9.2... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxml2/0002-Fix-missing-entities-after-CVE-2014-3660-fix.patch...
Running 'patch' for libxml2 2.9.2... OK
Running 'configure' for libxml2 2.9.2... OK
Running 'compile' for libxml2 2.9.2... OK
Running 'install' for libxml2 2.9.2... OK
Activating libxml2 2.9.2 (from /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/x86_64-apple-darwin14.1.0/libxml2/2.9.2)...
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxslt-1.1.28
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

Team Nokogiri will keep on doing their best to provide security
updates in a timely manner, but if this is a concern for you and want
to use the system library instead; abort this installation process and
reinstall nokogiri as follows:

    gem install nokogiri -- --use-system-libraries
        [--with-xml2-config=/path/to/xml2-config]
        [--with-xslt-config=/path/to/xslt-config]

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-darwin14.1.0/ports/libxslt/1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0001-Adding-doc-update-related-to-1.1.28.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0002-Fix-a-couple-of-places-where-f-printf-parameters-wer.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0003-Initialize-pseudo-random-number-generator-with-curre.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0004-EXSLT-function-str-replace-is-broken-as-is.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0006-Fix-str-padding-to-work-with-UTF-8-strings.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0007-Separate-function-for-predicate-matching-in-patterns.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0008-Fix-direct-pattern-matching.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0009-Fix-certain-patterns-with-predicates.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0010-Fix-handling-of-UTF-8-strings-in-EXSLT-crypto-module.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0013-Memory-leak-in-xsltCompileIdKeyPattern-error-path.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0014-Fix-for-bug-436589.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/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/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/x86_64-apple-darwin14.1.0/libxslt/1.1.28)...
checking for main() in -llzma... yes
checking for xmlParseDoc() in libxml/parser.h... no
checking for xmlParseDoc() in -lxml2... no
checking for xmlParseDoc() in -llibxml2... no
-----
libxml2 is missing.  Please locate mkmf.log to investigate how it is failing.
-----
*** 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/jdesilvio/.rvm/rubies/ruby-2.2.0/bin/$(RUBY_BASE_NAME)
    --help
    --clean
    --use-system-libraries
    --enable-static
    --disable-static
    --with-zlib-dir
    --without-zlib-dir
    --with-zlib-include
    --without-zlib-include=${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

extconf failed, exit code 1

Gem files will remain installed in /Users/jdesilvio/.rvm/gems/ruby-2.2.0@global/gems/nokogiri-1.6.6.2 for inspection.
Results logged to /Users/jdesilvio/.rvm/gems/ruby-2.2.0@global/extensions/x86_64-darwin-14/2.2.0-static/nokogiri-1.6.6.2/gem_make.out

我的操作系统是 OS X Yosemite 10.10.2

这是我到目前为止安装的，我使用 RMV 安装 Ruby:

$ ruby -v
ruby 2.2.0p0 (2014-12-25 revision 49005) [x86_64-darwin14]

$ xcode-select -p
/Applications/Xcode.app/Contents/Developer

$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --    with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.1.0
Thread model: posix

$ gem -v
2.4.6

我使用以下方法安装 Rails 并不断收到上述错误:

$ gem install rails --no-ri --no-rdoc

$ gem install rails -v 4.2.0

$ gem install nokogiri -- --use-system-libraries --with-xml2-include=/opt/local/include/libxml2 --with-xml2-lib=/opt/local/lib --with-xslt-dir=/opt/local

$ sudo gem install rails --no-ri --no-rdoc

我不知道还能做什么，请帮忙。

@rainkinz:

$ cat /Users/jdesilvio/.rvm/gems/ruby-2.2.0@global/extensions/x86_64-darwin-14/2.2.0-static/nokogiri-1.6.6.2/gem_make.out

/Users/jdesilvio/.rvm/rubies/ruby-2.2.0/bin/ruby -r ./siteconf20150409-82655-12gg3g1.rb extconf.rb
checking if the C compiler accepts ... yes
checking if the C compiler accepts -Wno-error=unused-command-line-argument-hard-error-in-future... no
Building nokogiri using packaged libraries.
checking for gzdopen() in -lz... yes
checking for iconv... yes
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxml2-2.9.2
with the following patches applied:
    - 0001-Revert-Missing-initialization-for-the-catalog-module.patch
    - 0002-Fix-missing-entities-after-CVE-2014-3660-fix.patch

Team Nokogiri will keep on doing their best to provide security
updates in a timely manner, but if this is a concern for you and want
to use the system library instead; abort this installation process and
reinstall nokogiri as follows:

    gem install nokogiri -- --use-system-libraries
        [--with-xml2-config=/path/to/xml2-config]
        [--with-xslt-config=/path/to/xslt-config]

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

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

Note, however, that nokogiri is not fully compatible with arbitrary
versions of libxml2 provided by OS/package vendors.
************************************************************************
Extracting libxml2-2.9.2.tar.gz into tmp/x86_64-apple-darwin14.1.0/ports/libxml2/2.9.2... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxml2/0001-Revert-Missing-initialization-for-the-catalog-module.patch...
Running 'patch' for libxml2 2.9.2... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxml2/0002-Fix-missing-entities-after-CVE-2014-3660-fix.patch...
Running 'patch' for libxml2 2.9.2... OK
Running 'configure' for libxml2 2.9.2... OK
Running 'compile' for libxml2 2.9.2... OK
Running 'install' for libxml2 2.9.2... OK
Activating libxml2 2.9.2 (from /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/x86_64-apple-darwin14.1.0/libxml2/2.9.2)...
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxslt-1.1.28
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

Team Nokogiri will keep on doing their best to provide security
updates in a timely manner, but if this is a concern for you and want
to use the system library instead; abort this installation process and
reinstall nokogiri as follows:

    gem install nokogiri -- --use-system-libraries
        [--with-xml2-config=/path/to/xml2-config]
        [--with-xslt-config=/path/to/xslt-config]

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-darwin14.1.0/ports/libxslt/1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0001-Adding-doc-update-related-to-1.1.28.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0002-Fix-a-couple-of-places-where-f-printf-parameters-wer.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0003-Initialize-pseudo-random-number-generator-with-curre.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0004-EXSLT-function-str-replace-is-broken-as-is.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0006-Fix-str-padding-to-work-with-UTF-8-strings.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0007-Separate-function-for-predicate-matching-in-patterns.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0008-Fix-direct-pattern-matching.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0009-Fix-certain-patterns-with-predicates.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0010-Fix-handling-of-UTF-8-strings-in-EXSLT-crypto-module.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0013-Memory-leak-in-xsltCompileIdKeyPattern-error-path.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/patches/libxslt/0014-Fix-for-bug-436589.patch...
Running 'patch' for libxslt 1.1.28... OK
Running patch with /Users/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/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/jdesilvio/.rvm/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/nokogiri-1.6.6.2/ports/x86_64-apple-darwin14.1.0/libxslt/1.1.28)...
checking for main() in -llzma... yes
checking for xmlParseDoc() in libxml/parser.h... no
checking for xmlParseDoc() in -lxml2... no
checking for xmlParseDoc() in -llibxml2... no
-----
libxml2 is missing.  Please locate mkmf.log to investigate how it is failing.
-----
*** 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/jdesilvio/.rvm/rubies/ruby-2.2.0/bin/$(RUBY_BASE_NAME)
    --help
    --clean
    --use-system-libraries
    --enable-static
    --disable-static
    --with-zlib-dir
    --without-zlib-dir
    --with-zlib-include
    --without-zlib-include=${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

extconf failed, exit code 1

** brew doctor 的输出:

$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Some directories in /usr/local/share/man aren't writable.
This can happen if you "sudo make install" software that isn't managed
by Homebrew. If a brew tries to add locale information to one of these
directories, then the install will fail during the link step.
You should probably `chown` them:

    /usr/local/share/man/mann

Warning: A newer Command Line Tools release is available.
Update them from Software Update in the App Store.

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:

  /opt/local/bin/libpng-config
  /opt/local/bin/libpng16-config
  /opt/local/bin/ncurses5-config
  /opt/local/bin/ncursesw5-config
  /opt/local/bin/pkg-config
  /opt/local/bin/python2.7-config
  /Users/jdesilvio/anaconda/bin/curl-config
  /Users/jdesilvio/anaconda/bin/freetype-config
  /Users/jdesilvio/anaconda/bin/libdynd-config
  /Users/jdesilvio/anaconda/bin/libpng-config
  /Users/jdesilvio/anaconda/bin/libpng15-config
  /Users/jdesilvio/anaconda/bin/llvm-config
  /Users/jdesilvio/anaconda/bin/python-config
  /Users/jdesilvio/anaconda/bin/python2-config
  /Users/jdesilvio/anaconda/bin/python2.7-config
  /Users/jdesilvio/anaconda/bin/xml2-config
  /Users/jdesilvio/anaconda/bin/xslt-config
  /Library/Frameworks/Python.framework/Versions/3.4/bin/python3-config
  /Library/Frameworks/Python.framework/Versions/3.4/bin/python3.4-config
  /Library/Frameworks/Python.framework/Versions/3.4/bin/python3.4m-config

Warning: Python is installed at /Library/Frameworks/Python.framework

Homebrew only supports building against the System-provided Python or a
brewed Python. In particular, Pythons installed to /Library can interfere
with other software installs.

Warning: You have MacPorts or Fink installed:
  /opt/local/bin/port

This can cause trouble. You don't have to uninstall them, but you may want to
temporarily move them out of the way, e.g.

  sudo mv /opt/local ~/macports

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:
    /usr/local/lib/libMonoPosixHelper.dylib
    /usr/local/lib/libSFFileMonitor.32.dylib
    /usr/local/lib/libSFIPC.32.dylib
    /usr/local/lib/libSFIPC.I.dylib
    /usr/local/lib/libSFsqlite3.7.4.dylib
    /usr/local/lib/libSFSyncEngine.I.dylib
    /usr/local/lib/libtcl8.6.dylib
    /usr/local/lib/libtk8.6.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
    /usr/local/include/fakemysql.h
    /usr/local/include/fakepq.h
    /usr/local/include/fakesql.h
    /usr/local/include/itcl.h
    /usr/local/include/itcl2TclOO.h
    /usr/local/include/itclDecls.h
    /usr/local/include/itclInt.h
    /usr/local/include/itclIntDecls.h
    /usr/local/include/itclMigrate2TclCore.h
    /usr/local/include/itclTclIntStubsFcn.h
    /usr/local/include/mysqlStubs.h
    /usr/local/include/odbcStubs.h
    /usr/local/include/pqStubs.h
    /usr/local/include/tcl.h
    /usr/local/include/tclDecls.h
    /usr/local/include/tclOO.h
    /usr/local/include/tclOODecls.h
    /usr/local/include/tclPlatDecls.h
    /usr/local/include/tclThread.h
    /usr/local/include/tclTomMath.h
    /usr/local/include/tclTomMathDecls.h
    /usr/local/include/tdbc.h
    /usr/local/include/tdbcDecls.h
    /usr/local/include/tdbcInt.h
    /usr/local/include/tk.h
    /usr/local/include/tkDecls.h
    /usr/local/include/tkPlatDecls.h

Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected .pc files:
    /usr/local/lib/pkgconfig/tcl.pc
    /usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected static libraries:
    /usr/local/lib/libtclstub8.6.a
    /usr/local/lib/libtkstub8.6.a

Warning: You have a non-Homebrew 'pkg-config' in your PATH:
  /opt/local/bin/pkg-config

`./configure` may have problems finding brew-installed packages using
this other pkg-config.

Warning: Your Xcode (6.2) is outdated
Please update to Xcode 6.3.
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Answer 1

根据您的 brew doctor 输出:

sudo mv /opt/local ~/macports
mv  /Users/jdesilvio/anaconda  /Users/jdesilvio/anaconda.back

gem install nokogiri

然后可选择放回 macports(您可能不应该同时拥有 macports 和 homebrew)并可选择放回 anaconda(无论是什么)。我的猜测是安装在 anaconda 目录中的 libxml2 弄乱了 nokogiri 安装的 libxml2 header 的路径。