Unable to bundle exec jekyll build because of missing gems - nokogiri issue

[sr-murthy]

Hi

I'm unable to bundle exec jekyll build my blog, it reports that the github-pages gem is missing:

Could not find gem 'github-pages (= 33) ruby' in the gems available on this machine.

So I tried bundle install but I run into the issue with nokigori again:

Fetching gem metadata from https://rubygems.org/..........
Resolving dependencies...
Using RedCloth 4.2.9
Using i18n 0.7.0
Using json 1.8.2
Using minitest 5.5.1
Using thread_safe 0.3.5
Using tzinfo 1.2.2
Using activesupport 4.2.1
Using blankslate 2.1.2.4
Using hitimes 1.2.2
Using timers 4.0.1
Using celluloid 0.16.0
Using fast-stemmer 1.0.2
Using classifier-reborn 2.0.3
Using coffee-script-source 1.9.1
Using execjs 2.4.0
Using coffee-script 2.3.0
Using colorator 0.1
Using ffi 1.9.8
Using gemoji 2.1.0
Using net-dns 0.8.0
Using public_suffix 1.5.0
Using github-pages-health-check 0.2.2
Using jekyll-coffeescript 1.0.1
Using jekyll-gist 1.2.1
Using jekyll-paginate 1.1.0
Using sass 3.4.13
Using jekyll-sass-converter 1.2.0
Using rb-fsevent 0.9.4
Using rb-inotify 0.9.5
Using listen 2.10.0
Using jekyll-watch 1.2.1
Using kramdown 1.5.0
Using liquid 2.6.1
Using mercenary 0.3.5
Using posix-spawn 0.3.10
Using yajl-ruby 1.2.1
Using pygments.rb 0.6.1
Using redcarpet 3.1.2
Using safe_yaml 1.0.4
Using parslet 1.5.0
Using toml 0.1.2
Using jekyll 2.4.0
Using mini_portile 0.6.2

Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -r ./siteconf20150402-12603-e1uja9.rb extconf.rb --use-system-libraries
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 system libraries.
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=/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
--help
--clean
--use-system-libraries
--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-xml2-dir
--without-xml2-dir
--with-xml2-include
--without-xml2-include=${xml2-dir}/include
--with-xml2-lib
--without-xml2-lib=${xml2-dir}/lib
--with-libxml-2.0-config
--without-libxml-2.0-config
--with-pkg-config
--without-pkg-config
--with-xslt-dir
--without-xslt-dir
--with-xslt-include
--without-xslt-include=${xslt-dir}/include
--with-xslt-lib
--without-xslt-lib=${xslt-dir}/lib
--with-libxslt-config
--without-libxslt-config
--with-exslt-dir
--without-exslt-dir
--with-exslt-include
--without-exslt-include=${exslt-dir}/include
--with-exslt-lib
--without-exslt-lib=${exslt-dir}/lib
--with-libexslt-config
--without-libexslt-config
--with-xml2lib
--without-xml2lib
--with-libxml2lib
--without-libxml2lib

extconf failed, exit code 1

Gem files will remain installed in /var/folders/md/qy7y7r3d2zn7wfmcpvc2mtk80000gn/T/bundler20150402-12603-19vuinn/nokogiri-1.6.6.2/gems/nokogiri-1.6.6.2 for inspection.
Results logged to /var/folders/md/qy7y7r3d2zn7wfmcpvc2mtk80000gn/T/bundler20150402-12603-19vuinn/nokogiri-1.6.6.2/extensions/universal-darwin-14/2.0.0/nokogiri-1.6.6.2/gem_make.out
An error occurred while installing nokogiri (1.6.6.2), and Bundler cannot continue.
Make sure that `gem install nokogiri -v '1.6.6.2'` succeeds before bundling.

I tried gem install nokogiri -v '1.6.6.2' but I had the usual error message which is

Building native extensions.  This could take a while...
ERROR:  Error installing nokogiri:
ERROR: Failed to build gem native extension.

/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -r ./siteconf20150402-7321-15frer3.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/ports/libxml2/2.9.2... OK
Running patch with /Library/Ruby/Gems/2.0.0/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 /Library/Ruby/Gems/2.0.0/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... ERROR, review '/Library/Ruby/Gems/2.0.0/gems/nokogiri-1.6.6.2/ext/nokogiri/tmp/x86_64-apple-darwin14/ports/libxml2/2.9.2/compile.log' to see what happened.
*** 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=/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/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
/Library/Ruby/Gems/2.0.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:279:in `block in execute': Failed to complete compile task (RuntimeError)
from /Library/Ruby/Gems/2.0.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:271:in `chdir'
from /Library/Ruby/Gems/2.0.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:271:in `execute'
from /Library/Ruby/Gems/2.0.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:70:in `compile'
from /Library/Ruby/Gems/2.0.0/gems/mini_portile-0.6.2/lib/mini_portile.rb:110:in `cook'
from extconf.rb:278:in `block in process_recipe'
from extconf.rb:177:in `tap'
from extconf.rb:177:in `process_recipe'
from extconf.rb:475:in `<main>'

extconf failed, exit code 1

Gem files will remain installed in /Library/Ruby/Gems/2.0.0/gems/nokogiri-1.6.6.2 for inspection.
Results logged to /Library/Ruby/Gems/2.0.0/extensions/universal-darwin-14/2.0.0/nokogiri-1.6.6.2    /gem_make.out

[sr-murthy]

I found a solution to the installation of the latest version of nokogiri, as reported here

sparklemotion/nokogiri#1166

by @dwt, and bunde install and bundle exec jekyll build are working fine now.