bundle update failing for github-pages - ruby-on-rails

Question

I'm trying to run bundle update as described at https://help.github.com/articles/using-jekyll-with-pages/ to update the github-pages gem on my Mac OS X 10.11.1. I get this error...
pschloss#polypay schlosslab.github.io (master) $ bundle update
Fetching gem metadata from https://rubygems.org/............
Fetching version metadata from https://rubygems.org/...
Fetching dependency metadata from https://rubygems.org/..
Resolving dependencies...
Using RedCloth 4.2.9
Using i18n 0.7.0
Using json 1.8.3
Using minitest 5.8.4
Using thread_safe 0.3.5
Using addressable 2.3.8
Using blankslate 2.1.2.4
Using fast-stemmer 1.0.2
Using coffee-script-source 1.10.0
Using execjs 2.6.0
Using colorator 0.1
Using ffi 1.9.10
Using multipart-post 2.0.0
Using gemoji 2.1.0
Using net-dns 0.8.0
Using public_suffix 1.5.3
Using jekyll-paginate 1.1.0
Using sass 3.4.21
Using rb-fsevent 0.9.7
Using kramdown 1.9.0
Using liquid 2.6.2
Using mercenary 0.3.5
Using posix-spawn 0.3.11
Using yajl-ruby 1.2.1
Using redcarpet 3.3.3
Using safe_yaml 1.0.4
Using jekyll-feed 0.3.1
Using mini_portile2 2.0.0
Using jekyll-sitemap 0.9.0
Using maruku 0.7.0
Using rdiscount 2.1.8
Using terminal-table 1.5.2
Using bundler 1.11.2
Using tzinfo 1.2.2
Using parslet 1.5.0
Using classifier-reborn 2.0.4
Using coffee-script 2.4.1
Using ethon 0.8.1
Using rb-inotify 0.9.5
Using faraday 0.9.2
Using jekyll-sass-converter 1.3.0
Using pygments.rb 0.6.3
Installing nokogiri 1.6.7.2 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
current directory: /Users/pschloss/Documents/websites/schlosslab.github.io/vendor/bundle/ruby/2.0.0/gems/nokogiri-1.6.7.2/ext/nokogiri
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -r ./siteconf20160201-14595-1a3dixy.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.
Using mini_portile version 2.0.0
checking for iconv.h... yes
checking for gzdopen() in -lz... yes
checking for iconv... no
-----
libiconv 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
--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
To see why this extension failed to compile, please check the mkmf.log which can be found here:
/Users/pschloss/Documents/websites/schlosslab.github.io/vendor/bundle/ruby/2.0.0/extensions/universal-darwin-15/2.0.0/nokogiri-1.6.7.2/mkmf.log
extconf failed, exit code 1
Gem files will remain installed in /Users/pschloss/Documents/websites/schlosslab.github.io/vendor/bundle/ruby/2.0.0/gems/nokogiri-1.6.7.2 for inspection.
Results logged to /Users/pschloss/Documents/websites/schlosslab.github.io/vendor/bundle/ruby/2.0.0/extensions/universal-darwin-15/2.0.0/nokogiri-1.6.7.2/gem_make.out
Using activesupport 4.2.5.1
Using toml 0.1.2
Using jekyll-coffeescript 1.0.1
Using typhoeus 0.8.0
Using listen 3.0.5
Using sawyer 0.6.0
An error occurred while installing nokogiri (1.6.7.2), and Bundler cannot continue.
Make sure that `gem install nokogiri -v '1.6.7.2'` succeeds before bundling.
As it suggests, I then run gem install nokogiri -v '1.6.7.2' and it installs fine. I repeat bundle update and get the same error as before. When I do nokogiri --version it comes back as 1.6.7.2:
$ nokogiri --version
# Nokogiri (1.6.7.2)
---
warnings: []
nokogiri: 1.6.7.2
ruby:
version: 2.3.0
platform: x86_64-darwin15
description: ruby 2.3.0p0 (2015-12-25 revision 53290) [x86_64-darwin15]
engine: ruby
libxml:
binding: extension
source: packaged
libxml2_path: "/Users/pschloss/.gem/ruby/2.3.0/gems/nokogiri-1.6.7.2/ports/x86_64-apple-darwin15.0.0/libxml2/2.9.2"
libxslt_path: "/Users/pschloss/.gem/ruby/2.3.0/gems/nokogiri-1.6.7.2/ports/x86_64-apple-darwin15.0.0/libxslt/1.1.28"
libxml2_patches:
- 0001-Revert-Missing-initialization-for-the-catalog-module.patch
- 0002-Fix-missing-entities-after-CVE-2014-3660-fix.patch
- 0003-Stop-parsing-on-entities-boundaries-errors.patch
- 0004-Cleanup-conditional-section-error-handling.patch
- 0005-CVE-2015-1819-Enforce-the-reader-to-run-in-constant-.patch
- 0006-Another-variation-of-overflow-in-Conditional-section.patch
- 0007-Fix-an-error-in-previous-Conditional-section-patch.patch
- 0008-CVE-2015-8035-Fix-XZ-compression-support-loop.patch
- 0009-Updated-config.guess.patch
- 0010-Fix-parsering-short-unclosed-comment-uninitialized-access.patch
- 0011-Avoid-extra-processing-of-MarkupDecl-when-EOF.patch
- 0012-Avoid-processing-entities-after-encoding-conversion-.patch
- 0013-CVE-2015-7497-Avoid-an-heap-buffer-overflow-in-xmlDi.patch
- 0014-CVE-2015-5312-Another-entity-expansion-issue.patch
- 0015-Add-xmlHaltParser-to-stop-the-parser.patch
- 0016-Detect-incoherency-on-GROW.patch
- 0017-CVE-2015-7500-Fix-memory-access-error-due-to-incorre.patch
- 0018-CVE-2015-8242-Buffer-overead-with-HTML-parser-in-pus.patch
- 0019-Do-not-print-error-context-when-there-is-none.patch
- 0020-xmlStopParser-reset-errNo.patch
- 0021-Reuse-xmlHaltParser-where-it-makes-sense.patch
libxslt_patches:
- 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
- 0016-Fix-for-type-confusion-in-preprocessing-attributes.patch
- 0017-Updated-config.guess.patch
compiled: 2.9.2
loaded: 2.9.2
Any suggestions? This doesn't seem like a nokogiri problem, but a github-pages or bundler problem (of course, I could be the problem too!)

Answer 1

The problem is with extension build process being unable to find libiconv for some reason.
Everyone around seems to be recommending the usage of an extra parameter for RubyGems, but the question explicitly states that gem alone actually installs the gem in question just fine. So this has something to do with the way your Bundler's bundle of gems is configured.
You can apply configuration to this specific bundle by using bundle config:
bundle config build.nokogiri --use-system-libraries
This, roughly, tells Bundler "whenever you install nokogiri, add --use-system-libraries".
...and then continue on:
bundle update
Credits to the fine people behind this answer.

Answer 2

Try the below code.
gem install nokogiri -- --use-system-libraries

Answer 3

Your bundle tries to install gem into vendor/bundle instead of system gems, that means that you probably tried --path vendor/bundle or --deployment - see cat .bundle/config
You can gem back to using system gems by running bundle install --system

Answer 4

I think same problem is faced many programmer before you & resolved this, if you ask anything on stackoverflow make sure this type of question have or not. anyway try this
gem install pg -- --with-pg-config= 'PATH_TO_YOUR_PG_CONFIG'
Thanks