I am using the IDE Cloud9 and wanted to upgrade the Ruby version (from 2.1.5. to 2.2.1). After installing RVM I said rvm use 2.2.1 and changed the Ruby version in the Gemfile to 2.2.1. Then I ran bundle install and got the following result:
Fetching gem metadata from https://rubygems.org/..........
Fetching version metadata from https://rubygems.org/...
Fetching dependency metadata from https://rubygems.org/..
Fetching https://github.com/leikind/wice_grid.git
Using rake 10.4.2
Installing CFPropertyList 2.3.1
Installing i18n 0.7.0
Installing json 1.8.3
Installing minitest 5.7.0
Installing thread_safe 0.3.5
Installing tzinfo 1.2.2
Installing activesupport 4.2.3
Installing builder 3.2.2
Installing erubis 2.7.0
Installing mini_portile 0.6.2
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
/usr/local/rvm/rubies/ruby-2.2.1/bin/ruby -r ./siteconf20150710-9483-je82d8.rb extconf.rb
checking if the C compiler accepts ... yes
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-unknown-linux-gnu/ports/libxml2/2.9.2... OK
Running patch with /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/gems/nokogiri-1.6.6.2/ports/x86_64-unknown-linux-gnu/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-unknown-linux-gnu/ports/libxslt/1.1.28... OK
Running patch with /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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 /usr/local/rvm/gems/ruby-2.2.1/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... ERROR, review '/usr/local/rvm/gems/ruby-2.2.1/gems/nokogiri-1.6.6.2/ext/nokogiri/tmp/x86_64-unknown-linux-gnu/ports/libxslt/1.1.28/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=/usr/local/rvm/rubies/ruby-2.2.1/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
/usr/local/rvm/gems/ruby-2.2.1/gems/mini_portile-0.6.2/lib/mini_portile.rb:279:in `block in execute': Failed to complete compile task (RuntimeError)
from /usr/local/rvm/gems/ruby-2.2.1/gems/mini_portile-0.6.2/lib/mini_portile.rb:271:in `chdir'
from /usr/local/rvm/gems/ruby-2.2.1/gems/mini_portile-0.6.2/lib/mini_portile.rb:271:in `execute'
from /usr/local/rvm/gems/ruby-2.2.1/gems/mini_portile-0.6.2/lib/mini_portile.rb:70:in `compile'
from /usr/local/rvm/gems/ruby-2.2.1/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:487:in `<main>'
extconf failed, exit code 1
Gem files will remain installed in /usr/local/rvm/gems/ruby-2.2.1/gems/nokogiri-1.6.6.2 for inspection.
Results logged to /usr/local/rvm/gems/ruby-2.2.1/extensions/x86_64-linux/2.2.0/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.
Also, Cloud9 generated a pop-up disk quota reached (I had over 200MB free space before running bundle install. I tried to run gem install nokogiri -v '1.6.6.2' just like the error message at the end instructed. But this fails with the error message pasted above. I think this might be due to lack of disk quota but I don't know for sure. I tried cleaning up using gem cleanup and rake tmp:clear but these generate the error: Could not find nokogiri-1.6.6.2 in any of the sources. Run 'bundle install' to install missing gems. How should I progress from here?
Remove your old version of ruby via rvm, this will free up space.
In the future you might try using rvm upgrade to upgrade in place, as it will upgrade ruby and them attempt to migrate all your gems over, and then offer you the option to remove the old ruby. But if you are space constrained due to quota you might run into similar issues.