Nokogiri : installer avec « Building native extensions » sous Mac OSX 10.12 Sierra

Si l’installation de la gem Nokogiri provoque une erreur telle que :

$ gem install nokogiri -v 1.6.7.1
Fetching: nokogiri-1.6.7.1.gem (100%)
Building native extensions.  This could take a while...
ERROR:  Error installing nokogiri:
  ERROR: Failed to build gem native extension.

    current directory: /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/ext/nokogiri
/Users/username/.rvm/rubies/ruby-2.3.1/bin/ruby -r ./siteconf20170214-68028-185u3z7.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 using --with-opt-* flags... 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
  - 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

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-darwin15.0.0/ports/libxml2/2.9.2... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0001-Revert-Missing-initialization-for-the-catalog-module.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0002-Fix-missing-entities-after-CVE-2014-3660-fix.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0003-Stop-parsing-on-entities-boundaries-errors.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0004-Cleanup-conditional-section-error-handling.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0005-CVE-2015-1819-Enforce-the-reader-to-run-in-constant-.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0006-Another-variation-of-overflow-in-Conditional-section.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0007-Fix-an-error-in-previous-Conditional-section-patch.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0008-CVE-2015-8035-Fix-XZ-compression-support-loop.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0009-Updated-config.guess.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0010-Fix-parsering-short-unclosed-comment-uninitialized-access.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0011-Avoid-extra-processing-of-MarkupDecl-when-EOF.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0012-Avoid-processing-entities-after-encoding-conversion-.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0013-CVE-2015-7497-Avoid-an-heap-buffer-overflow-in-xmlDi.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0014-CVE-2015-5312-Another-entity-expansion-issue.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0015-Add-xmlHaltParser-to-stop-the-parser.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0016-Detect-incoherency-on-GROW.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0017-CVE-2015-7500-Fix-memory-access-error-due-to-incorre.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxml2/0018-CVE-2015-8242-Buffer-overead-with-HTML-parser-in-pus.patch... 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/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/ports/x86_64-apple-darwin15.0.0/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
  - 0016-Fix-for-type-confusion-in-preprocessing-attributes.patch
  - 0017-Updated-config.guess.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-darwin15.0.0/ports/libxslt/1.1.28... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0001-Adding-doc-update-related-to-1.1.28.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0002-Fix-a-couple-of-places-where-f-printf-parameters-wer.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0003-Initialize-pseudo-random-number-generator-with-curre.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0004-EXSLT-function-str-replace-is-broken-as-is.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0006-Fix-str-padding-to-work-with-UTF-8-strings.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0007-Separate-function-for-predicate-matching-in-patterns.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0008-Fix-direct-pattern-matching.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0009-Fix-certain-patterns-with-predicates.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0010-Fix-handling-of-UTF-8-strings-in-EXSLT-crypto-module.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0013-Memory-leak-in-xsltCompileIdKeyPattern-error-path.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0014-Fix-for-bug-436589.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0015-Fix-mkdir-for-mingw.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0016-Fix-for-type-confusion-in-preprocessing-attributes.patch... OK
Running git apply with /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/patches/libxslt/0017-Updated-config.guess.patch... OK
Running 'configure' for libxslt 1.1.28... OK
Running 'compile' for libxslt 1.1.28... ERROR, review '/Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1/ext/nokogiri/tmp/x86_64-apple-darwin15.0.0/ports/libxslt/1.1.28/compile.log' to see what happened. Last lines are:
========================================================================
                      ^
xsltutils.c:1876:24: note: expanded from macro 'XSLT_CLOCK'
#    define XSLT_CLOCK CLOCK_REALTIME
                       ^
xsltutils.c:1886:23: error: use of undeclared identifier 'CLOCK_REALTIME'
        clock_gettime(XSLT_CLOCK, &startup);
                      ^
xsltutils.c:1876:24: note: expanded from macro 'XSLT_CLOCK'
#    define XSLT_CLOCK CLOCK_REALTIME
                       ^
xsltutils.c:1890:19: error: use of undeclared identifier 'CLOCK_REALTIME'
    clock_gettime(XSLT_CLOCK, &cur);
                  ^
xsltutils.c:1876:24: note: expanded from macro 'XSLT_CLOCK'
#    define XSLT_CLOCK CLOCK_REALTIME
                       ^
1 warning and 3 errors generated.
make[2]: *** [xsltutils.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
========================================================================
*** 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=/Users/username/.rvm/rubies/ruby-2.3.1/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
/Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/mini_portile2-2.0.0/lib/mini_portile2/mini_portile.rb:366:in `block in execute': Failed to complete compile task (RuntimeError)
  from /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/mini_portile2-2.0.0/lib/mini_portile2/mini_portile.rb:337:in `chdir'
  from /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/mini_portile2-2.0.0/lib/mini_portile2/mini_portile.rb:337:in `execute'
  from /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/mini_portile2-2.0.0/lib/mini_portile2/mini_portile.rb:111:in `compile'
  from /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/mini_portile2-2.0.0/lib/mini_portile2/mini_portile.rb:150:in `cook'
  from extconf.rb:289:in `block (2 levels) in process_recipe'
  from extconf.rb:182:in `block in chdir_for_build'
  from extconf.rb:181:in `chdir'
  from extconf.rb:181:in `chdir_for_build'
  from extconf.rb:288:in `block in process_recipe'
  from extconf.rb:187:in `tap'
  from extconf.rb:187:in `process_recipe'
  from extconf.rb:490:in `
' To see why this extension failed to compile, please check the mkmf.log which can be found here: /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/extensions/x86_64-darwin-15/2.3.0/nokogiri-1.6.7.1/mkmf.log extconf failed, exit code 1 Gem files will remain installed in /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/gems/nokogiri-1.6.7.1 for inspection. Results logged to /Users/username/.rvm/gems/ruby-2.3.1@test-gemset3/extensions/x86_64-darwin-15/2.3.0/nokogiri-1.6.7.1/gem_make.out

Vous pouvez essayer les solutions suivantes, en adaptant le numéro de version à celui voulu :
gem install nokogiri -v 1.6.8.1 -- --use-system-libraries
gem install nokogiri -v 1.6.8.1 -- --use-system-libraries=true --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/libxml2
brew uninstall libxml2 (fourni par Xcode) puis relancer gem install nokogiri -v 1.6.8.1 -- --use-system-libraries
brew reinstall xz --universal puis relancer gem install nokogiri -v 1.6.8.1 -- --use-system-libraries

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