Installing on Mac El Capitan 10.11.16

[Dave Lindberg]

While attempting to install Rails 5 (while running Ruby 2.3.1), Nokogiri install is failing. 

Here's the terminal response:

Using pkg-config version 1.1.7
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.
ERROR: cannot discover where libxml2 is located on your system. please make sure `pkg-config` is installed.
*** 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/dlindberg/.rvm/rubies/ruby-2.3.1/bin/$(RUBY_BASE_NAME)
        --help
        --clean
        --use-system-libraries
        --with-zlib-dir
        --without-zlib-dir
        --with-zlib-include
        --without-zlib-include=${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
To see why this extension failed to compile, please check the mkmf.log which can be found here:


  /Users/dlindberg/.rvm/gems/ruby-2.3.1@rails5.0/extensions/x86_64-darwin-15/2.3.0/nokogiri-1.6.8/mkmf.log


extconf failed, exit code 1

 

Meanwhile, the mkmf.log file looks like so:

"gcc -o conftest -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  conftest.c  -L. -L/Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib -L. -fstack-protector -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib     -lruby.2.3.0  -lpthread -ldl -lobjc  "

checked program was:

/* begin */

1: #include "ruby.h"

2: 

3: int main(int argc, char **argv)

4: {

5:   return 0;

6: }

/* end */

"gcc -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe    -Werror -c conftest.c"

checked program was:

/* begin */

1: #include "ruby.h"

2: 

3: int main() {return 0;}

/* end */

"gcc -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -Wno-error=unused-command-line-argument-hard-error-in-future   -Werror -c conftest.c"

error: unknown warning option '-Werror=unused-command-line-argument-hard-error-in-future'; did you mean '-Werror=unused-command-line-argument'? [-Werror,-Wunknown-warning-option]

checked program was:

/* begin */

1: #include "ruby.h"

2: 

3: int main() {return 0;}

/* end */

have_header: checking for iconv.h... -------------------- yes

"gcc -E -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline  conftest.c -o conftest.i"

checked program was:

/* begin */

1: #include "ruby.h"

2: 

3: #include <iconv.h>

/* end */

--------------------

have_library: checking for gzdopen() in -lz... -------------------- yes

"gcc -o conftest -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline conftest.c  -L. -L/Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib -L. -fstack-protector -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib     -lruby.2.3.0 -lz  -lpthread -ldl -lobjc  "

checked program was:

/* begin */

 1: #include "ruby.h"

 2: 

 3: #include <zlib.h>

 4: 

 5: /*top*/

 6: extern int t(void);

 7: int main(int argc, char **argv)

 8: {

 9:   if (argc > 1000000) {

10:     printf("%p", &t);

11:   }

12: 

13:   return 0;

14: }

15: int t(void) { void ((*volatile p)()); p = (void ((*)()))gzdopen; return !p; }

/* end */

--------------------

have_iconv?: checking for iconv using --with-opt-* flags... -------------------- yes

"gcc -o conftest -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline conftest.c  -L. -L/Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib -L. -fstack-protector -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib     -lruby.2.3.0  -lpthread -ldl -lobjc  "

Undefined symbols for architecture x86_64:

  "_iconv", referenced from:

      _main in conftest-2c43b9.o

  "_iconv_open", referenced from:

      _main in conftest-2c43b9.o

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)

checked program was:

/* begin */

 1: #include "ruby.h"

 2: 

 3: #include <stdlib.h>

 4: #include <iconv.h>

 5: 

 6: int main(void)

 7: {

 8:     iconv_t cd = iconv_open("", "");

 9:     iconv(cd, NULL, NULL, NULL, NULL);

10:     return EXIT_SUCCESS;

11: }

/* end */

"gcc -o conftest -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline conftest.c  -L. -L/Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib -L. -fstack-protector -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib     -lruby.2.3.0 -liconv -lpthread -ldl -lobjc  "

checked program was:

/* begin */

 1: #include "ruby.h"

 2: 

 3: #include <stdlib.h>

 4: #include <iconv.h>

 5: 

 6: int main(void)

 7: {

 8:     iconv_t cd = iconv_open("", "");

 9:     iconv(cd, NULL, NULL, NULL, NULL);

10:     return EXIT_SUCCESS;

11: }

/* end */

--------------------

Following the instructions to trouble-shoot RVM installations (from http://www.nokogiri.org/tutorials/installing_nokogiri.html), I tried  sudo apt-get install libgmp-dev, only to get back sudo: apt-get: command not found
  

Now stuck. Any assistance would be appreciated!

[Mike Dalessio]

Hi,

Please make sure you're following instructions for OSX in the installation tutorial. apt-get is a tool used on certain Linux distros.

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[Dave Lindberg]

Thanks for the reply and solid advice. :-) 

Followed MAC OSX installation:

1. Since I'm on a new mac running Yosemite, I ran gem update --system
2.  Running Homebrew 0.9.5 (git revision e15a; last commit 2016-02-03)
   
3. gem install nokogiri

Here are the current results: 

Fetching: nokogiri-1.6.8.gem (100%)

Building native extensions.  This could take a while...

ERROR:  Error installing nokogiri:

        ERROR: Failed to build gem native extension.

    current directory: /Users/dlindberg/.rvm/gems/ruby-2.3.1/gems/nokogiri-1.6.8/ext/nokogiri

/Users/dlindberg/.rvm/rubies/ruby-2.3.1/bin/ruby -r ./siteconf20160903-11926-1hjq811.rb extconf.rb

Using pkg-config version 1.1.7

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 2.1.0

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 libxml2-2.9.4.

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 libxml2-2.9.4.tar.gz into tmp/x86_64-apple-darwin15.6.0/ports/libxml2/2.9.4... OK

Running 'configure' for libxml2 2.9.4... OK

Running 'compile' for libxml2 2.9.4... ERROR, review '/Users/dlindberg/.rvm/gems/ruby-2.3.1/gems/nokogiri-1.6.8/ext/nokogiri/tmp/x86_64-apple-darwin15.6.0/ports/libxml2/2.9.4/compile.log' to see what happened. Last lines are:

========================================================================

    unsigned short* in = (unsigned short*) inb;

                         ^~~~~~~~~~~~~~~~~~~~~

encoding.c:815:27: warning: cast from 'unsigned char *' to 'unsigned short *' increases required alignment from 1 to 2 [-Wcast-align]

    unsigned short* out = (unsigned short*) outb;

                          ^~~~~~~~~~~~~~~~~~~~~~

4 warnings generated.

  CC       error.lo

  CC       parserInternals.lo

  CC       parser.lo

  CC       tree.lo

  CC       hash.lo

  CC       list.lo

  CC       xmlIO.lo

xmlIO.c:1450:52: error: use of undeclared identifier 'LZMA_OK'

    ret =  (__libxml2_xzclose((xzFile) context) == LZMA_OK ) ? 0 : -1;

                                                   ^

1 error generated.

make[2]: *** [xmlIO.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/dlindberg/.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/dlindberg/.rvm/rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:366:in `block in execute': Failed to complete compile task (RuntimeError)

        from /Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:337:in `chdir'

        from /Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:337:in `execute'

        from /Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:111:in `compile'

        from /Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib/ruby/gems/2.3.0/gems/mini_portile2-2.1.0/lib/mini_portile2/mini_portile.rb:150:in `cook'

        from extconf.rb:364:in `block (2 levels) in process_recipe'

        from extconf.rb:257:in `block in chdir_for_build'

        from extconf.rb:256:in `chdir'

        from extconf.rb:256:in `chdir_for_build'

        from extconf.rb:363:in `block in process_recipe'

        from extconf.rb:262:in `tap'

        from extconf.rb:262:in `process_recipe'

        from extconf.rb:555:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /Users/dlindberg/.rvm/gems/ruby-2.3.1/extensions/x86_64-darwin-15/2.3.0/nokogiri-1.6.8/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /Users/dlindberg/.rvm/gems/ruby-2.3.1/gems/nokogiri-1.6.8 for inspection.

Results logged to /Users/dlindberg/.rvm/gems/ruby-2.3.1/extensions/x86_64-darwin-15/2.3.0/nokogiri-1.6.8/gem_make.out

Here's the contents mkmf.log:

| pkg-config --libs libxml-2.0

=> "-lxml2\n"

"gcc -o conftest -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I.  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline conftest.c  -L. -L/Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib -L. -fstack-protector -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib     -lruby.2.3.0 -lxml2 -lpthread -ldl -lobjc  "

checked program was:

/* begin */

1: #include "ruby.h"

2: 

3: int main(int argc, char **argv)

4: {

5:   return 0;

6: }

/* end */

| pkg-config --cflags-only-I libxml-2.0

=> "-I/usr/include/libxml2\n"

| pkg-config --cflags-only-other libxml-2.0

=> "\n"

| pkg-config --libs-only-l libxml-2.0

=> "-lxml2\n"

package configuration for libxml-2.0

cflags: 

ldflags: 

libs: -lxml2

| pkg-config --libs libxslt

=> "-lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2\n"

"gcc -o conftest -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/include/libxml2  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline  conftest.c  -L. -L/Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib -L. -fstack-protector -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib      -lxml2 -lruby.2.3.0 -lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2 -lpthread -ldl -lobjc  "

checked program was:

/* begin */

1: #include "ruby.h"

2: 

3: int main(int argc, char **argv)

4: {

5:   return 0;

6: }

/* end */

| pkg-config --cflags-only-I libxslt

=> "-I/usr/include/libxml2\n"

| pkg-config --cflags-only-other libxslt

=> "\n"

| pkg-config --libs-only-l libxslt

=> "-lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2\n"

package configuration for libxslt

cflags: 

ldflags: 

libs: -lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2

| pkg-config --libs libexslt

=> "-lexslt -lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2\n"

"gcc -o conftest -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/include/libxml2 -I/usr/include/libxml2  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline   conftest.c  -L. -L/Users/dlindberg/.rvm/rubies/ruby-2.3.1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib -L. -fstack-protector -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl/lib       -lxml2 -lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2 -lruby.2.3.0 -lexslt -lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2 -lpthread -ldl -lobjc  "

checked program was:

/* begin */

1: #include "ruby.h"

2: 

3: int main(int argc, char **argv)

4: {

5:   return 0;

6: }

/* end */

| pkg-config --cflags-only-I libexslt

=> "-I/usr/include/libxml2\n"

| pkg-config --cflags-only-other libexslt

=> "\n"

| pkg-config --libs-only-l libexslt

=> "-lexslt -lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2\n"

package configuration for libexslt

cflags: 

ldflags: 

libs: -lexslt -lxslt -lxml2 -lz -lpthread -licucore -lm -lxml2

"gcc -E -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin15 -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I/Users/dlindberg/.rvm/rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/include/libxml2 -I/usr/include/libxml2 -I/usr/include/libxml2  -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -O3 -fno-fast-math -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens  -fno-common -pipe  -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline     conftest.c -o conftest.i"

conftest.c:3:10: fatal error: 'libxml/xmlversion.h' file not found

#include <libxml/xmlversion.h>

         ^

1 error generated.

checked program was:

/* begin */

1: #include "ruby.h"

2: 

3: #include <libxml/xmlversion.h>

/* end */

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[Dave Lindberg]

Reinstalled xcode and nokogiri is now successfully installed. Thanks!

:-)

[David Taylor]

Same for me, spend half a day trying everything else...    And after updating Xcode new version it all worked 

Thx