Nokogiri: Unable to install Nokogiri on Mac OS 10.13 with lzma from homebrew

Created on 20 Nov 2017 · 2Comments · Source: sparklemotion/nokogiri

Have you tried following [the installation tutorial][tutorial]?

Yes

What is the output of gem install?

/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/ext/builder.rb:76: warning: Insecure world writable dir /Library/Ruby/Gems/2.3.0/gems in PATH, mode 040777
Building native extensions.  This could take a while...
ERROR:  Error installing nokogiri:
    ERROR: Failed to build gem native extension.

    current directory: /Library/Ruby/Gems/2.3.0/gems/nokogiri-1.8.1/ext/nokogiri
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby -r ./siteconf20171120-34111-18b20qt.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 2.3.0
checking for iconv.h... yes
checking for gzdopen() in -lz... yes
checking for iconv... yes
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxml2-2.9.5.

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 libxml2-2.9.5.tar.gz into tmp/x86_64-apple-darwin17/ports/libxml2/2.9.5... OK
Running 'configure' for libxml2 2.9.5... OK
Running 'compile' for libxml2 2.9.5... ERROR, review '/Library/Ruby/Gems/2.3.0/gems/nokogiri-1.8.1/ext/nokogiri/tmp/x86_64-apple-darwin17/ports/libxml2/2.9.5/compile.log' to see what happened. Last lines are:
========================================================================
  CCLD     libxml2.la
  CC       testdso.lo
  CCLD     testdso.la
  CC       xmllint.o
  CCLD     xmllint
ld: warning: ignoring file /usr/local/Cellar/xz/5.2.3/lib/liblzma.dylib, file was built for x86_64 which is not the architecture being linked (i386): /usr/local/Cellar/xz/5.2.3/lib/liblzma.dylib
Undefined symbols for architecture i386:
  "_lzma_auto_decoder", referenced from:
      _xz_head in libxml2.a(xzlib.o)
  "_lzma_code", referenced from:
      _xz_decomp in libxml2.a(xzlib.o)
  "_lzma_end", referenced from:
      ___libxml2_xzclose in libxml2.a(xzlib.o)
  "_lzma_properties_decode", referenced from:
      _is_format_lzma in libxml2.a(xzlib.o)
ld: symbol(s) not found for architecture i386
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [xmllint] 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
    --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/2.3/usr/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
/Library/Ruby/Gems/2.3.0/gems/mini_portile2-2.3.0/lib/mini_portile2/mini_portile.rb:402:in `block in execute': Failed to complete compile task (RuntimeError)
    from /Library/Ruby/Gems/2.3.0/gems/mini_portile2-2.3.0/lib/mini_portile2/mini_portile.rb:373:in `chdir'
    from /Library/Ruby/Gems/2.3.0/gems/mini_portile2-2.3.0/lib/mini_portile2/mini_portile.rb:373:in `execute'
    from /Library/Ruby/Gems/2.3.0/gems/mini_portile2-2.3.0/lib/mini_portile2/mini_portile.rb:115:in `compile'
    from /Library/Ruby/Gems/2.3.0/gems/mini_portile2-2.3.0/lib/mini_portile2/mini_portile.rb:154:in `cook'
    from extconf.rb:365: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:364:in `block in process_recipe'
    from extconf.rb:262:in `tap'
    from extconf.rb:262:in `process_recipe'
    from extconf.rb:548:in `<main>'

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

  /Library/Ruby/Gems/2.3.0/extensions/universal-darwin-17/2.3.0/nokogiri-1.8.1/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /Library/Ruby/Gems/2.3.0/gems/nokogiri-1.8.1 for inspection.
Results logged to /Library/Ruby/Gems/2.3.0/extensions/universal-darwin-17/2.3.0/nokogiri-1.8.1/gem_make.out

What are the contents of the mkmf.log file?

"xcrun clang -o conftest -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin17 -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -iwithsysroot /usr/local/libressl/include  conftest.c  -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib -L.             -L /BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib -L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib   -arch x86_64 -arch i386   -lruby.2.3.0  -lpthread -ldl -lobjc  "
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/mkmf.rb:395: warning: Insecure world writable dir /Library/Ruby/Gems/2.3.0/gems in PATH, mode 040777
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib'
checked program was:
/* begin */
1: #include "ruby.h"
2: 
3: int main(int argc, char **argv)
4: {
5:   return 0;
6: }
/* end */

"xcrun clang -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin17 -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -iwithsysroot /usr/local/libressl/include   -arch x86_64 -arch i386  -c conftest.c"
checked program was:
/* begin */
1: #include "ruby.h"
2: 
3: int main() {return 0;}
/* end */

"xcrun clang -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin17 -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -iwithsysroot /usr/local/libressl/include  -Wno-error=unused-command-line-argument-hard-error-in-future  -arch x86_64 -arch i386  -c conftest.c"
warning: unknown warning option '-Werror=unused-command-line-argument-hard-error-in-future'; did you mean '-Werror=unused-command-line-argument'? [-Wunknown-warning-option]
1 warning generated.
warning: unknown warning option '-Werror=unused-command-line-argument-hard-error-in-future'; did you mean '-Werror=unused-command-line-argument'? [-Wunknown-warning-option]
1 warning generated.
checked program was:
/* begin */
1: #include "ruby.h"
2: 
3: int main() {return 0;}
/* end */

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

"xcrun clang -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin17 -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -iwithsysroot /usr/local/libressl/include   -arch x86_64 -arch i386  -c conftest.c"
checked program was:
/* begin */
1: #include "ruby.h"
2: 
3: #include <iconv.h>
/* end */

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

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

"xcrun clang -o conftest -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin17 -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -iwithsysroot /usr/local/libressl/include  conftest.c  -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib -L.             -L /BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib -L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib   -arch x86_64 -arch i386   -lruby.2.3.0 -lz  -lpthread -ldl -lobjc  "
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib'
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... -------------------- yes

"xcrun clang -o conftest -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin17 -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -iwithsysroot /usr/local/libressl/include  conftest.c  -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib -L.             -L /BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib -L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib   -arch x86_64 -arch i386   -lruby.2.3.0  -lpthread -ldl -lobjc  "
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib'
Undefined symbols for architecture x86_64:
  "_iconv", referenced from:
      _main in conftest-41807e.o
  "_iconv_open", referenced from:
      _main in conftest-41807e.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 */

"xcrun clang -o conftest -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/universal-darwin17 -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/include/ruby-2.3.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT    -g -Os -pipe -DHAVE_GCC_ATOMIC_BUILTINS -iwithsysroot /usr/local/libressl/include  conftest.c  -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib -L.             -L /BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib -L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib   -arch x86_64 -arch i386   -lruby.2.3.0 -liconv -lpthread -ldl -lobjc  "
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/libressl/lib'
ld: warning: directory not found for option '-L/BuildRoot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.Internal.sdk/usr/local/lib'
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 */

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

What operating system are you using?

ruby = /Users/mark/.rbenv/shims/ruby
ruby version = ruby 2.3.3p222 (2016-11-21 revision 56859) [universal.x86_64-darwin17]
os = Mac OS, 10.13.1 (17B48)

This appears to be an issue with the xz formula. I'll try removing it but wanted to make sure this was documented here first in case others have a similar issue. If it works I'll submit a PR to the installation guide.

Source