When I try to install Nokogiri using:
gem install nokogiri
I get this error:
ERROR: While executing gem ... (Errno::EACCES)
Permission denied # rb_sysopen - /usr/local/lib/ruby/gems/2.3.0/gems/nokogiri-1.6.8.1/.autotest
I ran both of these commands first:
gem update --system
xcode-select --install
Can anyone see what's wrong here?
If I run this using sudo I get:
ERROR: Error installing nokogiri:
ERROR: Failed to build gem native extension.
current directory: /usr/local/lib/ruby/gems/2.3.0/gems/nokogiri-1.6.8.1/ext/nokogiri
/usr/local/opt/ruby/bin/ruby -r ./siteconf20161127-35515-164lnl6.rb extconf.rb
checking if the C compiler accepts ... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.
and here's the log file:
"clang -o conftest -I/usr/local/Cellar/ruby/2.3.3/include/ruby-2.3.0/x86_64-darwin14 -I/usr/local/Cellar/ruby/2.3.3/include/ruby-2.3.0/ruby/backward -I/usr/local/Cellar/ruby/2.3.3/include/ruby-2.3.0 -I. -I/usr/local/opt/libyaml/include -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/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/usr/local/Cellar/ruby/2.3.3/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L. -fstack-protector -L/usr/local/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -lruby.2.3.0 -lpthread -ldl -lobjc "
Undefined symbols for architecture x86_64:
"start", referenced from:
implicit entry/start for main executable
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: int main(int argc, char **argv)
4: {
5: return 0;
6: }
/* end */
You can try to do this:
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/MacOSX10.11.sdk/usr/include/libxml2
So this turned out to be a mix of permissions and file ownership. Once that was all sorted out I just had to rerun the gem install and close then reopen the terminal before running rails -v.
Related
I'm trying to run rails server and there is problem with sqlite3.
When i run bin/rails server
Could not find gem 'sqlite3 (~> 1.4)' in locally installed gems.
Run bundle install to install missing gems.
So i try to run bundle install
Installing sqlite3 1.4.2 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
And the last thing I tried is checking the log file in /var/lib/gems/2.7.0/extensions/x86_64-linux/2.7.0/sqlite3-1.4.2/mkmf.log
package configuration for sqlite3 is not found find_header: checking
for sqlite3.h... -------------------- no
"x86_64-linux-gnu-gcc -o conftest
-I/usr/include/x86_64-linux-gnu/ruby-2.7.0 -I/usr/include/ruby-2.7.0/ruby/backward -I/usr/include/ruby-2.7.0 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ruby2.7-aN7IdK/ruby2.7-2.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC conftest.c -L. -L/usr/lib/x86_64-linux-gnu -L. -Wl,-z,relro
-Wl,-z,now -fstack-protector-strong -rdynamic -Wl,-export-dynamic -lruby-2.7 -lm -lc"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5: return !!argv[argc];
6: }
/* end */
"x86_64-linux-gnu-gcc -E -I/usr/include/x86_64-linux-gnu/ruby-2.7.0
-I/usr/include/ruby-2.7.0/ruby/backward -I/usr/include/ruby-2.7.0 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ruby2.7-aN7IdK/ruby2.7-2.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC conftest.c -o conftest.i" conftest.c:3:10: fatal error: sqlite3.h: No
such file or directory
3 | #include <sqlite3.h>
| ^~~~~~~~~~~ compilation terminated.
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: #include <sqlite3.h>
/* end */
Any suggestion?
Building a new Rails app and getting a problem with nokogiri. Said to try gem install nokogiri -v '1.6.8.1' which fails with output below. I tried deleting Gemfile.lock and using the Gemfile from another app which has no problem—bundle install still fails. The original failure is bundle install which continues to work in other apps.
From console:
gem install nokogiri -v '1.6.8.1'
Building native extensions. This could take a while...
ERROR: Error installing nokogiri:
ERROR: Failed to build gem native extension.
current directory: ~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1/ext/nokogiri
~/.rubies/ruby-2.3.1/bin/ruby -r ./siteconf20161008-60071-tmqi2l.rb extconf.rb
Ignoring byebug-6.0.2 because its extensions are not built. Try: gem pristine byebug --version 6.0.2
Ignoring byebug-3.4.0 because its extensions are not built. Try: gem pristine byebug --version 3.4.0
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-darwin16.1.0/ports/libxml2/2.9.4... OK
Running 'configure' for libxml2 2.9.4... OK
Running 'compile' for libxml2 2.9.4... ERROR, review '~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1/ext/nokogiri/tmp/x86_64-apple-darwin16.1.0/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=~/.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
~/.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 ~/.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 ~/.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 ~/.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 ~/.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:365:in `block (2 levels) in process_recipe'
from extconf.rb:258:in `block in chdir_for_build'
from extconf.rb:257:in `chdir'
from extconf.rb:257:in `chdir_for_build'
from extconf.rb:364:in `block in process_recipe'
from extconf.rb:263:in `tap'
from extconf.rb:263:in `process_recipe'
from extconf.rb:556:in `<main>'
To see why this extension failed to compile, please check the mkmf.log which can be found here:
~/.gem/ruby/2.3.1/extensions/x86_64-darwin-16/2.3.0-static/nokogiri-1.6.8.1/mkmf.log
extconf failed, exit code 1
Gem files will remain installed in ~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1 for inspection.
Results logged to ~/.gem/ruby/2.3.1/extensions/x86_64-darwin-16/2.3.0-static/nokogiri-1.6.8.1/gem_make.out
mkmf.log:
"clang -o conftest -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/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 -pipe conftest.c -L. -L~/.rubies/ruby-2.3.1/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -L. -fstack-protector -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -lruby-static -framework CoreFoundation -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 */
"clang -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/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 -pipe -Werror -c conftest.c"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main() {return 0;}
/* end */
"clang -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/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 -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
"clang -E -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/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 -pipe 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
"clang -o conftest -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/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 -pipe conftest.c -L. -L~/.rubies/ruby-2.3.1/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -L. -fstack-protector -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -lruby-static -framework CoreFoundation -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
"clang -o conftest -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/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 -pipe conftest.c -L. -L~/.rubies/ruby-2.3.1/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -L. -fstack-protector -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -lruby-static -framework CoreFoundation -lpthread -ldl -lobjc "
Undefined symbols for architecture x86_64:
"_iconv", referenced from:
_main in conftest-d46614.o
"_iconv_open", referenced from:
_main in conftest-d46614.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 */
"clang -o conftest -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/x86_64-darwin16 -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0/ruby/backward -I~/.rubies/ruby-2.3.1/include/ruby-2.3.0 -I. -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/libyaml/include -I/usr/local/opt/gdbm/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 -pipe conftest.c -L. -L~/.rubies/ruby-2.3.1/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -L. -fstack-protector -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/gdbm/lib -lruby-static -framework CoreFoundation -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 */
--------------------
gem_make.out:
current directory: ~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1/ext/nokogiri
~/.rubies/ruby-2.3.1/bin/ruby -r ./siteconf20161008-60071-tmqi2l.rb extconf.rb
Ignoring byebug-6.0.2 because its extensions are not built. Try: gem pristine byebug --version 6.0.2
Ignoring byebug-3.4.0 because its extensions are not built. Try: gem pristine byebug --version 3.4.0
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-darwin16.1.0/ports/libxml2/2.9.4... OK
Running 'configure' for libxml2 2.9.4... OK
Running 'compile' for libxml2 2.9.4... ERROR, review '~/.gem/ruby/2.3.1/gems/nokogiri-1.6.8.1/ext/nokogiri/tmp/x86_64-apple-darwin16.1.0/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=${opt-dir}/lib
--with-make-prog
--without-make-prog
--srcdir=.
--curdir
--ruby=~/.rubies/ruby-2.3.1/bin/$(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
~/.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 ~/.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 ~/.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 ~/.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 ~/.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:365:in `block (2 levels) in process_recipe'
from extconf.rb:258:in `block in chdir_for_build'
from extconf.rb:257:in `chdir'
from extconf.rb:257:in `chdir_for_build'
from extconf.rb:364:in `block in process_recipe'
from extconf.rb:263:in `tap'
from extconf.rb:263:in `process_recipe'
from extconf.rb:556:in `<main>'
To see why this extension failed to compile, please check the mkmf.log which can be found here:
~/.gem/ruby/2.3.1/extensions/x86_64-darwin-16/2.3.0-static/nokogiri-1.6.8.1/mkmf.log
extconf failed, exit code 1
Run this first:
xcode-select --install
Then rerun your bundle install
Reference: https://github.com/sparklemotion/nokogiri/issues/1483
I tried #the_basterd's recommendation. That didn't work, but the reference was good—thank you the_basterd. What worked from that reference was:
brew install libxml2
bundle config build.nokogiri --use-system-libraries --with-xml2-include=/usr/local/opt/libxml2/include/libxml2
Reference: https://github.com/sparklemotion/nokogiri/issues/1483
Later postings at that ref said that what I posted above "is strongly recommended against by the Nokogiri."
brew unlink xz; bundle install; brew link xz is preferred.
You can also encounter the same error message if you've downloaded XCode Tools but haven't yet agreed to the license.
From Terminal, run:
sudo xcodebuild -license
Enter your admin password, space through the agreement and type agree to accept. Run brew doctor and if necessary, brew update and you should be in good shape.
I ran into this issue with nokogiri-1.6.8.1 while using bundle install --path vendor/bundle to install directly into a project located within a Google Drive sync folder. The hangup seemed related to libxml2.
While reading through the GitHub issue referenced by #Greg and #the_basterd, I noticed that someone was having trouble installing into a Box sync folder. Moving my project folder to another location worked.
Not sure what the underlying problem is when installing to a sync folder, but I'd be interested to learn if anyone had any thoughts.
Haven't tested this with Dropbox, but perhaps that would cause problems, too.
I am working on Ruby On Rails and whenever I try to install nokogiri-1.6.7.2, I get the following error:
Building native extensions. This could take a while...
ERROR: Error installing nokogiri:
ERROR: Failed to build gem native extension.
current directory: /usr/local/opt/gems/gems/nokogiri-1.6.7.2/ext/nokogiri
/usr/local/bin/ruby -r ./siteconf20160607-19453-7k21kq.rb extconf.rb
Ignoring binding_of_caller-0.7.2 because its extensions are not built. Try: gem pristine binding_of_caller --version 0.7.2
Ignoring byebug-8.2.2 because its extensions are not built. Try: gem pristine byebug --version 8.2.2
Ignoring debug_inspector-0.0.2 because its extensions are not built. Try: gem pristine debug_inspector --version 0.0.2
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.
Ignoring nokogiri-1.6.7.2 because its extensions are not built. Try: gem pristine nokogiri --version 1.6.7.2
Ignoring sqlite3-1.3.11 because its extensions are not built. Try: gem pristine sqlite3 --version 1.3.11
*** 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/bin/$(RUBY_BASE_NAME)
--help
--clean
--use-system-libraries
/usr/local/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- openssl (LoadError)
from /usr/local/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
from /usr/local/lib/ruby/2.3.0/net/https.rb:23:in `<top (required)>'
from /usr/local/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
from /usr/local/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
from /usr/local/lib/ruby/gems/2.3.0/gems/mini_portile2-2.0.0/lib/mini_portile2/mini_portile.rb:3:in `<top (required)>'
from /usr/local/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
from /usr/local/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
from /usr/local/lib/ruby/gems/2.3.0/gems/mini_portile2-2.0.0/lib/mini_portile2.rb:2:in `<top (required)>'
from /usr/local/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
from /usr/local/lib/ruby/site_ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
from extconf.rb:397:in `<main>'
To see why this extension failed to compile, please check the mkmf.log which can be found here:
/usr/local/opt/gems/extensions/x86_64-darwin-15/2.3.0-static/nokogiri-1.6.7.2/mkmf.log
extconf failed, exit code 1
Gem files will remain installed in /usr/local/opt/gems/gems/nokogiri-1.6.7.2 for inspection.
Results logged to /usr/local/opt/gems/extensions/x86_64-darwin-15/2.3.0-static/nokogiri-1.6.7.2/gem_make.out
Due to this Rails Server too is not starting and giving me error.. please help the results of the mkmf.log is below:-
"clang -o conftest -I/usr/local/include/ruby-2.3.0/x86_64-darwin15 -I/usr/local/include/ruby-2.3.0/ruby/backward -I/usr/local/include/ruby-2.3.0 -I. -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 -pipe conftest.c -L. -L/usr/local/lib -L. -fstack-protector -L/usr/local/lib -lruby-static -framework CoreFoundation -lpthread -lgmp -ldl -lobjc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5: return 0;
6: }
/* end */
"clang -I/usr/local/include/ruby-2.3.0/x86_64-darwin15 -I/usr/local/include/ruby-2.3.0/ruby/backward -I/usr/local/include/ruby-2.3.0 -I. -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 -pipe -Werror -c conftest.c"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main() {return 0;}
/* end */
"clang -I/usr/local/include/ruby-2.3.0/x86_64-darwin15 -I/usr/local/include/ruby-2.3.0/ruby/backward -I/usr/local/include/ruby-2.3.0 -I. -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 -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 */
Can anyone please help me resolve this.
Thanks
The issue actually has nothing to do with nokogiri and more to do with rbenv (or specifically, ruby-build).
9 times out of 10, running xcode-select --install will fix the issue. If that doesn't, I would suggest reviewing this wiki article to make sure your build environment is properly configured.
If you need more help after that, I would suggest tagging your question with rbenv. Personally, I stopped using it because of annoyances like this.
try to install nodes:
sudo apt-get install nodejs
I am unable to run my bundle install after I upgraded to yosemite, the contents of mkmf.log are as follows
/usr/local/opt/gcc46/bin/gcc-4.6 -o conftest
-I/Users/mac/.rvm/rubies/ruby-1.9.3-p547/include/ruby-1.9.1/x86_64-darwin12.4.0
-I/Users/mac/.rvm/rubies/ruby-1.9.3-p547/include/ruby-1.9.1/ruby/backward
-I/Users/mac/.rvm/rubies/ruby-1.9.3-p547/include/ruby-1.9.1 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl/include -O3 -ggdb -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration -fno-common -pipe conftest.c -L. -L/Users/mac/.rvm/rubies/ruby-1.9.3-p547/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. -L/usr/local/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 -lruby.1.9.1 -lpthread -ldl -lobjc
and it seems like it is trying to use gcc-4.6 but when I do gcc -v it gives me this
Configured with:
--prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn) Target:
x86_64-apple-darwin14.0.0 Thread model: posix
I also tried doing a ln -s to link /usr/local/opt/gcc46/bin/gcc-4.6 but it was no help, I keep getting
/Users/mac/.rvm/rubies/ruby-1.9.3-p547/bin/ruby extconf.rb checking
if the C compiler accepts ... *** 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..
Any help would be really appreciated
try reinstall ruby with:
rvm get stable
rvm reinstall 1.9.3-p547
then bundle install
I had the same problem - turns out, I had to reinstall ruby in the newest version and build all gems pristine.
http://danielpuglisi.com/articles/2014/10/reinstall-ruby-after-upgrading-to-osx-yosemite
This solution worked perfectly, I removed all old versions that were listed in rbenv, then installed ruby 2.1.3 as described in the link, then used gem pristine --all, and I was good to go, no more annoying error messages.
The steps really depends on which one you are using, rbenv or rmv.
I'm having issues installing Rails 4 with rvm. I saw another solution with removing rvm from my system, but that is not an option because I need isolated gemsets. This is my terminal:
Edmunds-MacBook-Pro:pipetask edmundmai$ rvm current
ruby-2.0.0-p247#pipetask
Edmunds-MacBook-Pro:pipetask edmundmai$ ls
Gemfile README.rdoc app config db lib public
Gemfile.lock Rakefile bin config.ru gcc-4.2 log vendor
Edmunds-MacBook-Pro:pipetask edmundmai$ gem install rails -v=4.0.0
Building native extensions. This could take a while...
ERROR: Error installing rails:
ERROR: Failed to build gem native extension.
/Users/edmundmai/.rvm/rubies/ruby-2.0.0-p247/bin/ruby extconf.rb
*** 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=/Users/edmundmai/.rvm/rubies/ruby-2.0.0-p247/bin/ruby
--with-atomic_reference-dir
--without-atomic_reference-dir
--with-atomic_reference-include
--without-atomic_reference-include=${atomic_reference-dir}/include
--with-atomic_reference-lib
--without-atomic_reference-lib=${atomic_reference-dir}/
/Users/edmundmai/.rvm/rubies/ruby-2.0.0-p247/lib/ruby/2.0.0/mkmf.rb:434:in `try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
from /Users/edmundmai/.rvm/rubies/ruby-2.0.0-p247/lib/ruby/2.0.0/mkmf.rb:519:in `try_link0'
from /Users/edmundmai/.rvm/rubies/ruby-2.0.0-p247/lib/ruby/2.0.0/mkmf.rb:817:in `try_run'
from extconf.rb:26:in `<main>'
Gem files will remain installed in /Users/edmundmai/.rvm/gems/ruby-2.0.0-p247#pipetask/gems/atomic-1.1.14 for inspection.
Results logged to /Users/edmundmai/.rvm/gems/ruby-2.0.0-p247#pipetask/gems/atomic-1.1.14/ext/gem_make.out
Edmunds-MacBook-Pro:pipetask edmundmai$
How would I debug this? I don't even know which mkmf.log it is talking about, I have like 50 of them when I do locate mkmf.log. What is development tools? I have xcode 5 and command line tools.
==Update
This might be the mkmf.log file it was referring to?
Edmunds-MacBook-Pro:bin edmundmai$ more /Users/emai/mkmf.log
have_func: checking for rb_hash_foreach()... -------------------- yes
"clang -o conftest -I/Users/emai/.rvm/rubies/ruby-2.0.0-p0/include/ruby-2.0.0/x86_64-darwin11.4.2 -I/Users/emai/.rvm/rubies/ruby-2.0.0-p0/include/ruby-2.0.0/ruby/backward -I/Users/emai/.rvm/rubies/ruby-2.0.0-p0/include/ruby-2.0.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -I/Users/emai/.rvm/usr/include -I/Users/emai/.rvm/usr/include -O3 -g3 -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 -pipe conftest.c -L. -L/Users/emai/.rvm/rubies/ruby-2.0.0-p0/lib -L/Users/emai/.rvm/usr/lib -L. -fstack-protector -L/Users/emai/.rvm/usr/lib -L/Users/emai/.rvm/usr/lib -lruby-static -lpthread -ldl -lobjc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(void) {return 0;}
/* end */
"clang -o conftest -I/Users/emai/.rvm/rubies/ruby-2.0.0-p0/include/ruby-2.0.0/x86_64-darwin11.4.2 -I/Users/emai/.rvm/rubies/ruby-2.0.0-p0/include/ruby-2.0.0/ruby/backward -I/Users/emai/.rvm/rubies/ruby-2.0.0-p0/include/ruby-2.0.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -I/Users/emai/.rvm/usr/include -I/Users/emai/.rvm/usr/include -O3 -g3 -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 -pipe conftest.c -L. -L/Users/emai/.rvm/rubies/ruby-2.0.0-p0/lib -L/Users/emai/.rvm/usr/lib -L. -fstack-protector -L/Users/emai/.rvm/usr/lib -L/Users/emai/.rvm/usr/lib -lruby-static -lpthread -ldl -lobjc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: /*top*/
4: int main(void) {return 0;}
5: extern int t(void);
6: int t(void) { void ((*volatile p)()); p = (void ((*)()))rb_hash_foreach; return 0; }
/* end */
--------------------