Unable to install mysql gem after MacOS 10.14 install and brew update - mysql

Question

after macOS 10.14 install + Brew update my dev system is broken.
I am unable to install the mysql gem. When trying to install I get:
$ gem install mysql -v '2.8.1' --source 'http://rubygems.org/'
Building native extensions. This could take a while...
ERROR: Error installing mysql:
ERROR: Failed to build gem native extension.
current directory: /Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/gems/mysql-2.8.1/ext/mysql_api
/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/bin/ruby -r ./siteconf20180926-49343-waujia-0.rb extconf.rb
checking for mysql_ssl_set()... yes
checking for rb_str_set_len()... yes
checking for rb_thread_start_timer()... yes
checking for mysql.h... no
checking for mysql/mysql.h... no
*** 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/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/bin/ruby
--with-mysql-config
--without-mysql-config
To see why this extension failed to compile, please check the mkmf.log which can be found here:
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/extensions/x86-darwin-14/1.8/mysql-2.8.1/mkmf.log
extconf failed, exit code 1
Gem files will remain installed in /Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/gems/mysql-2.8.1 for inspection.
Results logged to /Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/extensions/x86-darwin-14/1.8/mysql-2.8.1/gem_make.out
the relative mkmf.log is:
have_func: checking for mysql_ssl_set()... -------------------- yes
"/usr/local/bin/gcc-4.9 -o conftest -I. -I/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib/ruby/1.8/i686-darwin14.4.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/Cellar/mysql/5.7.21/include/mysql -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl098/include -O2 -fno-tree-dce -fno-optimize-sibling-calls -fno-common -pipe -fno-common conftest.c -L. -L/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib -L. -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl098/lib -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -lruby-static -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -ldl -lobjc "
conftest.c: In function 't':
conftest.c:3:53: error: 'mysql_ssl_set' undeclared (first use in this function)
int t() { void ((*volatile p)()); p = (void ((*)()))mysql_ssl_set; return 0; }
^
conftest.c:3:53: note: each undeclared identifier is reported only once for each function it appears in
checked program was:
/* begin */
1: /*top*/
2: int main() { return 0; }
3: int t() { void ((*volatile p)()); p = (void ((*)()))mysql_ssl_set; return 0; }
/* end */
"/usr/local/bin/gcc-4.9 -o conftest -I. -I/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib/ruby/1.8/i686-darwin14.4.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/Cellar/mysql/5.7.21/include/mysql -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl098/include -O2 -fno-tree-dce -fno-optimize-sibling-calls -fno-common -pipe -fno-common conftest.c -L. -L/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib -L. -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl098/lib -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -lruby-static -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -ldl -lobjc "
ld: warning: directory not found for option '-L/usr/local/opt/openssl098/lib'
checked program was:
/* begin */
1: /*top*/
2: int main() { return 0; }
3: int t() { mysql_ssl_set(); return 0; }
/* end */
--------------------
have_func: checking for rb_str_set_len()... -------------------- yes
"/usr/local/bin/gcc-4.9 -o conftest -I. -I/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib/ruby/1.8/i686-darwin14.4.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/Cellar/mysql/5.7.21/include/mysql -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl098/include -O2 -fno-tree-dce -fno-optimize-sibling-calls -fno-common -pipe -fno-common conftest.c -L. -L/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib -L. -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl098/lib -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -lruby-static -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -ldl -lobjc "
conftest.c: In function 't':
conftest.c:3:53: error: 'rb_str_set_len' undeclared (first use in this function)
int t() { void ((*volatile p)()); p = (void ((*)()))rb_str_set_len; return 0; }
^
conftest.c:3:53: note: each undeclared identifier is reported only once for each function it appears in
checked program was:
/* begin */
1: /*top*/
2: int main() { return 0; }
3: int t() { void ((*volatile p)()); p = (void ((*)()))rb_str_set_len; return 0; }
/* end */
"/usr/local/bin/gcc-4.9 -o conftest -I. -I/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib/ruby/1.8/i686-darwin14.4.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/Cellar/mysql/5.7.21/include/mysql -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl098/include -O2 -fno-tree-dce -fno-optimize-sibling-calls -fno-common -pipe -fno-common conftest.c -L. -L/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib -L. -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl098/lib -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -lruby-static -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -ldl -lobjc "
ld: warning: directory not found for option '-L/usr/local/opt/openssl098/lib'
checked program was:
/* begin */
1: /*top*/
2: int main() { return 0; }
3: int t() { rb_str_set_len(); return 0; }
/* end */
--------------------
have_func: checking for rb_thread_start_timer()... -------------------- yes
"/usr/local/bin/gcc-4.9 -o conftest -I. -I/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib/ruby/1.8/i686-darwin14.4.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/Cellar/mysql/5.7.21/include/mysql -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl098/include -O2 -fno-tree-dce -fno-optimize-sibling-calls -fno-common -pipe -fno-common conftest.c -L. -L/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib -L. -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl098/lib -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -lruby-static -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -ldl -lobjc "
conftest.c: In function 't':
conftest.c:3:53: error: 'rb_thread_start_timer' undeclared (first use in this function)
int t() { void ((*volatile p)()); p = (void ((*)()))rb_thread_start_timer; return 0; }
^
conftest.c:3:53: note: each undeclared identifier is reported only once for each function it appears in
checked program was:
/* begin */
1: /*top*/
2: int main() { return 0; }
3: int t() { void ((*volatile p)()); p = (void ((*)()))rb_thread_start_timer; return 0; }
/* end */
"/usr/local/bin/gcc-4.9 -o conftest -I. -I/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib/ruby/1.8/i686-darwin14.4.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/Cellar/mysql/5.7.21/include/mysql -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl098/include -O2 -fno-tree-dce -fno-optimize-sibling-calls -fno-common -pipe -fno-common conftest.c -L. -L/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib -L. -L/usr/local/opt/libyaml/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/libksba/lib -L/usr/local/opt/openssl098/lib -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -lruby-static -L/usr/local/Cellar/mysql/5.7.21/lib -lmysqlclient -lssl -lcrypto -ldl -lobjc "
ld: warning: directory not found for option '-L/usr/local/opt/openssl098/lib'
checked program was:
/* begin */
1: /*top*/
2: int main() { return 0; }
3: int t() { rb_thread_start_timer(); return 0; }
/* end */
--------------------
have_header: checking for mysql.h... -------------------- no
"/usr/local/bin/gcc-4.9 -E -I. -I/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib/ruby/1.8/i686-darwin14.4.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/Cellar/mysql/5.7.21/include/mysql -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl098/include -O2 -fno-tree-dce -fno-optimize-sibling-calls -fno-common -pipe -fno-common conftest.c -o conftest.i"
In file included from conftest.c:1:0:
/usr/local/Cellar/mysql/5.7.21/include/mysql/mysql.h:35:23: fatal error: sys/types.h: No such file or directory
#include <sys/types.h>
^
compilation terminated.
checked program was:
/* begin */
1: #include <mysql.h>
/* end */
--------------------
have_header: checking for mysql/mysql.h... -------------------- no
"/usr/local/bin/gcc-4.9 -E -I. -I/Users/MYACCOUNT/.rvm/rubies/ruby-1.8.7-p374/lib/ruby/1.8/i686-darwin14.4.0 -I. -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -I/usr/local/Cellar/mysql/5.7.21/include/mysql -I/usr/local/opt/libyaml/include -I/usr/local/opt/readline/include -I/usr/local/opt/libksba/include -I/usr/local/opt/openssl098/include -O2 -fno-tree-dce -fno-optimize-sibling-calls -fno-common -pipe -fno-common conftest.c -o conftest.i"
In file included from conftest.c:1:0:
/usr/local/include/mysql/mysql.h:35:23: fatal error: sys/types.h: No such file or directory
#include <sys/types.h>
^
compilation terminated.
checked program was:
/* begin */
1: #include <mysql/mysql.h>
/* end */
--------------------
I have mysql installed via Brew and keep mysql, mysql#5.6 or mysql#5.7 active. Path is set in .bash_profile:
### Customize path for MYSQL
MYSQL=/usr/local/mysql/bin
export PATH=$PATH:$MYSQL
export DYLD_LIBRARY_PATH=/usr/local/mysql/lib:$DYLD_LIBRARY_PATH
When I switch to mysql#5.6 or 5.7 I change the path accordingly.
There appears to be some problem with mysql in general.
While one webapp in Ruby 1.8.7, Rails 3.2.5 with mysql database is running, two other webapps with the same technology stack are unable to either reinstall the mysql gem or connect to the database.
$ rake db:migrate --trace
** Invoke db:migrate (first_time)
** Invoke environment (first_time)
** Execute environment
rake aborted!
Mysql::Error: Table 'dev_WEBPROJECT.safts' doesn't exist: SHOW FULL FIELDS FROM `safts`
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/gems/activerecord-3.2.5/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:243:in `query'
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/gems/activerecord-3.2.5/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:243:in `execute'
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/gems/activerecord-3.2.5/lib/active_record/connection_adapters/abstract_adapter.rb:280:in `log'
.
.
.
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/gems/rake-0.9.6/lib/rake/application.rb:70:in `run'
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/gems/rake-0.9.6/bin/rake:37
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/bin/rake:22:in `load'
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/bin/rake:22
/Users/MYACCOUNT/.rvm/gems/ruby-1.8.7-p374#WEBPROJECT/bin/ruby_executable_hooks:15
Tasks: TOP => db:migrate => environment
Can anyone help?

Answer 1

Mojave changed the location of header files necessary for compiling C extensions. You might need to run the following command to install mysql gem:
sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /
Ref: https://gorails.com/setup/osx/10.14-mojave

Answer 2

Do you have xcode installed? /usr/bin/xcodebuild -version