AndreaNobili AndreaNobili - 17 days ago 6
Ruby Question

Why I obtain these error messages when I try to install gem bundler on Ubuntu? (Could not create Makefile)

I am not a Ruby developer and I am finding many difficult to install Redmine (that is developed in Ruby) on an Ububuntu 16.04 server.

I am following this official tutorial: http://www.redmine.org/projects/redmine/wiki/HowTo_Install_Redmine_on_Ubuntu_step_by_step

It seems very simple but I am finding many difficult when it "ensure that the bundler GEM is installed".

I am not sure about what exactly is this bundler GEM that have to be installed. From what I have understand (correct me if I am doing wrong assertion) a GEM is something that packages excutable Ruby application (something like a JAR file in Java).

So, the problem is that when I perform this statment in the bash console:

sudo gem update


I obtain many error messages like this:

root@Betrivius-VPS:~# sudo gem update
Updating installed gems
Updating molinillo
Fetching: molinillo-0.5.4.gem (100%)
Successfully installed molinillo-0.5.4
Parsing documentation for molinillo-0.5.4
Installing ri documentation for molinillo-0.5.4
Installing darkfish documentation for molinillo-0.5.4
Done installing documentation for molinillo after 1 seconds
Parsing documentation for molinillo-0.5.4
Done installing documentation for molinillo after 0 seconds
Updating mysql2
Building native extensions. This could take a while...
ERROR: Error installing mysql2:
ERROR: Failed to build gem native extension.

current directory: /var/lib/gems/2.3.0/gems/mysql2-0.4.5/ext/mysql2
/usr/bin/ruby2.3 -r ./siteconf20161115-29205-1v41srl.rb extconf.rb
checking for rb_absint_size()... yes
checking for rb_absint_singlebit_p()... yes
checking for ruby/thread.h... yes
checking for rb_thread_call_without_gvl() in ruby/thread.h... yes
checking for rb_thread_blocking_region()... no
checking for rb_wait_for_single_fd()... yes
checking for rb_hash_dup()... yes
checking for rb_intern3()... yes
checking for rb_big_cmp()... yes
checking for mysql_query() in -lmysqlclient... no
-----
mysql client is missing. You may need to 'apt-get install libmysqlclient-dev' or 'yum install mysql-devel', and try again.
-----
*** 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/bin/$(RUBY_BASE_NAME)2.3
--with-mysql-dir
--without-mysql-dir
--with-mysql-include
--without-mysql-include=${mysql-dir}/include
--with-mysql-lib
--without-mysql-lib=${mysql-dir}/lib
--with-mysql-config
--without-mysql-config
--with-mysql-dir
--without-mysql-dir
--with-mysql-include
--without-mysql-include=${mysql-dir}/include
--with-mysql-lib
--without-mysql-lib=${mysql-dir}/lib
--with-mysqlclientlib
--without-mysqlclientlib

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

/var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/mysql2-0.4.5/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /var/lib/gems/2.3.0/gems/mysql2-0.4.5 for inspection.
Results logged to /var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/mysql2-0.4.5/gem_make.out
Updating nokogiri
Building native extensions. This could take a while...
ERROR: Error installing nokogiri:
ERROR: Failed to build gem native extension.

current directory: /var/lib/gems/2.3.0/gems/nokogiri-1.6.8.1/ext/nokogiri
/usr/bin/ruby2.3 -r ./siteconf20161115-29205-11qd2.rb extconf.rb
checking if the C compiler accepts ... yes
Building nokogiri using packaged libraries.
Using mini_portile version 2.1.0
checking for gzdopen() in -lz... no
zlib is missing; necessary for building libxml2
*** 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/bin/$(RUBY_BASE_NAME)2.3
--help
--clean
--use-system-libraries
--enable-static
--disable-static
--with-zlib-dir
--without-zlib-dir
--with-zlib-include
--without-zlib-include=${zlib-dir}/include
--with-zlib-lib
--without-zlib-lib=${zlib-dir}/lib
--enable-cross-build
--disable-cross-build

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

/var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/nokogiri-1.6.8.1/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /var/lib/gems/2.3.0/gems/nokogiri-1.6.8.1 for inspection.
Results logged to /var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/nokogiri-1.6.8.1/gem_make.out
Updating psych
Fetching: psych-2.2.0.gem (100%)
Building native extensions. This could take a while...
Successfully installed psych-2.2.0
Parsing documentation for psych-2.2.0
Installing ri documentation for psych-2.2.0
Installing darkfish documentation for psych-2.2.0
Done installing documentation for psych after 2 seconds
Parsing documentation for psych-2.2.0
Done installing documentation for psych after 1 seconds
Updating rmagick
Building native extensions. This could take a while...
ERROR: Error installing rmagick:
ERROR: Failed to build gem native extension.

current directory: /var/lib/gems/2.3.0/gems/rmagick-2.16.0/ext/RMagick
/usr/bin/ruby2.3 -r ./siteconf20161115-29205-1qfeji3.rb extconf.rb
checking for gcc... yes
checking for Magick-config... no
checking for pkg-config... no
Can't install RMagick 2.16.0. Can't find Magick-config or pkg-config in /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin

*** 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/bin/$(RUBY_BASE_NAME)2.3

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

/var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/rmagick-2.16.0/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /var/lib/gems/2.3.0/gems/rmagick-2.16.0 for inspection.
Results logged to /var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/rmagick-2.16.0/gem_make.out
Updating sqlite3
Building native extensions. This could take a while...
ERROR: Error installing sqlite3:
ERROR: Failed to build gem native extension.

current directory: /var/lib/gems/2.3.0/gems/sqlite3-1.3.12/ext/sqlite3
/usr/bin/ruby2.3 -r ./siteconf20161115-29205-1mvfxcm.rb extconf.rb
checking for sqlite3.h... no
sqlite3.h is missing. Try 'brew install sqlite3',
'yum install sqlite-devel' or 'apt-get install libsqlite3-dev'
and check your shared library search path (the
location where your sqlite3 shared library is located).
*** 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/bin/$(RUBY_BASE_NAME)2.3
--with-sqlite3-config
--without-sqlite3-config
--with-pkg-config
--without-pkg-config
--with-sqlite3-dir
--without-sqlite3-dir
--with-sqlite3-include
--without-sqlite3-include=${sqlite3-dir}/include
--with-sqlite3-lib
--without-sqlite3-lib=${sqlite3-dir}/lib

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

/var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/sqlite3-1.3.12/mkmf.log

extconf failed, exit code 1


In these error messages it say that I have to check the /var/lib/gems/2.3.0/extensions/x86_64-linux/2.3.0/sqlite3-1.3.12/mkmf.log file content, this is its content (that maybe could give some additional information to understand where is the probem):

package configuration for sqlite3 is not found
find_header: checking for sqlite3.h... -------------------- no

"gcc -o conftest -I/usr/include/x86_64-linux-gnu/ruby-2.3.0 -I/usr/include/ruby-2.3.0/ruby/backward -I/usr/include/ruby-2.3.0 -I. -Wdate-t$
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5: return 0;
6: }
/* end */

"gcc -E -I/usr/include/x86_64-linux-gnu/ruby-2.3.0 -I/usr/include/ruby-2.3.0/ruby/backward -I/usr/include/ruby-2.3.0 -I. -Wdate-time -D_FO$
conftest.c:3:21: fatal error: sqlite3.h: No such file or directory
compilation terminated.
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: #include <sqlite3.h>
/* end */

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


So, reading the previous log file, it seems that the problem could be related to:

fatal error: sqlite3.h: No such file or directory


It seems that a C header file is missing but I really don't know why.

Why I have this problem? What am I missing? How can I try to fix this issue?

Tnx

Answer

I am not sure about what exactly is this bundler GEM that have to be installed

-> bundler is package manager for ruby code libraries aka ruby gems.


mysql gem would not install unless you install the binary dependencies of the library. try

$ sudo apt-get install libmysql-ruby libmysqlclient-dev
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