Related
PROBLEM:
bundler fails to build ffi and so my rails apps are broken in my development environment.
None of the posts that I've read have solutions that work for me. I get the same error in a number of rails apps.
What other troubleshooting steps can I take?
How do I fix this issue?
BACKGROUND:
After an upgrade to Mountain Lion from Snow Leopard, Xcode upgrade, Clean Homebrew install, I did a clean install of rvm. Now I am trying to recreate the gemsets used by my rails apps. I did:
gem install rails -v3.2.16 (to get the base rails gems installed)
rvm gemset import ruby-1.9.3-p545#CLIENTNAME.gems (to import gems)
bundle install (to install dependencies and resync gemfile.lock)
ISSUE:
bundle install fails with this error message:
An error occurred while installing ffi (1.9.3), and Bundler cannot continue.
Make sure that gem install ffi -v '1.9.3' succeeds before bundling.
The complete gem_make.out is here: https://gist.github.com/mattmartini/b2f8ad3b4e6c57325d38
The mkmf.log is here: https://gist.github.com/mattmartini/d3256cb52e5eafb2346b
The config.log is here: https://gist.github.com/mattmartini/69407e118e92cadda2b0
I would like to stay on ruby 1.9.3 as the Production servers are using this.
OBSERVATIONS:
One of the errors thrown is that 'C compiler cannot create executables' - this is not true. I can compile C programs and bundler built nokogiri without a problem.
I did just notice that libffi, which was installed (along with gcc46) by rvm, is keg only. Would bundler be able to use the lib in creating the gem?
ENVIRONMENT:
Mac OS X 10.8.5 (Mountain Lion)
Xcode 5.0.2 (command line tools installed)
Homebrew 0.9.5 (recent fresh install)
rvm 1.25.25 (stable)
ruby 1.9.3-p545
libffi 3.0.13 (brew via rvm)
gcc46 (brew via rvm)
REVIEWED:
I reviewed a number of posts of similar issues, but none had a solution that worked for me, including:
https://github.com/ffi/ffi/issues/286
Note I had a bunch of stack overflow links here but I couldn't submit this question with them.
My hunch about libffi being keg only was correct. After linking libffi, bundle used this lib instead of trying to compile it. This resolves the issue of getting the gem installed, but doesn't resolve why it fails to compile.
Since the lib is keg only you have to force it to link:
brew link libffi --force
After updating to OS X 10.9 Mavericks I tried to start a Rails 3 app, but the connection to the PG database was not working. Checking on PGAdmin III, the database is still there and it works fine.
So I tried to reinstall the pg gem:
gem uninstall pg
gem install pg
But the last command doesn't succeed, and gives the following error:
Building native extensions. This could take a while... ERROR: Error
installing pg:
ERROR: Failed to build gem native extension.
/Users/XXX/.rvm/rubies/ruby-1.9.3-p194/bin/ruby extconf.rb checking for pg_config... yes Using config values from
/usr/local/bin/pg_config
* 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.
/Users/XXX/.rvm/rubies/ruby-1.9.3-p194/lib/ruby/1.9.1/mkmf.rb:381:in
`try_do': The compiler failed to generate an executable file.
(RuntimeError) You have to install development tools first. from
/Users/XXX/.rvm/rubies/ruby-1.9.3-p194/lib/ruby/1.9.1/mkmf.rb:461:in
try_link0' from
/Users/XXX/.rvm/rubies/ruby-1.9.3-p194/lib/ruby/1.9.1/mkmf.rb:476:in
try_link' from extconf.rb:39:in `'
I guess the problem is related to the Xcode developer tools. I updated Xcode to the latest version, but that didn't solve the problem. Do you know how to fix it?
You're right that the problem is related to the Xcode developer tools. It's not a bad idea to make sure you have all the developer tools installed (as opposed to solely installing gcc as mentioned in the previous answer):
Open up Xcode
In the application menu item "Xcode" select Open Developer Tool > More Developer Tools...
This takes you to a site with a bunch of software. Go ahead and download and install "Command Line Tools (OS X Mavericks) for Xcode - Late October 2013".
You will now be able to properly install the gem.
For anyone else coming to this issue off of a fresh install of the Postgres 9.3.0 app on Mac OS X Mavericks (i.e. you're not using homebrew for your Postgres installation) you may notice that even though you can build the pg gem you cannot run rake because of a dylib issue:
rake aborted!
dlopen(/Users/[USERNAME]/.rbenv/versions/2.0.0-p195/lib/ruby/gems/2.0.0/gems/pg-0.15.1/lib/pg_ext.bundle, 9): Library not loaded: #loader_path/../lib/libpq.5.dylib
Referenced from: /Users/[USERNAME]/.rbenv/versions/2.0.0-p195/lib/ruby/gems/2.0.0/gems/pg-0.15.1/lib/pg_ext.bundle
Reason: image not found - /Users/[USERNAME]/.rbenv/versions/2.0.0-p195/lib/ruby/gems/2.0.0/gems/pg-0.15.1/lib/pg_ext.bundle
Unfortunately this is a problem with the current release version of 9.3.0 of Postgres. Winding back to a previous version will fix it for you:
uninstall the pg gem: gem uninstall pg
delete your 9.3.0 Postgres app by dragging it to the trash and emptying the trash
install version 9.2.2.0 of the Postgres app here: http://postgres-app.s3.amazonaws.com/PostgresApp-9-2-2-0.zip
reinstall the pg gem: gem install pg
*Thanks to the comment by jhiro009 on this thread for pointing me in the right direction on this last Postgres app part of the issue although the 9.2.4.3 version that he mentioned didn't work for me.
Using homebrew fixed this for me:
gem uninstall pg
brew install apple-gcc42
gem install pg
EDIT: I also manually installed "devtools"
xcode-select --install
On OS X Mavericks
sudo ln -s /usr/bin/llvm-gcc /usr/bin/gcc-4.2
gem uninstall pg; gem install pg;
works with homebrew Postgresql (9.3.1) installation and Apple Command Line Tools installed (pg 0.17.0).
None of the previous solutions worked for me (I just upgraded to Mavericks and updated XCode). Instead, I installed Postgress.app. and called
gem install pg -- --with-pg-config=/Applications/Postgres.app/Contents/MacOS/bin/pg_config
None of the solutions worked for me, and I didn't want to use MacPorts. Try and download the Postgres App and put it into the Application directory.
Then, specify the location of newly downloaded pg_config, which resides inside the app:
gem install pg -- --with-pg-config=/Applications/Postgres.app/Contents/MacOS/bin/pg_config
If you run in to missing headers problem, try specifying the include directory of the app:
gem install pg -- --with-pg-include='/Applications/Postgres.app/Contents/MacOS/include/'
If you are looking for just a quick fix, add the following to your database.yml file:
host: localhost
I had the exact problem, added that line, and now all is well.
I had luck following this post from the guys at New-Bamboo:
3 Quick Tips for Coding with OS X 10.9 Mavericks
After installing the xcode dev tools, the third step sorted everything out:
brew tap homebrew/versions && brew install apple-gcc42
brew link --force apple-gcc42
ln -nsf $(which gcc-4.2) /usr/bin/gcc-4.2
I had this problem the first time I tried to install pg. Through various trials and errors I found something that worked. Thankfully, my notes also worked when Mavericks broke everything.
Hope this helps:
Do not do any brewing.
download the enterpriseDB one-click installer, mount and run.
If it doesn't work, run it through the command line (unattended mode) and it will change the memory settings. Restart, run again.
Makes a user called postgres with the password you supply. Also installs pgadmin III.
run this in app directory:
env ARCHFLAGS="-arch x86_64" gem install pg -- --with-pg-include=/Library/PostgreSQL/9.2/include/ --with-pg-lib=/Library/PostgreSQL/9.2 sudo env ARCHFLAGS='-arch i386' gem install pg/lib/
Open pgadmin3 and create a user and password for rails, then add it to config.
psql [database_name] # to check on your db. Or use pgadmin III
I used to have no problems at all with ruby, gems and all related stuff. But after installing X Code Developer Tools and upgrading to Lion the gems do not install.
I get the following error for every gem. This is the message for sqlite as an example:
Building native extensions. This could take a while...
ERROR: Error installing sqlite3:
ERROR: Failed to build gem native extension.
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby extconf.rb
mkmf.rb can't find header files for ruby at /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/ruby.h
Gem files will remain installed in /Library/Ruby/Gems/1.8/gems/sqlite3-1.3.4 for inspection.
Results logged to /Library/Ruby/Gems/1.8/gems/sqlite3-1.3.4/ext/sqlite3/gem_make.out
What went wrong? How to fix it?
I had to install the Command Line Tools in the latest Xcode-Version (4.3.1) and
sudo gem install rails
worked like a charm.
To install Command Line Tools, go to Xcode Preferences > Downloads or use the following command in terminal (thx #Purell):
xcode-select --install
I'm using Mavericks and Ruby 2.0.0 and I also got this error (mkmf.rb can't find header files) when installing gems. I solved this issue by creating some symbolic links in Terminal.
#First install developer tools again:
xcode-select --install
#Create symbolic link to Ruby include (updated for 10.9)
sudo ln -s /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0 /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/include
#Create symbolic link to config.h (updated for 10.9)
sudo ln -s /System/Library/Frameworks/Ruby.framework/Versions/2.0/Headers/ruby/config.h /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0/ruby/config.h
I faced same problem while trying to install rails on my Lion. This is how i could solve it.
Install rvm
$ curl https://raw.github.com/wayneeseguin/rvm/master/binscripts/rvm-installer | bash -s stable
Install osx-gcc-installer
https://github.com/kennethreitz/osx-gcc-installer
Installed new version of ruby
rvm install 1.9.3
Typed to following command to show the requirements
rvm requirements
To use an RVM installed Ruby as default, instead of the system ruby:
rvm system ; rvm gemset export system.gems ; rvm 1.9.3 ; rvm gemset import system.gems # migrate your gems
rvm alias create default 1.9.3
Installed rails:
sudo gem install rails
My Mac is now read for rails!! YAY!!
Not a direct solution to your problem, but I'd suggest using rvm to install fresh rubies and gems. That should take care of it.
While installing Rails I had the error :
can't find header files for ruby at /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/ruby.h
As i had already Xcode installed, I had just to install Command Line Tools to resolve this problem
You need to have XCode installed, it includes ruby.h as well as some other important files needed to compile other native gems.
Hello i'm sorry i can't test this answer but i would suggest to change the default search paths in your bashrc and extconf.rb since the Library files seem to be moved in Lion.
(P.S. if he wants to work with the default 1.8 Version, rvm would be an unneeded hassle)
Update to the latest version of xcode, that fixed the problem for me. Make sure xcodebuild is in your path.
running xcodebuild -version in a terminal window should output 4.2.1 (4.x at least).
After a OS-Update make sure that you do accept the X-Code license even when you have used command-line-tools before. Only then some header-files will be available. To accept the license you have to run X-Code once.
I just forgot to run it with the sudo command.
sudo gem install sqlite3
not:
gem install sqlite3
I always worked my way around Nokogiri installation issues by following the documentation in the "Installing Nokogiri" tutorial.
But this time, even after installing all the dependencies, Nokogiri hasn't been installed. I get the following error:
libxml2 is missing. please visit <http://nokogiri.org/tutorials/installing_nokogiri.html>
I tried installing it by specifying the libxml2 and libxslt directories:
sudo gem install nokogiri -- --with-xml2-include=/usr/include/libxml2 --with-xml2-lib=/usr/lib --with-xslt-dir=/usr/
but it returned the same error.
I followed all the other related Stack Overflow articles and none helped. Does anyone have a solution?
You may actually need to install both of these packages
sudo apt-get install libxslt-dev libxml2-dev
First, install the dependencies:
sudo apt-get install libxslt-dev libxml2-dev
If you still receive the error, you may be missing a compiler toolchain:
sudo apt-get install build-essential
You'll get the "libxml2 is missing" error if you're missing a build toolchain (at least I ran into this issue on Debian Lenny).
The Nokogiri build test-compiles a libxml2 header file to verify that it is present, however, it doesn't differentiate between "libxml2 is missing" and "a compiler to test libxml2 is missing".
In Mac OS X (Mavericks), installing the libraries with brew and setting NOKOGIRI_USE_SYSTEM_LIBRARIES=1 before installing the gem did the trick for me.
Summarising:
If previously installed, uninstall the gem:
gem uninstall nokogiri
Use Homebrew to install libxml2, libxslt and libiconv:
brew install libxml2 libxslt libiconv
Install the gem specifying the paths to the libraries to be linked against:
NOKOGIRI_USE_SYSTEM_LIBRARIES=1 gem install nokogiri -- --use-system-libraries --with-iconv-dir="$(brew --prefix libiconv)" --with-xml2-config="$(brew --prefix libxml2)/bin/xml2-config" --with-xslt-config="$(brew --prefix libxslt)/bin/xslt-config"
I just had the same issue on Fedora 13. After a frustrating and unsuccessful search to make
gem install nokogiri
work for me, I was able to install it and get around the libxml2 error via yum.
Simply install the gem via yum instead of the gem command:
su
yum search rubygem-nokogiri #this find the proper package name
yum install rubygem-nokogiri.i686
This helped me find the right answer for Fedora and, as I am using RVM for Ruby package management,
yum install rubygem-nokogiri
will pull in all the Ruby gems and dependencies into the system, not into my RVM environment, and in my experience that leads to a very frustrating and humbling experience.
So, taking your find of the Nokogiri yum gem you can use:
yum provides rubygem-nokogiri
and get a list of the dependencies for rubygem-Nokogiri which showed me the libraries that were missing. After that I ran:
yum install libxml2-devel libxslt libxslt-devel
Now Nokogiri compiles in Fedora and Nokogiri installs. D'oh!, we need the headers to compile Nokogiri from the devel libraries.
In Mac OS X (Mavericks) if none of these solutions work, try:
ARCHFLAGS="-arch x86_64" gem install nokogiri
or
ARCHFLAGS="-arch i386" gem install nokogiri
depending on your system's architecture.
You usually need development files for building gems. Try:
sudo apt-get install libxslt-dev libxml2-dev
(I just saw that Eric suggested the same in a comment.)
I was able to get this installed with Chocolatey, Windows 8.1 x64, and DevKit x64.
cinst libxml2
cinst libxslt
cinst libiconv
gem install nokogiri --
--with-xml2-include=C:\Chocolatey\lib\libxml2.2.7.8.7\build\native\include
--with-xml2-lib=C:\Chocolatey\lib\libxml2.redist.2.7.8.7\build\native\bin\v110\x64\Release\dynamic\cdecl
--with-iconv-include=C:\Chocolatey\lib\libiconv.1.14.0.11\build\native\include
--with-iconv-lib=C:\Chocolatey\lib\libiconv.redist.1.14.0.11\build\native\bin\v110\x64\Release\dynamic\cdecl
--with-xslt-include=C:\Chocolatey\lib\libxslt.1.1.28.0\build\native\include
--with-xslt-lib=C:\Chocolatey\lib\libxslt.redist.1.1.28.0\build\native\bin\v110\x64\Release\dynamic
You'll have to verify the version number in the paths are correct.
You may possibly need to add Microsoft's NuGet repository:
-Source "https://go.microsoft.com/fwlink/?LinkID=230477"
It will be:
sudo yum install -y libxml2 libxml2-devel
on RHEL servers.
At macOS none of above/below had really worked for me until I explicitly provided XCode libxml2 path to --with-xml2-include.
gem install nokogiri -- --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/libxml2 --use-system-libraries
I was able to install Nokogiri 1.6.5 on Fedora 20 by doing:
export NOKOGIRI_USE_SYSTEM_LIBRARIES=true
Then running:
gem install nokogiri
For anyone else experiencing this issue, I solved it by running this command within the project directory
gem install nokogiri -- --use-system-libraries
Update: I ran into this again and tried just updating the gem which worked for me...
gem update nokogiri
Have you tried installing libxml2? Not from rubygems, but via the standard install process for your operating system. On Ubuntu/Debian for example:
sudo apt-get install libxml2
On any recent version of OS X it should already be installed.
For OSX users, if you've had success installing Nokogiri before, yet are getting errors installing it on, say, using a new version of Ruby that you've added and that error that includes a message like:
The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
This could be indicative of a XCode upgrade having happened via the App Store, either manually or automatically, and you not having opened it since that time.
If so, you should be able to open XCode, agree to the new license, and then install Nokogiri successfully.
On Mac OS X Yosemite my mistake was that I tried to use sudo gem install when it's a rule of thumb to not use superuser privileges when installing gems.
In my case it tried to modify the system installation of Ruby, and that's not a good idea. I installed rbenv, installed Ruby 2.2.2 thru it and set it as global, which is a term from rbenv's documentation. After that Nokogiri could install itself with a simple
gem install nokogiri
No hacks or workarounds were necessary, just a properly set environment; Nokogiri does the rest perfectly.
Was able to install vagrant-awe by following the above post but using the command as follow:
NOKOGIRI_USE_SYSTEM_LIBRARIES=1 vagrant plugin install vagrant-aws
For Windows x64:
gem inst nokogiri --pre --platform ruby
For more information check this thread: https://github.com/sparklemotion/nokogiri/issues/864
I was able to install Nokogiri by running the following packages:
$ dnf group install "C Development Tools and Libraries"
$ dnf install ruby-devel libxml2-devel patch
=== TLDR ===
As the instructions state, build Ruby with the latest clang compiler, or at least the same version that Rubygems will use to compile Nokogiri's native extensions libxml and libxsl.
If using RVM, building from source with the --with-ggc=clang flag was what did it for me:
rvm install 2.2 --with-gcc=clang
Replace 2.2 with whatever version you want. --with-gcc=clang ensures RVM builds from source and uses clang to do so; otherwise RVM may a pre-built binary Ruby, which is what tripped me up.
Then, install Nokogiri as normal using Bundler or Rubygems.
=== IN DEPTH ===
I struggled with this for a while. gem install nokogiri gave me:
checking for xmlParseDoc() in libxml/parser.h... no
checking for xmlParseDoc() in -lxml2... no
checking for xmlParseDoc() in -llibxml2... no
Digging into mkmf.log I saw:
conftest.c:15:27: error: too few arguments to function call, single argument 'cur' was not specified
int t(void) { xmlParseDoc(); return 0; }
Nokogiri supplies its own libxml and libxsl (as of 1.6.4). The signature defined in Nokogiri's local copy of parser.h (found under the gem install directory) is:
xmlParseDoc (const xmlChar *cur);
So I was at a loss as to how the method call in the hermetically sealed conftest.c file usage couldn't match up with the header file for parser.h.
When I realized I had probably installed a binary Ruby I removed and reinstalled using --with-gcc=clang (to force compilation and use clang) and the problem was solved:
rvm uninstall 2.2
rvm install 2.2 --with-gcc=clang
gem install nokogiri
I'm not exactly sure why that works as the system libxml header /usr/include/libxml2/libxml/parser.h has the same signature as Nokogiri's local copy.
It's weird, but it worked. Just make sure you compile a Ruby with clang.
gem install nokogiri -- --with-xml2-include=/usr/local/Cellar/libxml2/2.7.8/include/libxml2 --with-xml2-lib=/usr/local/Cellar/libxml2/2.7.8/lib --with-xslt-dir=/usr/local/Cellar/libxslt/1.1.26 --with-iconv-include=/usr/local/Cellar/libiconv/1.14/include --with-iconv-lib=/usr/local/Cellar/libiconv/1.14/lib
Change your version with it.
I'm try to install the SQLite gem on a Fedora 9 Linux box with Ruby 1.8.6, Rails 2.2.2, gem 1.3, and sqlite-3.5.9. Here's the command I'm running and its results:
sudo gem install sqlite3-ruby
Building native extensions. This could take a while...
ERROR: Error installing sqlite3-ruby:
ERROR: Failed to build gem native extension.
/usr/bin/ruby extconf.rb install sqlite3-ruby
can't find header files for ruby.
Gem files will remain installed in /usr/lib/ruby/gems/1.8/gems/sqlite3-ruby-1.2.4 for inspection.
Results logged to /usr/lib/ruby/gems/1.8/gems/sqlite3-ruby-1.2.4/ext/sqlite3_api/gem_make.out
gem_make.out just repeats what was already sent to the console. How can I install this gem?
The SQLite RubyGem isn't actually a RubyGem, it's a "CGem", IOW it's written in C. This means it has to be compiled and linked to the Ruby interpreter when you install it and in order to do that it needs the C header files for the Ruby interpreter.
If you compile Ruby yourself, those header files will be installed automatically, however, in RedHat-ish systems, such header files are usually packaged in a seperate package, called <whatever>-dev. So, in this case you will need to install the ruby-dev package and possibly the libsqlite3-dev (Ubuntu) or sqlite-devel (Fedora) package as well.
However, you might be better off just installing your Operating System's pre-packaged libsqlite3-ruby package, that way all the dependencies are automatically satisfied.
(Note: all package names pulled out of thin air, might be different on your system.)
You probably need the ruby dev package. For Ubuntu you have to install ruby1.8-dev which includes the ruby header files. A quick google says that the yum package is ruby-devel. so run this:
sudo yum install ruby-devel
I faced problem installing sqlite3-ruby gem on my fedora 13 box.
It was fixed after sudo yum install sqlite-devel
When I had that problem:
gem install sqlite3 -v '1.3.9'
Building native extensions. This could take a while...
ERROR: Error installing sqlite3:
ERROR: Failed to build gem native extension.
For me worked, installing the "libsqlite3-dev" with:
apt-get install libsqlite3-dev
sudo apt-get install ruby-dev
Fixed it for me.
On Ubuntu 9 and 10 try:
sudo apt-get install ruby-dev
sudo apt-get install sqlite3-dev
Then run
gem install sqlite3
Run the following for Fedora OS:
yum install rubygem-sqlite3
On alpine, you need to install the sqlite-dev package.
I also faced this same issue, the problem is that your Linux installation requires the development libraries for SQLite3 to be installed in order to build the gem.
Here's how I fixed the issue
Open your terminal and run the following commands
sudo apt-get install sqlite3
sudo apt-get install libsqlite3-dev
And then try installing Sqlite3 gem again using this command
gem install sqlite3
That's all.
I hope this helps
Do you have all the source code required to build sqlite3-ruby? Gem is trying to compile some C code and cannot find the headers. You can probably use a fedora rpm for sqlite3-ruby (I don't use fedora, but I'm sure one exists) if you prefer to forgo compiling. Personally for ruby stuff, I prefer to use gem rather than a distro's packaging system.
I'm not really familiar with Fedora, but in Ubuntu when you are installing packages you have apt-get, and you have to install the build-essentials which includes gcc and other compilation tools for C. I would say that could be your issue, and you make look into how that can be install either using RPM or apt-get on Fedora.
I fixed the problem on my OLPC (Fedora 9) by installing 'gcc' oddly enough. It seems like it should have been one of those dev packages, but no.
Also, regarding the other packages, the suffix is "-devel", not "-dev", so make sure you get those ending right: "ruby-devel", "sqlite-devel"...
Once you get that installed, if you get errors about your gems being too old "< 1.3.1" when you try to run various rails scripts, eg: script/server or script/console, google "upgrade_rubygems" to fix that problem...
HTH...
Run "sudo yum install sqlite-devel" and then "gem install sqlite3". Had the same problem on my Fedora 15.
I had this same exact issue...instead of gem'ing the missing pieces I used synaptic on unbuntu.
The key package for me was libsqlite-ruby1.9.1 ... I documented my experience (for reference) with this error at :
Sqlite3-gem-error-during-bundle-install
I encountered this error while running bundle install after generating a react-rails app on Fedora 29. I was able to identify a suitable development package by running dnf search sqlite3, then installed it dnf install libsqlite3x-devel. This fixed it for me.