Hi Matt,
The best place to send Open Babel questions is to the mailing list. Otherwise,
you get stuck in my overfull e-mail box which I tend to ignore.
I'm afraid I don't know much about Ruby, the OB gem, or Heroku. However, I do
know that others on the list do know about this (e.g., there's now a "Rubabel"
project). I also noticed that in the error messages, it's complaining about not
being able to find Open Babel installed, so it's trying to build the sources.
I suspect if you pre-install Open Babel, the gem will go through fine. If not,
it looks like it's hunting for pkg-config to find libopenbabel and so you may
need to install pkg-config to help things out.
Hope that helps,
-Geoff
On Mar 13, 2014, at 4:22 PM, Matt Berlin <mgber...@gmail.com> wrote:
> Dr Hutchison,
> I'm a chemist new to programming in Ruby/Rails, and am currently trying to
> deploy an app to Heroku that uses OpenBabel. I'm trying to use the openbabel
> gem, along with openbabel-heroku. I feel like I've tried everything and can't
> get it to deploy. Do you think you could offer some advice? My repo can be
> found at https://github.com/mgberlin/chemInv and I've pasted the deployment
> errors below. I'd really appreciate any help,
>
> Thanks,
> Matt Berlin
>
> git push heroku master
> Fetching repository, done.
> Counting objects: 32, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (29/29), done.
> Writing objects: 100% (29/29), 3.22 KiB, done.
> Total 29 (delta 20), reused 0 (delta 0)
>
> -----> Fetching custom git buildpack... done
> -----> Multipack app detected
> =====> Downloading Buildpack:
> https://github.com/Cominch/heroku-buildpack-openbabel.git
> =====> Detected Framework: openbabel detection
> -----> Creating directories in /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644
> -----> Preparing to install OpenBabel
> -----> Downloading precompiled OpenBabel
> % Total % Received % Xferd Average Speed Time Time Time
> Current
> Dload Upload Total Spent Left Speed
> 100 22.1M 100 22.1M 0 0 562k 0 0:00:40 0:00:40 --:--:-- 708k
> -----> openbabel done
> =====> Downloading Buildpack:
> https://github.com/heroku/heroku-buildpack-ruby.git
> =====> Detected Framework: Ruby
> -----> Compiling Ruby/Rails
> -----> Using Ruby version: ruby-1.9.3
> -----> Installing dependencies using 1.5.2
> Ruby version change detected. Clearing bundler cache.
> Old: ruby 2.0.0p451 (2014-02-24 revision 45167) [x86_64-linux]
> New: ruby 1.9.3p545 (2014-02-24 revision 45159) [x86_64-linux]
> Running: bundle install --without development:test --path
> vendor/bundle --binstubs vendor/bundle/bin -j4 --deployment
> Fetching gem metadata from https://rubygems.org/..........
> Fetching additional metadata from https://rubygems.org/..
> Fetching git://github.com/Cominch/openbabel-heroku-gem.git
> Installing multi_json (1.9.0)
> Installing i18n (0.6.9)
> Installing minitest (4.7.5)
> Installing rake (10.1.1)
> Installing builder (3.1.4)
> Installing erubis (2.7.0)
> Installing atomic (1.1.15)
> Installing tzinfo (0.3.38)
> Installing rack (1.5.2)
> Installing mime-types (1.25.1)
> Installing polyglot (0.3.4)
> Installing andand (1.3.3)
> Installing activerecord-deprecated_finders (1.0.3)
> Installing arel (4.0.2)
> Installing execjs (2.0.2)
> Installing coffee-script-source (1.7.0)
> Installing thor (0.18.1)
> Installing hike (1.2.3)
> Installing subexec (0.2.3)
> Using openbabel-heroku (2.3.2.0) from
> git://github.com/Cominch/openbabel-heroku-gem.git (at master)
> Installing bcrypt (3.1.7)
> Using bundler (1.5.2)
> Installing json (1.8.1)
> Installing tilt (1.4.1)
> Installing rails_serve_static_assets (0.0.2)
> Installing rails_stdout_logging (0.0.3)
> Installing thread_safe (0.2.0)
> Installing sass (3.2.14)
> Installing rack-test (0.6.2)
> Gem::Installer::ExtensionBuildError: ERROR: Failed to build gem native
> extension.
>
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/bin/ruby
> extconf.rb
> Downloading OpenBabel sources
> % Total % Received % Xferd Average Speed Time Time Time
> Current
> Dload Upload Total Spent Left Speed
> 100 19.2M 100 19.2M 0 0 6779k 0 0:00:02 0:00:02 --:--:--
> 8678k 497
> Configuring OpenBabel
> checking for main() in -lopenbabel... no
> OpenBabel not installed. Compiling sources.
> make: *** No targets specified and no makefile found. Stop.
> make: *** No rule to make target `install'. Stop.
> Compiling and instaling OpenBabel Ruby bindings.
> Package openbabel-2.0 was not found in the pkg-config search path.
> Perhaps you should add the directory containing `openbabel-2.0.pc'
> to the PKG_CONFIG_PATH environment variable
> No package 'openbabel-2.0' found
> Package openbabel-2.0 was not found in the pkg-config search path.
> Perhaps you should add the directory containing `openbabel-2.0.pc'
> to the PKG_CONFIG_PATH environment variable
> No package 'openbabel-2.0' found
> extconf.rb:6: Use RbConfig instead of obsolete and deprecated Config.
> checking for inchi_api.h in
> /usr/include/inchi,/usr/include,./../../include... yes
> checking for main() in -lopenbabel... 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=/tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/bin/ruby
> --with-openbabel-dir
> --without-openbabel-dir
> --with-openbabel-include=${openbabel-dir}/include
> --with-openbabel-lib=${openbabel-dir}/lib
> --with-openbabellib
> --without-openbabellib
> Install Open Babel first. If you've already compiled and installed
> Open Babel, you may need to run ldconfig.
> sed: can't read Makefile: No such file or directory
> make: *** No targets specified and no makefile found. Stop.
> *** 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=/tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/bin/ruby
> --with-openbabellib
> --without-openbabellib
>
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:1515:in
> `stat': No such file or directory -
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/bundle/ruby/1.9.1/gems/openbabel-2.3.1.9/src/openbabel-2.3.1/scripts/ruby/openbabel.so
> (Errno::ENOENT)
> from
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:1515:in
> `block in fu_each_src_dest'
> from
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:1529:in
> `fu_each_src_dest0'
> from
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:1513:in
> `fu_each_src_dest'
> from
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:395:in
> `cp'
> from extconf.rb:45:in `<main>'
> Gem files will remain installed in
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/bundle/ruby/1.9.1/gems/openbabel-2.3.1.9
> for inspection.
> Results logged to
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/bundle/ruby/1.9.1/gems/openbabel-2.3.1.9/ext/openbabel/gem_make.out
> Installing coffee-script (2.2.0)
> Installing treetop (1.4.15)
> Installing pg (0.17.1)
> An error occurred while installing openbabel (2.3.1.9), and Bundler
> cannot
> continue.
> Make sure that `gem install openbabel -v '2.3.1.9'` succeeds before
> bundling.
> Bundler Output: Fetching gem metadata from
> https://rubygems.org/..........
> Fetching additional metadata from https://rubygems.org/..
> Fetching git://github.com/Cominch/openbabel-heroku-gem.git
> Installing multi_json (1.9.0)
> Installing i18n (0.6.9)
> Installing minitest (4.7.5)
> Installing rake (10.1.1)
> Installing builder (3.1.4)
> Installing erubis (2.7.0)
> Installing atomic (1.1.15)
> Installing tzinfo (0.3.38)
> Installing rack (1.5.2)
> Installing mime-types (1.25.1)
> Installing polyglot (0.3.4)
> Installing andand (1.3.3)
> Installing activerecord-deprecated_finders (1.0.3)
> Installing arel (4.0.2)
> Installing execjs (2.0.2)
> Installing coffee-script-source (1.7.0)
> Installing thor (0.18.1)
> Installing hike (1.2.3)
> Installing subexec (0.2.3)
> Using openbabel-heroku (2.3.2.0) from
> git://github.com/Cominch/openbabel-heroku-gem.git (at master)
> Installing bcrypt (3.1.7)
> Using bundler (1.5.2)
> Installing json (1.8.1)
> Installing tilt (1.4.1)
> Installing rails_serve_static_assets (0.0.2)
> Installing rails_stdout_logging (0.0.3)
> Installing thread_safe (0.2.0)
> Installing sass (3.2.14)
> Installing rack-test (0.6.2)
>
> Gem::Installer::ExtensionBuildError: ERROR: Failed to build gem native
> extension.
>
>
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/bin/ruby
> extconf.rb
> Downloading OpenBabel sources
> % Total % Received % Xferd Average Speed Time Time Time
> Current
> Dload Upload Total Spent Left Speed
> 100 19.2M 100 19.2M 0 0 6779k 0 0:00:02 0:00:02 --:--:--
> 8678k 497
> Configuring OpenBabel
> checking for main() in -lopenbabel... no
> OpenBabel not installed. Compiling sources.
> make: *** No targets specified and no makefile found. Stop.
> make: *** No rule to make target `install'. Stop.
> Compiling and instaling OpenBabel Ruby bindings.
> Package openbabel-2.0 was not found in the pkg-config search path.
> Perhaps you should add the directory containing `openbabel-2.0.pc'
> to the PKG_CONFIG_PATH environment variable
> No package 'openbabel-2.0' found
> Package openbabel-2.0 was not found in the pkg-config search path.
> Perhaps you should add the directory containing `openbabel-2.0.pc'
> to the PKG_CONFIG_PATH environment variable
> No package 'openbabel-2.0' found
> extconf.rb:6: Use RbConfig instead of obsolete and deprecated Config.
> checking for inchi_api.h in
> /usr/include/inchi,/usr/include,./../../include... yes
> checking for main() in -lopenbabel... 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=/tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/bin/ruby
> --with-openbabel-dir
> --without-openbabel-dir
> --with-openbabel-include=${openbabel-dir}/include
> --with-openbabel-lib=${openbabel-dir}/lib
> --with-openbabellib
> --without-openbabellib
> Install Open Babel first. If you've already compiled and installed
> Open Babel, you may need to run ldconfig.
> sed: can't read Makefile: No such file or directory
> make: *** No targets specified and no makefile found. Stop.
> *** 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=/tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/bin/ruby
> --with-openbabellib
> --without-openbabellib
>
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:1515:in
> `stat': No such file or directory -
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/bundle/ruby/1.9.1/gems/openbabel-2.3.1.9/src/openbabel-2.3.1/scripts/ruby/openbabel.so
> (Errno::ENOENT)
> from
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:1515:in
> `block in fu_each_src_dest'
> from
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:1529:in
> `fu_each_src_dest0'
> from
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:1513:in
> `fu_each_src_dest'
> from
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/ruby-1.9.3/lib/ruby/1.9.1/fileutils.rb:395:in
> `cp'
> from extconf.rb:45:in `<main>'
>
>
> Gem files will remain installed in
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/bundle/ruby/1.9.1/gems/openbabel-2.3.1.9
> for inspection.
> Results logged to
> /tmp/build_dc55137d-170c-48cc-b696-1c0cc967b644/vendor/bundle/ruby/1.9.1/gems/openbabel-2.3.1.9/ext/openbabel/gem_make.out
> Installing coffee-script (2.2.0)
> Installing treetop (1.4.15)
> Installing pg (0.17.1)
> An error occurred while installing openbabel (2.3.1.9), and Bundler
> cannot
> continue.
> Make sure that `gem install openbabel -v '2.3.1.9'` succeeds before
> bundling.
> !
> ! Failed to install gems via Bundler.
> !
>
> ! Push rejected, failed to compile Multipack app
>
> To g...@heroku.com:peaceful-shore-4036.git
> ! [remote rejected] master -> master (pre-receive hook declined)
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