Hi,
First time trying out sequenceserver. Looks like a great tool, looking forward to getting it going. I am trying to install on a ubuntu server. With the following command, I get the following error:
`
sudo gem install sequenceserver
Building native extensions. This could take a while…
ERROR: Error installing sequenceserver:
ERROR: Failed to build gem native extension.
/usr/bin/ruby1.9.1 extconf.rb
/usr/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in require': cannot load such file -- mkmf (LoadError) from /usr/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in require’
from extconf.rb:2:in `’
Gem files will remain installed in /var/lib/gems/1.9.1/gems/eventmachine-1.0.7 for inspection.
Results logged to /var/lib/gems/1.9.1/gems/eventmachine-1.0.7/ext/gem_make.out
`
Here are the versions of ruby and gem I currently have:
`
gem -v
1.8.11
ruby -v
ruby 1.8.7 (2011-06-30 patchlevel 352) [x86_64-linux]
`
Any insight would be greatly appreciated!
Thanks
Hey Phil,
Could you try installing SequenceServer after running the command below and let us know if that worked?
sudo apt-get install ruby-dev
– Priyam
Hi Anurag,
Thanks for the quick response. I ran that command and installed rub-dev, that part was successful. Unfortunately, I still receive the exact same error after this when I run ‘sudo gem install sequenceserver’.
As an update, I attempted to setup the dev setup from github. I get a very similar error during that process at the command below.
`
sudo gem install bundler && bundle
Fetching: bundler-1.8.5.gem (100%)
Successfully installed bundler-1.8.5
1 gem installed
Installing ri documentation for bundler-1.8.5…
Installing RDoc documentation for bundler-1.8.5…
Fetching gem metadata from http://rubygems.org/…
Fetching version metadata from http://rubygems.org/…
Resolving dependencies…
Installing rake 10.4.2
Installing ast 2.0.0
Installing parser 2.2.0.3
Installing astrolabe 1.3.0
Installing mime-types 2.4.3
Installing mini_portile 0.6.2
Gem::Installer::ExtensionBuildError: ERROR: Failed to build gem native extension.
/usr/bin/ruby1.9.1 extconf.rb
/usr/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in require': cannot load such file -- mkmf (LoadError) from /usr/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in require’
from extconf.rb:4:in `’
Gem files will remain installed in /tmp/bundler20150312-8024-1fnlboo/nokogiri-1.6.6.2/gems/nokogiri-1.6.6.2 for inspection.
Results logged to /tmp/bundler20150312-8024-1fnlboo/nokogiri-1.6.6.2/gems/nokogiri-1.6.6.2/ext/nokogiri/gem_make.out
An error occurred while installing nokogiri (1.6.6.2), and Bundler cannot continue.
Make sure that gem install nokogiri -v '1.6.6.2' succeeds before bundling.
`
I have not really ever used ruby or gem. So they might not be setup properly? Although they are definitely installed and up to date…
It’s due to some missing dependencies on your system.
Can you post me the output of “apt-cache show ruby-dev” It’s possible that ruby-dev on your version of Ubuntu points to a later Ruby. And it’s also possible that ‘make’ is missing. So I would ask you to try:
sudo apt-get install ruby1.8-dev build-essentials
And then try installing SequenceServer again.
– Priyam
Output of apt-get show rub-dev
`
apt-cache show ruby-dev
Package: ruby-dev
Priority: optional
Section: devel
Installed-Size: 32
Maintainer: Ubuntu Developers ubuntu-devel-discuss@lists.ubuntu.com
Original-Maintainer: akira yamada akira@debian.org
Architecture: all
Source: ruby-defaults
Version: 4.8
Depends: ruby1.8-dev (>> 1.8.7.334-1)
Filename: pool/main/r/ruby-defaults/ruby-dev_4.8_all.deb
Size: 4572
MD5sum: 8ca9e04c6eb0177155bc9a8e5b507513
SHA1: 293181748d30cd76dac6204845b3e081a42eedea
SHA256: f94762d2cdac81d9bb1a0013cb62fc2f0da34b6a220f52dabecd5e8d61f3145e
Description-en: Transitional package for ruby1.8-dev
This is a transitional package which ensures that users of ruby-dev will use
ruby1.8-dev in the future. It can safely be removed.
Homepage: http://www.ruby-lang.org/
Description-md5: 3cef48fc8299c9a557429a0bfc978a4a
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu
Supported: 18m
`
Ah yes, I did read about build-essential elsewhere too. I tried that command and then sequenceserver and still same issue…
Thanks again for these quick responses and suggestions!
So I ran
`
sudo apt-get install ruby1.9.1-dev
`
and it has installed successfully! Thank you for your help!
I am now working to upgrade my blast from 2.2.25.
Hi Anurag,
I’m running into the same problem installing on a fresh ubuntu install. Tried Phil’s solutions (191-dev etc.) but i am still getting the error. Any suggestions? Thanks
gem -v 1.8.23
ruby -v ruby 1.9.3p484
ERROR: Error installing sequenceserver:
ERROR: Failed to build gem native extension.
/usr/bin/ruby1.9.1 extconf.rb
Creating Makefile for ruby version 1.9.3 on x86_64-linux <<<<<
creating Makefile
extconf.rb:66:in ``’: No such file or directory - make clean (Errno::ENOENT)
from extconf.rb:66:in `’
Resolved. gcc not properly installed.