Error installing

[Phil Rees]

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 `<main>'

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

[Anurag Priyam]

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

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[Phil Rees]

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'.

[Phil Rees]

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 `<main>'

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..

[Anurag Priyam]

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

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[Phil Rees]

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-dev...@lists.ubuntu.com>

Original-Maintainer: akira yamada <ak...@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! 

[Phil Rees]

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.

On Thursday, March 12, 2015 at 2:20:24 PM UTC-4, Phil Rees wrote:

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>

[Anurag Priyam]

Cool.

-- Priyam

To view this discussion on the web visit https://groups.google.com/d/msgid/sequenceserver/217e5085-e04e-4989-99c9-cfda10608426%40googlegroups.com.

[Jeffrey Kim]

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 `<main>'

On Friday, March 13, 2015 at 3:48:55 AM UTC-7, Anurag Priyam wrote:

Cool.

-- Priyam

On Fri, Mar 13, 2015 at 12:20 AM Phil Rees <phil...@gmail.com> wrote:

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.

On Thursday, March 12, 2015 at 2:20:24 PM UTC-4, Phil Rees wrote:

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-dev...@lists.ubuntu.com>

[Jeffrey Kim]

Resolved. gcc not properly installed.