[BioRuby] samtools-ruby
Michal
mictadlo at gmail.com
Thu Feb 3 11:23:40 UTC 2011
Hi Philipp,
Bundle solved this problem, but after rake install I can not call rake test.
$ bundle install
Fetching source index for http://rubygems.org/
Using rake (0.8.7)
Installing bio (1.4.1)
Using bundler (1.0.10)
Using ffi (1.0.5)
Installing git (1.2.5)
Installing jeweler (1.5.2)
Installing rcov (0.9.9) with native extensions
Installing shoulda (2.11.3)
Your bundle is complete! Use `bundle show [gemname]` to see where a
bundled gem is installed.
$ rake install
(in /home/mictadlo/Downloads/git/bioruby-samtools)
WARNING: no rubyforge_project specified
Successfully built RubyGem
Name: bio-samtools
Version: 0.0.0
File: bio-samtools-0.0.0.gem
Executing "ruby -S gem install ./pkg/bio-samtools-0.0.0.gem":
ruby -S gem install ./pkg/bio-samtools-0.0.0.gem
Successfully installed bio-samtools-0.0.0
1 gem installed
Installing ri documentation for bio-samtools-0.0.0...
Installing RDoc documentation for bio-samtools-0.0.0...
$ rake test
(in /home/mictadlo/Downloads/git/bioruby-samtools)
/home/mictadlo/apps/ruby/bin/ruby -I"lib:lib:test"
"/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb"
"test/test_bio-samtools.rb"
/home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:75:in
`block in ffi_lib': Could not open library
'/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.a':
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/libbam.a:
invalid ELF header (LoadError)
from
/home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in
`map'
from
/home/mictadlo/apps/ruby/lib/ruby/gems/1.9.1/gems/ffi-1.0.5/lib/ffi/library.rb:54:in
`ffi_lib'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:12:in `<module:Tools>'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:8:in
`<module:SAM>'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:7:in
`<module:DB>'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:6:in
`<module:Bio>'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam/bam.rb:5:in
`<top (required)>'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in
`require'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio/db/sam.rb:2:in
`<top (required)>'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in
`require'
from
/home/mictadlo/Downloads/git/bioruby-samtools/lib/bio-samtools.rb:2:in
`<top (required)>'
from
/home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `require'
from
/home/mictadlo/Downloads/git/bioruby-samtools/test/helper.rb:15:in `<top
(required)>'
from test/test_bio-samtools.rb:1:in `require'
from test/test_bio-samtools.rb:1:in `<top (required)>'
from
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `load'
from
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in
`block in <main>'
from
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in `each'
from
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader.rb:5:in
`<main>'
rake aborted!
Command failed with status (1): [/home/mictadlo/apps/ruby/bin/ruby
-I"lib:l...]
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:993:in `block in sh'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `call'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1008:in `sh'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `sh'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1027:in `ruby'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1092:in `ruby'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:115:in `block
(2 levels) in define'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1110:in `verbose'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/testtask.rb:100:in `block
in define'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `call'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:634:in `block in execute'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `each'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:629:in `execute'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:595:in `block in
invoke_with_call_chain'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/monitor.rb:201:in `mon_synchronize'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:588:in
`invoke_with_call_chain'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:581:in `invoke'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2041:in `invoke_task'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block (2
levels) in top_level'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `each'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2019:in `block in top_level'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in
`standard_exception_handling'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2013:in `top_level'
/home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1992:in `run'
/home/mictadlo/apps/ruby/bin/rake:31:in `<main>'
What did I wrong?
Michal
On 02/03/2011 08:06 PM, Philipp Comans wrote:
> Hi Michal,
> have you tried running
>
> bundle install
> rake install
>
> In order to install the missing gems?
> I see that you have bio installed but maybe it's missing something else.
>
> The error about "marshal data too short" went through the mailing list a few days ago, I think it is currently being worked on.
>
> Hope that helps!
>
> Best,
>
> Philipp
>
> Am 03.02.2011 um 10:55 schrieb Michal:
>
>> Hi Philipp,
>> Bundler fix one problem, but I have got a new one:
>>
>> $ gem install bundler
>> Successfully installed bundler-1.0.10
>> 1 gem installed
>> Installing ri documentation for bundler-1.0.10...
>> Installing RDoc documentation for bundler-1.0.10...
>>
>> ~/Downloads/git/bioruby-samtools$ rake test
>> (in /home/uqmlore1/Downloads/git/bioruby-samtools)
>> Could not find bio-1.4.1 in any of the sources
>> Run `bundle install` to install missing gems
>>
>> $ irb
>> irb(main):001:0> require "bio"
>> => true
>> irb(main):002:0> exit
>>
>> $ bioruby
>> Loading config (/home/uqmlore1/.bioruby/shell/session/config) ... done
>> Loading object (/home/uqmlore1/.bioruby/shell/session/object) ... Error: Failed to load (/home/uqmlore1/.bioruby/shell/session/object) : marshal data too short
>> done
>>
>> . . . B i o R u b y i n t h e s h e l l . . .
>>
>> Version : BioRuby 1.4.1 / Ruby 1.9.2
>>
>>
>> Thank you in advance.
>>
>> Michal
>>
>>
>> On 02/03/2011 07:03 PM, Philipp Comans wrote:
>>> Try gem install bundler
>>>
>>> Am 03.02.2011 um 09:16 schrieb Michal<mictadlo at gmail.com>:
>>>
>>>> Dear Raoul,
>>>> I have tried out bioruby-samtools unsuccessful on Ubuntu 10.10 64bit in the following way:
>>>> $ tar xvfz ruby-1.9.2-p136.tar.gz
>>>> $ cd ruby-1.9.2-p136/
>>>> $ ./configure --prefix=/home/mictadlo/apps/ruby
>>>> $ make
>>>> $ make install
>>>> $ vim ~/.bashrc
>>>> export APPS=/home/mictadlo/apps
>>>> export RUBY_HOME=$APPS/ruby
>>>> export LD_LIBRARY_PATH=/RUBY_HOME/lib
>>>> PATH=$RUBY_HOME/bin:$PATH
>>>> $ . ~/.bashrc
>>>> $ ruby -v
>>>> ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux]
>>>>
>>>> $ gem install ffi
>>>> Building native extensions. This could take a while...
>>>> Successfully installed ffi-1.0.5
>>>> 1 gem installed
>>>> Installing ri documentation for ffi-1.0.5...
>>>> Installing RDoc documentation for ffi-1.0.5...
>>>>
>>>> ~/Downloads/git$ git clone https://github.com/helios/bioruby-samtools.git
>>>> Initialized empty Git repository in /home/mictadlo/Downloads/git/bioruby-samtools/.git/
>>>> remote: Counting objects: 92, done.
>>>> remote: Compressing objects: 100% (84/84), done.
>>>> remote: Total 92 (delta 21), reused 0 (delta 0)
>>>> Unpacking objects: 100% (92/92), done.
>>>>
>>>> ~/Downloads/git/bioruby-samtools$ rake test
>>>> (in /home/mictadlo/Downloads/git/bioruby-samtools)
>>>> rake aborted!
>>>> no such file to load -- bundler
>>>> <internal:lib/rubygems/custom_require>:29:in `require'
>>>> <internal:lib/rubygems/custom_require>:29:in `require'
>>>> /home/mictadlo/Downloads/git/bioruby-samtools/Rakefile:2:in `<top (required)>'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `load'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2373:in `raw_load_rakefile'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2007:in `block in load_rakefile'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2058:in `standard_exception_handling'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:2006:in `load_rakefile'
>>>> /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake.rb:1991:in `run'
>>>> /home/mictadlo/apps/ruby/bin/rake:31:in `<main>'
>>>>
>>>> What did I wrong?
>>>>
>>>> Thank you in advance.
>>>>
>>>> Michal
>>>>
>>>> On 01/31/2011 08:11 PM, Raoul Bonnal wrote:
>>>>> Dear Michal,
>>>>> please check this out:
>>>>>
>>>>> https://github.com/helios/bioruby-samtools
>>>>>
>>>>> This is the inital port of samtools-ruby as plugin. It comes with library for osx and linux, no windows.
>>>>> I need to test the linux library because I'm developing under osx.
>>>>> If the libbam.a is wrong please give me the right one and I'll add it to the repo.
>>>>> Also note that the library has been compiled for 64bit.
>>>>>
>>>>> Ciao!
>>>>>
>>>>> On 30/gen/2011, at 12.42, Michal wrote:
>>>>>
>>>>>> Hi,
>>>>>> I have tried to install samtools-ruby on ruby 1.9.2, but I have failed. I have already posted this problem on https://github.com/homonecloco/samtools-ruby/issues#issue/3 , but I have not got any response.
>>>>>>
>>>>>> What did I wrong?
>>>>>>
>>>>>> Michal
>>>>>> _______________________________________________
>>>>>> BioRuby Project - http://www.bioruby.org/
>>>>>> BioRuby mailing list
>>>>>> BioRuby at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>>>> --
>>>>> R.J.P.B.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> BioRuby Project - http://www.bioruby.org/
>>>> BioRuby mailing list
>>>> BioRuby at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>
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