[BioRuby] samtools-ruby

[Michal]

Hi,
I have tried the svn version and I have got the following error:

~/Downloads/svn/ $ svn co 
https://samtools.svn.sourceforge.net/svnroot/samtools samtools
Checked out revision 910.
~/Downloads/svn/samtools/trunk/samtools$ make dylib
~/Downloads/svn/samtools/trunk/samtools$ cp libbam.so.1 
~/Downloads/git/bioruby-samtools/lib/bio/db/sam/external/
~/Downloads/svn/samtools/trunk/samtools$ cd ~/Downloads/git/bioruby-samtools
~/Downloads/git/bioruby-samtools$ 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"
Loaded suite /home/mictadlo/apps/ruby/lib/ruby/1.9.1/rake/rake_test_loader
Started
F
Finished in 0.000371 seconds.

   1) Failure:
test: BioSamtools should probably rename this file and start testing for 
real. (TestBioSamtools) [test/test_bio-samtools.rb:5]:
hey buddy, you should probably rename this file and start testing for real

1 tests, 1 assertions, 1 failures, 0 errors, 0 skips

Test run options: --seed 16981
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>'
~/Downloads/git/bioruby-samtools$

I understand how difficult it is to keep track and it is a good idea to 
ship bioruby-samtools with a working samtools version like Raoul does it.

What I have forgotten to do?

Thank you in advance.

Michal

On 02/04/2011 06:31 PM, Tomoaki NISHIYAMA wrote:
> Hi,
>
>> ~/Downloads/samtools-0.1.12a
>
> The *latest* samtools which I used was r910 via svn yesterday.
> r854 produced the same error as you have shown.
>
> Samtools is under very active development, as seen from the mailing 
> list flow.
> So, some change in the samtools code made this difference,
> and its a bit difficult to keep track with all the update.
>
> --
>
> Tomoaki NISHIYAMA
>
>
> Advanced Science Research Center,
>
> Kanazawa University,
>
> 13-1 Takara-machi,
>
> Kanazawa, 920-0934, Japan
>
>
>