[BioRuby] Bio::Blat::Report

[Naohisa GOTO]

Hi,

Thanks for reporting bugs.

On Wed, 3 Sep 2008 11:45:05 +0200
Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it> wrote:

> Hi, after installing the last version from git (http://github.com/ 
> bioruby/bioruby), I have a couple of warnings using my application:
>
> NOTE: the file test.psl I am using for testing is without psl headers
> 
> Oni:~/code/Ruby/bioruby tucano$ ./blatanalyzer list blatanalyzerdir/ 
> test/test.psl
> /usr/local/lib/ruby/site_ruby/1.8/bio/io/flatfile/splitter.rb:81:  
> warning: private attribute?
(snip)
> /usr/local/lib/ruby/site_ruby/1.8/bio/appl/blat/report.rb:89:  
> warning: instance variable @header_lines not initialized

The warning message "warning: instance variable @header_lines
not initialized" was a bug during header parsing.

The messages "warning: private attribute?" are harmless now,
but I've changed not to be shown by explicitly specifying
private attributes using "private".

I've just fixed them in git repository.
http://github.com/bioruby/bioruby/commit/3ff940988b76bdff75679cdf0af4c836f76fa3a1
http://github.com/bioruby/bioruby/commit/1440b766202a2b66ac7386b9b46928834a9c9873

Could you please try again with new version?

FYI: When reporting, please show which Ruby version, OS, and
architecture (type of CPU) you are using, with BioRuby version.
In addition, please show a short script and test data to reproduce
the bug, or please show all your scripts and data (If very large,
put them to your homepage or blog). Note that in this case, I can
find problem without these information, and you don't need to do so
unless the bugs are not fixed well.

> The previuos version I was using don't give warnings
> 
> here the diff of changes in the new git version and in the previous  
> report.rb:
> 
> diff oldreport.rb /usr/local/lib/ruby/site_ruby/1.8/bio/appl/blat/ 
> report.rb

Please don't show diffs between already committed versions,
except when you can clearly point out what is wrong.

Normally, to see diffs with commit messages, doing
  % git log -p lib/bio/appl/blat/report.rb
is enough.

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org