[BioRuby] marshal data too short

[Toshiaki Katayama]

Hi Michal,

When I remove the ~/.bioruby directory, I could reproduce the same error with Ruby 1.9.2.

The ~/.bioruby/shell/session/object file was empty because BioRuby shell failed to save the file.

Saving object (/Users/ktym/.bioruby/shell/session/object) ... Error: Failed to save (/Users/ktym/.bioruby/shell/session/object) : can't convert Symbol into String

I'll try to fix this.

Toshiaki



On 2011/01/28, at 21:18, Michal wrote:

> Hi Toshiaki,
> On my system was not Ruby installed before and I just installed the latest version in my home directory:
> $ ls -l ~/.bioruby/shell/session/object
> -rw-r--r-- 1 mictadlo mictadlo 0 2011-01-25 19:40 /home/mictadlo/.bioruby/shell/session/object
> $ ruby -e 'p ARGF.read.unpack("cc")' ~/.bioruby/shell/session/object
> [nil, nil]
> $ ruby -rubygems -rbio -e 'p Marshal.load(ARGF.read)' ~/.bioruby/shell/session/object
> -e:1:in `load': marshal data too short (ArgumentError)
>    from -e:1:in `<main>'
> 
> Do you need another information?
> 
> Thank you in advance.
> 
> Michal
> 
> 
> On 01/27/2011 02:09 AM, Toshiaki Katayama wrote:
>> Hi Michal,
>> 
>> Could you give me some additional information?
>> 
>> % ls -l ~/.bioruby/shell/session/object
>> -rw-r--r--  1 ktym  staff  17401  1 19 13:09 /Users/ktym/.bioruby/shell/session/object
>> 
>> % ruby -e 'p ARGF.read.unpack("cc")' ~/.bioruby/shell/session/object
>> [4, 8]
>> 
>> Have you ever used the bioruby shell with the old version of Ruby before?
>> 
>> If your file is not corrupted, this might be due to the backward
>> incompatibility of the Marshal file format (if so, does anyone know
>> whether there are any workaround to convert old marshal data into 1.9's?).
>> 
>> Note that, in my environment, both Ruby 1.8.7 and 1.9.2 can successfully
>> restore the saved objects:
>> 
>> % ruby -rubygems -rbio -e 'p Marshal.load(ARGF.read)' ~/.bioruby/shell/session/object
>> 
>> Toshiaki
>> 
>> 
>> On 2011/01/26, at 9:41, Michal wrote:
>> 
>>> Hi,
>>> I installed on Ubuntu 10.10 (Linux Mint) Ruby 1.9.2 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]
>>> 
>>> $ tar xvfz bioruby-1.4.1.tar.gz
>>> $ cd bioruby-1.4.1/
>>> $ ruby setup.rb
>>> $ bioruby
>>>    Loading config (/home/mitlox/.bioruby/shell/session/config) ... done
>>>    Loading object (/home/mitlox/.bioruby/shell/session/object) ... Error: Failed to load (/home/mitlox/.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
>>> 
>>>    bioruby>  exit
>>> 
>>> How can I fix the error in BioRuby?
>>> 
>>> Thank you in advance.
>>> 
>>> Michal
>>> 
>>> _______________________________________________
>>> BioRuby Project - http://www.bioruby.org/
>>> BioRuby mailing list
>>> BioRuby at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>> 
>