[BioRuby] marshal data too short

[Toshiaki Katayama]

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
> 
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