[BioRuby] marshal data too short

[Michal]

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
>