I'm also having the same problem with the version in Jaunty.

$ apt-cache policy pbzip2
pbzip2:
  Installed: 1.0.3-1
  Candidate: 1.0.3-1
  Version table:
 *** 1.0.3-1 0
        500 http://mirror.lcsee.wvu.edu jaunty/universe Packages
        100 /var/lib/dpkg/status

However when my office was running Hardy, pbzip2 vesrion 1.0.2-0, we had
no issues with large files.

I've grabbed and compiled the 1.0.2-0 version on jaunty with debugging
enabled. On a large 14 GB file the 1.0.2-0 version operates correctly.

The reason that pbzip2 isn't working is related to the off_t variable.
In hardy it's correctly getting set to 8 while in hardy it's 4 after
it's compiled.

Testing a 14GB file against pbzip-1.0.2-0 on Jaunty with PBZIP_DEBUG
enabled:

$ pbzip2 -v -t large_file.tar.bz2 
argv[1]: -v   Len: 2
argv[2]: -t   Len: 2
Parallel BZIP2 v1.0.2 - by: Jeff Gilchrist [http://compression.ca]
[July 25, 2007]             (uses libbzip2 by Julian Seward)
off_t size: 8    uint size: 4
-------------------------------------------
      File #: 1 of 1
     Testing: large_file.tar.bz2 
^C
 *Control-C or similar caught, quitting...
 Infile: (null)   Outfile: (null)


Testing a 14GB file against pbzip2-1.0.3-1 on Jaunty with PBZIP_DEBUG enabled:


$ pbzip2 -v -t large_file.tar.bz2
argv[1]: -v   Len: 2
argv[2]: -t   Len: 2
Parallel BZIP2 v1.0.3 - by: Jeff Gilchrist [http://compression.ca]
[Oct. 31, 2008]             (uses libbzip2 by Julian Seward)
off_t size: 4    uint size: 4

 *WARNING: off_t variable size only 32 bits!
 You will only able to compress files smaller than 2GB in size.

-------------------------------------------
      File #: 1 of 1
     Testing: large_file.tar.bz2
 *ERROR: Could not open input file [large_file.tar.bz2]!  Skipping...
-------------------------------------------

 Start Time: 1255969853 + 12994
 Stop Time : 1255969853 + 13730

     Wall Clock: 0.000736 seconds

-- 
pbzip2 does not see big files
https://bugs.launchpad.net/bugs/363793
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