I have the same problem:

ubuntu 11.10 64 bit llvm3.0 dragonEgg3.0 llvm-gcc-4.6

http://stackoverflow.com/questions/9447318/im-getting-llvm-gcc-
potential-incompatible-plug-in-version

Then when I try

buse@buseZenbook:~$ llvm-gcc -flto hello.c -c -o hello.bc
Potential incompatible plugin version. GCC: 4.6. Expected: 4.6.1
Defines 'dragonegg_disable_version_check' as env variable to remove this warning
Please note that unexpected errors might occur.
/tmp/ccUI7YSa.s: Assembler messages:
/tmp/ccUI7YSa.s:1: Error: junk at end of line, first unrecognized character is 
`e'
/tmp/ccUI7YSa.s:2: Error: no such instruction: `target 
triple="x86_64--linux-gnu"'
/tmp/ccUI7YSa.s:4: Error: no such instruction: `module asm "\09.ident\09\22GCC: 
(Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 LLVM: exported\22"'
/tmp/ccUI7YSa.s:6: Error: junk at end of line, first unrecognized character is 
`@'
/tmp/ccUI7YSa.s:8: Error: no such instruction: `define i32@main(...)nounwind 
uwtable ssp{'
/tmp/ccUI7YSa.s:10: Error: junk at end of line, first unrecognized character is 
`%'
/tmp/ccUI7YSa.s:11: Error: junk at end of line, first unrecognized character is 
`%'
/tmp/ccUI7YSa.s:12: Error: junk at end of line, first unrecognized character is 
`%'
/tmp/ccUI7YSa.s:13: Error: no such instruction: `br label %"2"'
/tmp/ccUI7YSa.s:15: Error: junk at end of line, first unrecognized character is 
`"'
/tmp/ccUI7YSa.s:15: Error: bad expression
/tmp/ccUI7YSa.s:15: Error: junk at end of line, first unrecognized character is 
`e'
/tmp/ccUI7YSa.s:16: Error: junk at end of line, first unrecognized character is 
`%'
/tmp/ccUI7YSa.s:17: Error: no such instruction: `store i32 0,i32* %memtmp,align 
1'
/tmp/ccUI7YSa.s:18: Error: no such instruction: `br label %return'
/tmp/ccUI7YSa.s:20: Error: bad expression
/tmp/ccUI7YSa.s:20: Error: junk at end of line, first unrecognized character is 
`"'
/tmp/ccUI7YSa.s:21: Error: junk at end of line, first unrecognized character is 
`%'
/tmp/ccUI7YSa.s:22: Error: operand size mismatch for `ret'
/tmp/ccUI7YSa.s:23: Error: junk at end of line, first unrecognized character is 
`}'
/tmp/ccUI7YSa.s:25: Error: no such instruction: `declare i32@puts(i8*)'

Hence -flto didn't work in my case.

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https://bugs.launchpad.net/bugs/712199

Title:
  -emit-llvm makes invalid bytecode

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