[Debian-med-packaging] Sambamba release

Andreas Tille andreas at fam-tille.de
Tue Oct 9 07:27:07 BST 2018


Hi Matthias,

On Thu, Oct 04, 2018 at 02:54:47PM +0200, Matthias Klumpp wrote:
> Well, your initial request for help with the Sambamba issue was way older ^^
> 
> > Thanks again for all your help
> 
> I've had a small amount of spare time at work just now and decided to
> quickly look into the issue.
> This patchset against BioD will resolve the problem you currently
> have: https://github.com/biod/BioD/pull/38 - so Sambamba will find all
> the things it depends on again.

I've uploaded libbiod including these patches.
 
> However, when trying to build sambamba now, I get a linking error:
> 
> ```
> 'sambamba at exe/thirdparty_mergesort.d.o'
> 'sambamba at exe/thirdparty_unstablesort.d.o'
> 'sambamba at exe/ldc_version_info_.d.o' -L=-lundead
> -L=-L/usr/local/lib/x86_64-linux-gnu -L=-lbiod -L=-llz4 -L=-lhts
> /usr/bin/ld: /usr/local/lib/x86_64-linux-gnu/libbiod.so: undefined
> reference to `_D6object__T8__equalsTxPS3std11parallelism__T4TaskS_D4bio211bgzf_writer16bgzfCompressFuncFAhiQdDFQhQjZvZSQDc8typecons__T5TupleTQBlTQBpTDFQBvQByZvZQBaTQCiTiTQCoTQzZQEoTxQFpZQGeFNaNbNiNfAxQGhQfZb'
> /usr/bin/ld: /usr/local/lib/x86_64-linux-gnu/libbiod.so: undefined
> reference to `_D3std11parallelism__T4TaskS_D4bio211bgzf_writer16bgzfCompressFuncFAhiQdDFQhQjZvZS3std8typecons__T5TupleTQBmTQBqTDFQBwQBzZvZQBaTQCjTiTQCpTQzZQEp6__initZ'
> /usr/bin/ld: /usr/local/lib/x86_64-linux-gnu/libbiod.so: undefined
> reference to `_D3std11parallelism__T4TaskS_D4bio211bgzf_writer16bgzfCompressFuncFAhiQdDFQhQjZvZSQDc8typecons__T5TupleTQBlTQBpTDFQBvQByZvZQBaTQCiTiTQCoTQzZQEo10yieldForceMFNcNdNjNeZQDh'
> /usr/bin/ld: /usr/local/lib/x86_64-linux-gnu/libbiod.so: undefined
> reference to `_D3bio4core5utils8roundbuf__T8RoundBufTPS3std11parallelism__T4TaskS_D4bio211bgzf_writer16bgzfCompressFuncFAhiQdDFQhQjZvZSQDc8typecons__T5TupleTQBlTQBpTDFQBvQByZvZQBaTQCiTiTQCoTQzZQEoZQFy6__initZ'
> collect2: error: ld returned 1 exit status
> Error: /usr/bin/gcc failed with status: 1
> ```

I can reproduce this issue here.

 
> This looks *very* similar to an issue that appears when ldc is passed
> the export-dynamic flag (see
> https://github.com/ldc-developers/ldc/issues/2846 ), but that is not
> the case here.
> So, I am not yet sure what exactly the culprit is in this case (needs
> more time to investigate).
> In any case, this might help you to move a bit further :-)

Thanks again, waiting for further information. ;-)

Kind regards

        Andreas.

-- 
http://fam-tille.de



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