[Debian-med-packaging] Sambamba release

[Matthias Klumpp]

Am Do., 4. Okt. 2018 um 11:19 Uhr schrieb Andreas Tille <andreas at fam-tille.de>:
>
> On Thu, Oct 04, 2018 at 11:14:15AM +0200, Matthias Klumpp wrote:
> > I moved to a new place last week, and I am still without internet
> > connection at my new home, hence the really slow replies, sorry for
> > that.
>
> Pretty quick for a "slow response" - thanks a lot.  I'll wait for some
> comments from Pjotr.

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.

However, when trying to build sambamba now, I get a linking error:

```
[3/28] Linking target sambamba.
FAILED: sambamba
ldc2  -of=sambamba 'sambamba at exe/sambamba_main.d.o'
'sambamba at exe/sambamba_depth.d.o' 'sambamba at exe/sambamba_fixbins.d.o'
'sambamba at exe/sambamba_flagstat.d.o' 'sambamba at exe/sambamba_index.d.o'
'sambamba at exe/sambamba_markdup.d.o'
'sambamba at exe/sambamba_markdup2.d.o' 'sambamba at exe/sambamba_merge.d.o'
'sambamba at exe/sambamba_pileup.d.o' 'sambamba at exe/sambamba_slice.d.o'
'sambamba at exe/sambamba_sort.d.o' 'sambamba at exe/sambamba_subsample.d.o'
'sambamba at exe/sambamba_validate.d.o'
'sambamba at exe/sambamba_utils_common_bed.d.o'
'sambamba at exe/sambamba_utils_common_file.d.o'
'sambamba at exe/sambamba_utils_common_filtering.d.o'
'sambamba at exe/sambamba_utils_common_intervaltree.d.o'
'sambamba at exe/sambamba_utils_common_ldc_gc_workaround.d.o'
'sambamba at exe/sambamba_utils_common_overwrite.d.o'
'sambamba at exe/sambamba_utils_common_pratt_parser.d.o'
'sambamba at exe/sambamba_utils_common_progressbar.d.o'
'sambamba at exe/sambamba_utils_common_queryparser.d.o'
'sambamba at exe/sambamba_utils_common_readstorage.d.o'
'sambamba at exe/sambamba_utils_common_tmpdir.d.o'
'sambamba at exe/sambamba_utils_view_alignmentrangeprocessor.d.o'
'sambamba at exe/sambamba_utils_view_headerserializer.d.o'
'sambamba at exe/sambamba_view.d.o' 'sambamba at exe/utils_lz4.d.o'
'sambamba at exe/utils_strip_bcf_header.d.o'
'sambamba at exe/utils_version_.d.o' 'sambamba at exe/cram_exception.d.o'
'sambamba at exe/cram_htslib.d.o' 'sambamba at exe/cram_reader.d.o'
'sambamba at exe/cram_reference.d.o' 'sambamba at exe/cram_slicereader.d.o'
'sambamba at exe/cram_wrappers.d.o' 'sambamba at exe/cram_writer.d.o'
'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
```

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 :-)

Cheers,
    Matthias

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