[Debian-med-packaging] Bug#907489: Bug#938431: Fixing sambamba 0.8.6

[Michael Crusoe]

On Sun, Dec 15, 2019 at 3:18 AM Matthias Klumpp <matthias at tenstral.net>
wrote:

> Am Do., 28. Nov. 2019 um 16:37 Uhr schrieb Pjotr Prins <
> pjotr2018 at thebird.nl>:
> >
> > When 1.18 arrives I think it is a good time to get sambamba and biod
> > in Debian again.
>
> They always were in Debian, just not in a release because the packages
> were broken ^^
> The LDC transition went really well this time, I don't think it has
> ever been this smooth! No regressions this time, hurray!
>

Huzzah, indeed!


> There are also two brand new remaining issues: Apparently, for some
> reason, SONAME isn't set correctly for BioD, producing a Lintian error
> - not sure what happens there, and which component is to blame for
> that (Meson or LDC, most likely). Also, Sambamba doesn't *actually*
> build yet:
> ```
> roup -L=-rpath
> -L=/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu
> slicereader.d:71: error: undefined reference to 'cram_to_bam'
> collect2: error: ld returned 1 exit status
> ```
> The cram_to_bam is private in htslib, so it shouldn't be used by other
> applications. Not sure whether htslib or Sambamba needs to be changed
> here, I simply worked around this issue for testing, and when this is
> resolved, Sambamba builds & works.
>

You'll be wanting libhts-private-dev, but libhts is broken in unstable
right now; sorry!


-- 
Michael R. Crusoe
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