[Debian-med-packaging] Bug#948925: pbseqlib ftbfs with libpbbam1.0.6

[Andreas Tille]

Hi Paul,

thanks for your bug report.

On Tue, Jan 14, 2020 at 09:45:59PM +0100, Paul Gevers wrote:
> Source: pbseqlib
> Version: 5.3.1+dfsg-2.1
> Severity: serious
> Justification: ftbfs
> Tags: ftbfs sid bullseye
> 
> Dear maintainer,
> 
> pbbam started a transition and I scheduled binNMUs for pbseqlib.
> However, they failed. Please investigate.
> 
> Paul
> 
> https://buildd.debian.org/status/package.php?p=pbseqlib
> 
> Tail of log for pbseqlib on amd64:
> 
> /usr/include/pbbam/BamRecord.h:19:10: fatal error:
> pbcopper/data/MappedRead.h: No such file or directory
>    19 | #include <pbcopper/data/MappedRead.h>
>       |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
> compilation terminated.

I admit there are lots of problems currently with PacBio software
(packages mostly start with pb*).  We tried hard to get the latest
versions libpbcopper and libpbbam to build but upstream has quite a weak
release management and besides this has on some projects disabled the
issue tracker effectively preventing us from issues like this.  The
only way to do the transition is removing blockers like this from
testing for the moment.

In addition to the complex situation the former Uploader Afif had to
reduce his involvement and so I try to take this stack on my shoulders
as well.  We need to see how this might work out until next freeze but
may be we need to drop some of the packages from Debian.  Since its not
clear for the moment whether we can fix these issues after a new
upstream release easily I do not think that the time for removal has
come right now - so simply lets drop it from testing for the moment.

Kind regards and thanks for your QA work

       Andreas.

-- 
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