[Debian-med-packaging] Bug#753485: Bug#753485: Status of samtools

[Charles Plessy]

Le Tue, Sep 16, 2014 at 08:14:43AM +0200, Andreas Tille a écrit :
> On Tue, Sep 16, 2014 at 08:16:19AM +0900, Charles Plessy wrote:
>  
> > What I can do is rename the old samtools source package "libbam", make it build
> > libbam-dev only, and upload it to NEW.  What do you think about this ?
> 
> This sounds like the most straightforward way to get libbam-dev back.
> We need it seriously since a chain of dependency is based on it.  We
> also should ping ftpmaster for fast-processing since I see several
> packages in danger not to make it into Jessie.

Hi Andreas,

thanks for pinging the FTP team.

I have not uploaded yet samtools 1.0 to Unstable, because it strangely fails to
build in a chroot, where two regression tests do not pass.

When comparing the logs of the building with git-buildpackage (local, works)
and sbuild (chroot, fails), the only significant difference that I see is for
the failure itself:

	 test_usage_subcommand:
		samtools stats
	-.. ok
	+
	+       did not have Usage:
	+.. failed ...
	+
	+
	+       usage did not mention samtools stats
	+.. failed ...

I am very puzzled and for the moment I could not find any hint on why only
these tests fail, that is: I am blocked.

By the way, I just saw on BioStars that we will need to patch at least TopHat
does not work with samtools 1.0…

    https://www.biostars.org/p/112749/

Cheers,

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan