Bug#859111: [Debian-med-packaging] Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted

[Sascha Steinbiss]

forwarded 859111 https://github.com/sanger-pathogens/ariba/issues/170
tags 859111 upstream
thanks

Hi all,

> On Thu, Mar 30, 2017 at 06:20:16PM +0300, Adrian Bunk wrote:
>> Control: retitle -1 ariba FTBFS with bowtie2 2.3.1-1
> [...]
>> This is actually not related to the ariba version but to the bowtie2 version,
>> ariba 2.6.1+ds-1 in stretch builds with the stretch bowtie2 2.3.0-2 but 
>> FTBFS with the sid bowtie2 2.3.1-1
> 
> Do we already know whether the newer upstream version fixes this?

No, it doesn't. I just tested it. Given that the test failure seems to
be caused by differences between result and reference, and bowtie2 2.3.1
introduced different default values for one of the parameters [1], it
might be likely that it's connected to that. I have contacted upstream
[2] -- they are usually quite responsive.

Cheers
Sascha

[1] http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
[2] https://github.com/sanger-pathogens/ariba/issues/170

Bug#859111: [Debian-med-packaging] Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted

[Sascha Steinbiss]

Hi all,

>> Control: retitle -1 ariba FTBFS with bowtie2 2.3.1-1
> [...]
>> This is actually not related to the ariba version but to the bowtie2 version,
>> ariba 2.6.1+ds-1 in stretch builds with the stretch bowtie2 2.3.0-2 but 
>> FTBFS with the sid bowtie2 2.3.1-1
> 
> Do we already know whether the newer upstream version fixes this?
> 
> Sascha: could you try to import it and pehaps upload it to unstable?
> Given there is already a difference between testing and unstable (2.6.1
> vs 2.7.1) it shouldn't make much difference at this point even in the
> freeze…

Sure, I can do this later today when I find some time. I'm a bit busy
atm with unrelated work but will get back to it.

Cheers
Sascha



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