Bug squashing in December (Was: December)

2017-12-06 Thread Andreas Tille
Hi Debian Med fans, may be the subject of the original mail was not catchy enough and people did not realised that we are doing a 24 day internet wide bug squashing party. Believers in different tradition than advent are welcome to join as well, for sure. I admit I have not realised a dramatic b

Re: December: tophat

2017-12-06 Thread Fabian Klötzl
Hi Andreas, On 04.12.2017 17:33, Andreas Tille wrote: > On Mon, Dec 04, 2017 at 02:09:48PM +0100, Fabian Klötzl wrote: >> I just pushed some changes to build tophat with our version of libbam. >> Not sure if the previously mentioned issue in [1] is fixed; can't test, > > Thanks to the test suite

Re: December: tophat

2017-12-06 Thread Andreas Tille
Hi Fabian, On Wed, Dec 06, 2017 at 03:53:09PM +0100, Fabian Klötzl wrote: > On 04.12.2017 17:33, Andreas Tille wrote: > > > > Thanks to the test suite we now know that the issue is not solved yet: > > > > $ sh run-unit-test > > That should be done with my recent commit; The new samtools versio

Re: December: tophat

2017-12-06 Thread Fabian Klötzl
On 06.12.2017 16:20, Andreas Tille wrote: > Hi Fabian, > > On Wed, Dec 06, 2017 at 03:53:09PM +0100, Fabian Klötzl wrote: >> On 04.12.2017 17:33, Andreas Tille wrote: >>> >>> Thanks to the test suite we now know that the issue is not solved yet: >>> >>> $ sh run-unit-test >> >> That should be do

bug squashing target: Probably bowtie 1.2.1.1 issue (Was: Bug#880347: bioperl-run: FTBFS: Test failures)

2017-12-06 Thread Andreas Tille
Hi, this bug report has a time correlation to the upload of the new version of bowtie (1.2.1.1): On Mon, Oct 30, 2017 at 09:08:15PM +0100, Lucas Nussbaum wrote: > Source: bioperl-run > Version: 1.7.2-1 > Severity: serious > ... > > Relevant part (hopefully): > > ok 9 # skip Required executable f