Bug#954511: Can someone habe a look at bioperl-run in connection with kalign (was: bioperl-run is marked for autoremoval from testing]

2020-03-30 Thread Pranav Ballaney
Hi, Yes, Kalign is on v3 now. I've pushed some patches to fix this bug. All build-time tests pass now. Autopkgtests don't, however, but that issue seems to be unrelated. Please take a look at https://salsa.debian.org/med-team/bioperl-run and verify the patches. This is my first time working with

Bug#954511: Can someone habe a look at bioperl-run in connection with kalign (was: bioperl-run is marked for autoremoval from testing]

2020-03-30 Thread Christopher Fields
I have seen per exit codes of 256 for other bioperl-run wrappers in the past where the application API changed (constant game of playing catchup unfortunately). That seems to be the case here based on the error. Is kalign is now at v3? chris On 3/30/20, 2:57 AM, "Andreas Tille" wrote:

Bug#954511: Can someone habe a look at bioperl-run in connection with kalign (was: bioperl-run is marked for autoremoval from testing]

2020-03-30 Thread Andreas Tille
Control: tags -1 help Hi, currently bioperl-run fails. I think the issue is: > # Failed test 'Code tested only on kalign versions >= 2' > # at t/Kalign.t line 23. > # got: '' > # expected: '1' > [2020-03-22 03:18:02] : ERROR : Input alignment format could not be >