Hi Andreas, I've added some more tests to kalign, but there's a slight problem. As specified in the README file, kalign supports two ways of taking input: one is through stdin and the other through the -i flag (or even without it). For some reason, all tests using the -i flag fail inside my testing chroot, but work perfectly outside the chroot. However, inside the chroot and outside, stdin input works as expected.
In the run-unit-test file, all the tests take input from stdin, and all the tests pass. It's the same as what happened with loki earlier, I guess. Please uncomment the lines with -i and try running them on your system. Maybe if they work on yours and others', it's just an issue with my chroot. Here are the errors generated when commands using -i are run inside the chroot: LOG : kalign -i BB11001.tfa -f msf -o out.msf ERROR : Input alignment format could not be detected. (rwalign.c line 314) ERROR : Function "detect_alignment_format(b, &type)" failed. (rwalign.c line 187) ERROR : Function "tmp_msa = read_input(param->infile[i],tmp_msa)" failed. (run_kalign.c line 383) ERROR : Function "run_kalign(param)" failed. (run_kalign.c line 353) Regards, Pranav On Thu, Mar 19, 2020 at 10:18 PM Andreas Tille <andr...@an3as.eu> wrote: > Hi, > > On Thu, Mar 19, 2020 at 11:49:28AM +0100, Steffen Möller wrote: > > > > > https://salsa.debian.org/med-team/kalign > > > > I expected a kalign3 package and then did not investigate any further. > > Sorry. It almost happened :o) > > I had a look and was running routine-update on it. I was close to > uploading but realised that autopkgtest fails. (Steffen, please do > NOT upload, I just added this as TODO and this should be done before > uploading.) > > Any volunteer to fix the test? > > Kind regards > > Andreas. > > -- > http://fam-tille.de > > ᐧ
