On November 9, 2017 2:32:56 AM EST, Diane Trout <di...@ghic.org> wrote: >On Thu, 2017-11-09 at 02:03 -0500, Afif Elghraoui wrote: >> > - TODO Split private cram headers off into a new libhts-private-dev >> > package >> >> I'd rather be in favor of restoring the bundled htslib to seqlib as >> the short term solution. Putting a private package in the archive may >> exacerbate the problem and is odd nevertheless. > >The no convenience copies of libraries is a pretty strong rule of >Debian, and there are good maintenance reasons for it.
Yes, I understand that, but we don't have good options right now. I don't see the maintenance advantages for seqlib as worth requiring a transition for every htslib update to make sure it doesn't break--in addition to putting a package in the archive and telling users/developers not to install it. > Although I'm not >opposed to it I'd like several people to agree that its the best option >first. > >On the plus side overriding it would allow us to drop the patch that is >making the cram symbols public, on the downside we'd have to remember >that bugs involving htslib also impact libseqlib. If this whole situation is primarily seqlib's problem, I think it's only fair for it to bear the kludges required for its approach. Otherwise, we have the kludge in htslib and the need for a htslib transition with every update, right? In fact, lofreq never entered Debian because it needs to use samtools as a library and we were not going to bundle it [1]. I felt that would be an RC bug. > >I think we'd need to use the Built-Using tag? I haven't used that >before. > >On the other hand upstream did suggest that the private-dev library was >a viable temporary solution. (Though doing that would push htslib into >NEW). Well, I think they were saying that if we were going to go so far as to misrepresent htslib, we should at the very least make a division and distribute htslib proper as such. I read that as saying anything would be better than the current situation--not necessarily that they're equally better. > >> >> And there is another action item-- >> TODO update the htslib package to the latest release. > >Very true.... I did try building 1.6 and there was a problem with >running tests that I haven't investigated yet. > Regards Afif 1. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=808895