Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

On Thu, Nov 09, 2017 at 10:11:30PM -0500, Afif Elghraoui wrote: > On November 9, 2017 6:20:03 PM EST, Diane Trout wrote: > > > [...] > > > >Anyone want to review? or should I go ahead and release? > > I think you can release. Yes please release it, and IMHO close this bug with

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

On November 9, 2017 6:20:03 PM EST, Diane Trout wrote: > [...] > >Anyone want to review? or should I go ahead and release? > I think you can release. However, it appears the changelog wasn't updated in git since the last upload [1] you'll need to go for a 1.5-3. regards

Bug#879886: libhts2: libhts2 needs to handle ABI changes

> As a gotcha, remember that this bug was born out of the fact that > there > was a package requiring a >= 1.5 dependency. I recommend you compile > the symbol file with something << 1.5 (i.e. 1.4 or just re-add the > file > that was removed) and then update it appropriately so there will be >

Bug#879886: libhts2: libhts2 needs to handle ABI changes

On Thu, Nov 09, 2017 at 03:14:27AM -0500, Afif Elghraoui wrote: > >If you find issues getting stuff sponsored, please do point me to it > >privately (I know you are on IRC, that tends to often work best for > >me). > > Diane's a DD. Oops, sorry! Then I take back my offer to sponsor, but still

Bug#879886: libhts2: libhts2 needs to handle ABI changes

On November 9, 2017 3:06:32 AM EST, Mattia Rizzolo wrote: >On Wed, Nov 08, 2017 at 04:58:49PM -0800, Diane Trout wrote: >> > > I was wondering if we should split the cram headers into a >> > > libhts-private-dev so we can at least track what is depending on >> > > the >> > >

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

On Wed, Nov 08, 2017 at 11:32:56PM -0800, Diane Trout wrote: > I think we'd need to use the Built-Using tag? I haven't used that > before. No, that's needed when doing static linking for GPL compliance (and other kind of things, but all related to static linking that thanks god is not a topic

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

On November 9, 2017 2:32:56 AM EST, Diane Trout 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 >>

Bug#879886: libhts2: libhts2 needs to handle ABI changes

On Wed, Nov 08, 2017 at 04:58:49PM -0800, Diane Trout wrote: > - TODO Recommit symbols file > > > Symbols file are strange to work with because their update usually > > goes > > through a build failure that outputs a patch, which is not very > > intuitive. And then the patched symbols file has

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

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

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

Hi, Diane, Thanks for working on this. On November 8, 2017 7:58:49 PM EST, Diane Trout wrote: >One of the htslib developers filed a new bug, > >https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881170 > >asking us to not make their private libraries public. His suggestions >are

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

Dear Diane, On Wed, Nov 08, 2017 at 04:58:49PM -0800, Diane Trout wrote: > > Should I push these proposed changes to a clone of the htslib packaging > repository? A branch of the alioth repository, or just push it to the > alioth master? Thanks for your sane considerations and pleas push to

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

One of the htslib developers filed a new bug, https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881170 asking us to not make their private libraries public. His suggestions are fairly similar to whats Charles proposed. What I'm thinking is: - TODO Recommit symbols file - TODO Split private

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

Hi Diane and everybody, Le Tue, Nov 07, 2017 at 05:09:34PM -0800, Diane Trout a écrit : > > I do think we should bring back the symbols file I think so too. Symbols file are strange to work with because their update usually goes through a build failure that outputs a patch, which is not very

Bug#879886: libhts2: libhts2 needs to handle ABI changes

On Fri, Oct 27, 2017 at 12:52:31AM -0400, Afif Elghraoui wrote: > We've been doing this for every htslib suite release and can confirm > upstream's explanation. It seems to me the most "interesting" argument in #822701#26 is this: | What's described in that thread is undocumented internal

Bug#879886: [Debian-med-packaging] Bug#879886: Bug#879886: libhts2: libhts2 needs to handle ABI changes

Hi, Mattia and all, على الخميس 26 تشرين الأول 2017 ‫15:44، كتب Mattia Rizzolo: > On Thu, Oct 26, 2017 at 12:12:05PM -0700, Diane Trout wrote: >> libhts2 introduced an ABI change which broke python-pysam, and a new >> version of python-pysam needed to be released to update to the new ABI. > >

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

On Thu, Oct 26, 2017 at 12:12:05PM -0700, Diane Trout wrote: > libhts2 introduced an ABI change which broke python-pysam, and a new > version of python-pysam needed to be released to update to the new ABI. FTR, this is what changed between the symbols of the version 1.4.1-5 and 1.5-1: ---

Bug#879886: libhts2: libhts2 needs to handle ABI changes

Package: libhts2 Version: 1.5-1 Severity: critical Dear Maintainer, libhts2 introduced an ABI change which broke python-pysam, and a new version of python-pysam needed to be released to update to the new ABI. libhts2 probably needs a proper symbols file to make it easier to see when the ABI is