Updating Build-Depends for R packages

2017-11-09 Thread Graham Inggs
Hi! I noticed the following build failures in Ubuntu recently: r-bioc-genomicfeatures 1.30.0+dfsg-1 Error : package ‘GenomicRanges’ 1.28.6 was found, but >= 1.29.14 is required by ‘GenomicFeatures’ r-bioc-genomicalignments 1.14.0-1 Error : package ‘GenomicRanges’ 1.28.6 was found, but >=

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

2017-11-09 Thread Diane Trout
> 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 >

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

2017-11-09 Thread Mattia Rizzolo
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

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

2017-11-09 Thread Afif Elghraoui
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 >> > >

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

2017-11-09 Thread Mattia Rizzolo
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

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

2017-11-09 Thread Afif Elghraoui
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 >>

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

2017-11-09 Thread Mattia Rizzolo
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