[Debian-med-packaging] Bug#927166: Any chance to get libbiod compiling again?

[Pjotr Prins]

Hi all,

Libundead was removed as dependency for biod, but it may be there are
some other issues now because the D ecosystem keeps moving.

My main interest is sambamba and we are working on a fix for one of
the main outstanding bugs building against the latest D compilers.

I suggest to drop the packages until we have fixed them. Not many
takers anyway (right now).

Andreas, I think we'll meet in Paris in November. May be a good time
to hack.

Pj.

On Wed, Sep 18, 2019 at 08:39:52PM +0200, Andreas Tille wrote:
> Hi,
> 
> [Pjotr as upstream in CC]
> 
> On Wed, Sep 18, 2019 at 04:54:16PM +0200, Matthias Klumpp wrote:
> > Am Fr., 13. Sept. 2019 um 22:51 Uhr schrieb Andreas Tille <andreas at an3as.eu>:
> > >
> > > On Fri, Sep 13, 2019 at 03:37:32PM +0200, Matthias Klumpp wrote:
> > > > Am Fr., 13. Sept. 2019 um 15:21 Uhr schrieb Andreas Tille <andreas at an3as.eu>:
> > > > > /usr/bin/ld.gold: error: bin/biod_tests.o: multiple definition of '_d_execBssBegAddr'
> > > > > /usr/bin/ld.gold: contrib/undead/*/__main.o: previous definition here
> > > > > /usr/bin/ld.gold: error: bin/biod_tests.o: multiple definition of '_d_execBssEndAddr'
> > > > > /usr/bin/ld.gold: contrib/undead/*/__main.o: previous definition here
> > > > > collect2: error: ld returned 1 exit status
> > > > > [...]
> > > >
> > > > It's very likely that undeaD needs to be updated first in order to
> > > > compile this again.
> > > > Has upgrading that been attempted yet?
> > >
> > > I just upgraded libundead and re-added it to libbiod (I assumed libundead
> > > would not have been needed for libbiod any more and thus it was removed)
> > > Now the error is:
> > 
> > When I try to compile libbiod now, I get this error:
> > ```
> > ../bio/bam/baseinfo.d-mixin-165(165): Error: Options at
> > ../bio/bam/baseinfo.d(579) conflicts with Options at
> > ../bio/bam/baseinfo.d(482)
> > ../bio/bam/baseinfo.d(175):        called from here: getRangeMethods()
> > ../bio/bam/baseinfo.d(278): Error: template instance
> > `bio.bam.baseinfo.PerBaseInfo!(BamRead, "FZ", "MD", cast(Option)0,
> > cast(Option)1, cast(Option)2, cast(Option)3)` error instantiating
> > ../test/unittests.d(382):        instantiated from here:
> > basesWith!(BamRead, MixinArg!(string, "flowOrder"), MixinArg!(string,
> > "keySequence"))
> > [100/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d
> > -enable-color -O -g -release -wi -unittest
> > -of='biod_test at exe/bio_bam_cigar.d.o' -c ../bio/bam/cigar.d
> > [101/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d
> > -enable-color -O -g -release -wi -unittest
> > -of='biod_test at exe/bio_bam_tagvalue.d.o' -c ../bio/bam/tagvalue.d
> > [102/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d
> > -enable-color -O -g -release -wi -unittest
> > -of='biod_test at exe/bio_bam_bai_indexing.d.o' -c
> > ../bio/bam/bai/indexing.d
> > [103/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d
> > -enable-color -O -g -release -wi -unittest
> > -of='biod_test at exe/bio_bam_iontorrent_flowcall.d.o' -c
> > ../bio/bam/iontorrent/flowcall.d
> > [104/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d
> > -enable-color -O -g -release -wi -unittest
> > -of='biod_test at exe/bio_bam_thirdparty_msgpack.d.o' -c
> > ../bio/bam/thirdparty/msgpack.d
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion
> > not done for -header, use '-preview=intpromote' switch or
> > -cast(int)(header)
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion
> > not done for -header, use '-preview=intpromote' switch or
> > -cast(int)(header)
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion
> > not done for -cast(byte)-header, use '-preview=intpromote' switch or
> > -cast(int)(cast(byte)-header)
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion
> > not done for -header, use '-preview=intpromote' switch or
> > -cast(int)(header)
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion
> > not done for -cast(short)-header, use '-preview=intpromote' switch or
> > -cast(int)(cast(short)-header)
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion
> > not done for -header, use '-preview=intpromote' switch or
> > -cast(int)(header)
> > ninja: build stopped: subcommand failed.
> > dh_auto_build: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j6 -v
> > returned exit code 1
> > ```
> > This is definitely an error in BioD itself, caused by a deprecation
> > that turned into an error in recent LDC versions.
> > So, libbiod will need to be upgraded for sure to fix this.
> 
> @Pjotr: Can you comment on this?
> 
> > In order to support all architectures and generate a pkg-config file I
> > would have to reintroduce the Meson build definition (which upstream
> > apparently has removed) or apply some hacks around the existing
> > Makefile to make that work in a Debian context, which is quite a bit
> > more work.
> 
> As I told you before:  I have no idea about meson.  It would be great if
> we could get it working but if we restrict the package to those
> architectures where it builds out of the box and save some manpower I
> bet the world will keep on turning round.
>  
> > Btw, if libundead has no users anymore, removing it completely may be
> > a good idea - we don't need to maintain something that's dead and has
> > no users.
> 
> I was about to file a removal request to ftpmaster before you said in
> your last mail that the former build issue might have been caused due
> to the lack of libundead.  I would really love to get rid of unneeded
> packages.
> 
> Kind regards
> 
>       Andreas.
> 
> -- 
> http://fam-tille.de