[Debian-med-packaging] [Pkg-d-devel] Libbiod and libundead packaged but sambamba does not build (Was: Next D project question: sambamba needs rdmd)

[Andreas Tille]

Hi,

I wonder whether I made something wrong with htslib since I can not
confirm that the suggested change would help.

Kind regards

    Andreas.

On Thu, May 04, 2017 at 11:14:58AM +0200, Andreas Tille wrote:
> Hi Matthias,
> 
> thanks a lot for your commitment to this package.  Its really
> appreciated since I'd otherwise would be totally clueless.
> 
> On Sun, Apr 30, 2017 at 06:12:29PM +0200, Matthias Klumpp wrote:
> > > I'll make a patch and see if that works okay.
> > 
> > I now committed a couple of changes to the sambamba packaging repo,
> > which will make the thing build - in theory.
> 
> Thanks again.
> 
> > To actually make the build process work, this patch needs to be
> > applied to htslib:
> >  https://github.com/UMCUGenetics/guix-additions/blob/master/htslib-add-cram_to_bam.patch
> 
> I commited this patch to htslib git and build locally (even if
> distribution is set to experimental I did not uploaded yet).
> 
> > Then the build finishes
> 
> Hmmm, not at my side.  Despite I have changed
> 
> sambamba(master) $ git diff
> diff --git a/debian/control b/debian/control
> index 7058e73..0d7a65e 100644
> --- a/debian/control
> +++ b/debian/control
> @@ -6,7 +6,7 @@ Uploaders: Andreas Tille <tille at debian.org>
>  Build-Depends: debhelper (>= 10),
>                 ldc,
>                 libbiod-dev,
> -               libhts-dev,
> +               libhts-dev (>= 1.4-3),
>                 liblz4-dev,
>                 libundead-dev,
>                 meson (>= 0.40),
> 
> 
> when trying to build sambamba in pbuilder I get
> 
> ...
> Writing extended state information...
> Get: 1 file:/var/cache/pbuilder/extra/release ./ libhts2 1.4-3 [294 kB]
> Get: 2 file:/var/cache/pbuilder/extra/release ./ libhts-dev 1.4-3 [397 kB]
> ...
> 
>    debian/rules override_dh_auto_configure
> make[1]: Entering directory '/build/sambamba-0.6.6'
> mkdir build
> (cd build && meson --prefix=/usr --buildtype=plain ..)
> The Meson build system
> Version: 0.40.0
> Source dir: /build/sambamba-0.6.6
> Build dir: /build/sambamba-0.6.6/build
> Build type: native build
> Project name: Sambamba
> Native d compiler: ldc2 (llvm 1.1.1)
> Appending DFLAGS from environment: '-O3 -g -release'
> Appending LDFLAGS from environment: '-Wl,-z,relro'
> Build machine cpu family: x86_64
> Build machine cpu: x86_64
> Found pkg-config: /usr/bin/pkg-config (0.29)
> Native dependency undead found: YES 1.0.6
> Native dependency biod found: YES 0.1.0
> Native dependency liblz4 found: YES 131
> 
> Meson encountered an error in file meson.build, line 80, column 0:
> Could not generate cargs for htslib:
> 
> 
> debian/rules:26: recipe for target 'override_dh_auto_configure' failed
> 
> 
> 
> Is there any chance that you did not commited the last state of your
> meson file?
> 
> 
> > and we get a binary, which doesn't launch:
> > 
> > Fatal Error while loading '/usr/lib/x86_64-linux-gnu/libbiod.so.0':
> >         The module 'undead.stream' is already defined in './sambamba'.
> > 
> > This probably is an LDC bug, it looks like it doesn't like the undeaD
> > static library being compiled into both the executable and shared lib.
> > The issue could probably be worked around by making the undead library
> > a shared library instead, that way, both BLOBs would be forced to use
> > the same code copy.
> > (in order to make undead a shared library, change the "shared_library"
> > instruction in its meson.build file to just "library", and recompile
> > BioD with the new package).
> 
> I can perfectly do so but in any case feel free to commit those helpful
> changes to Git if you have done those changes locally anyway.
>  
> I'd happily try the latter once the first issue is settled.
> 
> Thanks a lot again for your very great help
> 
>         Andreas.
> 
> -- 
> http://fam-tille.de
> 
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