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

[Matthias Klumpp]

2017-05-13 23:34 GMT+02:00 Andreas Tille <tille at debian.org>:
> Hi,
>
> I wonder whether I made something wrong with htslib since I can not
> confirm that the suggested change would help.

I saw that cargs error once, the culprit was an issue with the
pkg-config file of htslib (finding it properly). I forgot how I solved
this though, it was one of these issues where you think little about.
I can try building this again when home, weird that you get this issue
while I didn't.
To debug, use the pkg-config command to query cflags for htslib manually.

Cheers,
    Matthias

> 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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>>
>
> --
> http://fam-tille.de



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