[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
tille at debian.org
Thu May 18 13:16:48 UTC 2017
On Thu, May 18, 2017 at 12:39:37AM +0200, Matthias Klumpp wrote:
> Hmm, I just tested this in a pristine sid chroot (using pbuilder) and
> the compilation went just fine.
> What are you doing to trigger this?
By doing exatly the same. I'm using pbuilder + the extra local
repository featuring libhts-dev (>= 1.4-3).
However, if I try with only debuild on my testing machinge (with meson
from unstable + libhts-dev (>= 1.4-3) installed manually) the package
builds. This seems to indicate some missing (versioned) Build-Depends -
no idea which one.
Kind regards
Andreas.
>
> 2017-05-17 12:53 GMT+02:00 Matthias Klumpp <mak at debian.org>:
> > 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
> >
> >
> >
> > --
> > I welcome VSRE emails. See http://vsre.info/
>
>
>
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