[Debian-med-packaging] Sambamba release

[Andreas Tille]

Hi Pjotr,

On Thu, Oct 04, 2018 at 09:03:03AM +0200, Pjotr Prins wrote:
> Hi Andreas,
> 
> I released a new version of sambamba. Sorry for the delay.

Thanks a lot for the prompt information.  That's very helpful.
Unfortunately there seems to be an issue with the meson.build file[1].
Matthias once added this to enable an easy build but I think its a bit
unfortunate if we maintain in Debian a separate build system which
always needs adaption (which is hard for me since I neither speak D nor
meson :-().

@Matthias: What was your initial motivation to replace the Makefile
provided by sambamba by meson?  I was able to adapt it for the
0.6.8-pre3 release but now it fails with:

[1/80] ldc2 -I=sambamba at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi   -of='sambamba at exe/sambamba_main.d.o' -c ../sambamba/main.d
FAILED: sambamba at exe/sambamba_main.d.o 
ldc2 -I=sambamba at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi   -of='sambamba at exe/sambamba_main.d.o' -c ../sambamba/main.d
../sambamba/markdup2.d(46): Error: module `reader` is in file 'bio2/bam/reader.d' which cannot be read
import path[0] = sambamba at exe
import path[1] = .
import path[2] = ..
import path[3] = /usr/include/d
import path[4] = /usr/lib/ldc/x86_64-linux-gnu/include/d/ldc
import path[5] = /usr/lib/ldc/x86_64-linux-gnu/include/d
import path[6] = /usr/include/d
[2/80] ldc2 -I=sambamba at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi   -of='sambamba at exe/sambamba_flagstat.d.o' -c ../sambamba/flagstat.d
[3/80] ldc2 -I=sambamba at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi   -of='sambamba at exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
[4/80] ldc2 -I=sambamba at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi   -of='sambamba at exe/sambamba_depth.d.o' -c ../sambamba/depth.d
ninja: build stopped: subcommand failed.
dh_auto_build: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1
make: *** [debian/rules:9: build] Error 1


@Pjotr: Do you see any advantage of meson over make and would like to
maintain it?  I admit I would also need to adapt the Makefile since
currently it fails with

$ make
make: *** No rule to make target 'lz4/lib/lz4.c', needed by 'lz4/lib/liblz4.a'.  Stop.


(There is no point in building that lib since it is provided by the
package liblz4-dev in /usr/lib/<TRIPLET>/liblz4.a - so I need to remove
that dependency inside the Makefile.)

I'm just curious what kind of build system looks promising to build new
versions of sambamba out of the box without requiring manual edits for
the packaging.

Kind regards

        Andreas.


[1] https://salsa.debian.org/med-team/sambamba/blob/master/debian/patches/01_add_meson.patch 

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