[Debian-med-packaging] Bug#909071: pbbam: FTBFS on every release architecture where it previously built (fwd)

[Steve Langasek]

On Tue, Feb 05, 2019 at 11:10:15PM +0200, Adrian Bunk wrote:
> On Tue, Feb 05, 2019 at 12:06:22PM -0800, Steve Langasek wrote:
> > On Tue, Feb 05, 2019 at 09:35:23AM +0200, Adrian Bunk wrote:
> > > And then there is the unrelated #908269 that currently prevents testing 
> > > migration of pbbam.

> > > Steve seems to be addressing this with
> > > http://launchpadlibrarian.net/409374477/pbbam_0.19.0+dfsg-1ubuntu3_0.19.0+dfsg-1ubuntu4.diff.gz

> > Yes, but the net result of this change is that now the autopkgtest fails by
> > running out of memory during the package build at test time, which is why I
> > haven't submitted a better patch to the BTS.

> > I think the ideal here would be to either have a way to generate just the
> > single data file we need for the tests, or to capture that file from the
> > package build and ship it in a binary package, so that we don't have to do a
> > full rebuild during the autopkgtests.

> The file is generated during configure, not build.

> As proof of concept, it works to do

> override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in))
> ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
> 	dh_auto_configure -O--buildsystem=meson
> ...

Indeed, with this pbbam now passes its autopkgtests on all three
architectures in Ubuntu.  Attached is a complete patch against pbbam
0.19.0+dfsg-3 for this.

Thanks,
-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                   https://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
-------------- next part --------------
diff -Nru pbbam-0.19.0+dfsg/debian/rules pbbam-0.19.0+dfsg/debian/rules
--- pbbam-0.19.0+dfsg/debian/rules	2019-02-04 02:47:51.000000000 -0800
+++ pbbam-0.19.0+dfsg/debian/rules	2019-02-05 13:58:07.000000000 -0800
@@ -26,6 +26,7 @@
 
 override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in))
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	dh_auto_configure -O--buildsystem=meson
 	mkdir -p $(generated_data_dir)
 	python tests/scripts/generate_data.py $(CURDIR)/tests/data $(generated_data_dir)
 	# Fix broken PATH
diff -Nru pbbam-0.19.0+dfsg/debian/tests/control pbbam-0.19.0+dfsg/debian/tests/control
--- pbbam-0.19.0+dfsg/debian/tests/control	2019-02-02 22:57:09.000000000 -0800
+++ pbbam-0.19.0+dfsg/debian/tests/control	2019-02-05 13:58:07.000000000 -0800
@@ -1,11 +1,5 @@
 Test-Command: debian/rules override_dh_auto_test
 Depends:
-	make,
-	python,
+	@builddeps@,
 	pbbamtools,
-	python-cram,
-	samtools
-Restrictions:
-	rw-build-tree,
-	allow-stderr,
-	build-needed
+Restrictions: rw-build-tree, allow-stderr
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20190205/d3fef0ec/attachment.sig>