On Tue, Feb 05, 2019 at 03:59:55PM -0800, Steve Langasek wrote:
> 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, I've done NMUs for both this problem and removal of the libpbbam
provides that caused FTBFS of blasr and pbdagcon.
debdiffs are attached.
> Thanks,
cu
Adrian
--
"Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
"Only a promise," Lao Er said.
Pearl S. Buck - Dragon Seed
diff -Nru pbbam-0.19.0+dfsg/debian/changelog pbbam-0.19.0+dfsg/debian/changelog
--- pbbam-0.19.0+dfsg/debian/changelog 2019-02-04 12:50:20.000000000 +0200
+++ pbbam-0.19.0+dfsg/debian/changelog 2019-02-06 08:53:24.000000000 +0200
@@ -1,3 +1,12 @@
+pbbam (0.19.0+dfsg-3.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Apply autopkgtest regression fix from Steve Langasek.
+ (Closes: #908269)
+ * libpbbam0.19.0: Remove the incorrect Provides: libpbbam.
+
+ -- Adrian Bunk <b...@debian.org> Wed, 06 Feb 2019 08:53:24 +0200
+
pbbam (0.19.0+dfsg-3) unstable; urgency=medium
* Team upload.
diff -Nru pbbam-0.19.0+dfsg/debian/control pbbam-0.19.0+dfsg/debian/control
--- pbbam-0.19.0+dfsg/debian/control 2019-02-03 09:00:28.000000000 +0200
+++ pbbam-0.19.0+dfsg/debian/control 2019-02-06 08:52:32.000000000 +0200
@@ -50,7 +50,6 @@
${misc:Depends}
Pre-Depends: ${misc:Pre-Depends}
Breaks: libpbbam (<< ${source:Version})
-Provides: libpbbam
Replaces: libpbbam
Description: Pacific Biosciences binary alignment/map (BAM) library
The BAM format is a binary, compressed, record-oriented container format
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 12:47:51.000000000 +0200
+++ pbbam-0.19.0+dfsg/debian/rules 2019-02-06 08:52:46.000000000 +0200
@@ -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 2019-02-03 08:57:09.000000000
+0200
+++ pbbam-0.19.0+dfsg/debian/tests/control 2019-02-06 08:52:46.000000000
+0200
@@ -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
diff -Nru pbseqlib-5.3.1+dfsg/debian/changelog
pbseqlib-5.3.1+dfsg/debian/changelog
--- pbseqlib-5.3.1+dfsg/debian/changelog 2019-01-28 12:27:41.000000000
+0200
+++ pbseqlib-5.3.1+dfsg/debian/changelog 2019-02-06 09:02:44.000000000
+0200
@@ -1,3 +1,12 @@
+pbseqlib (5.3.1+dfsg-2.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Remove manual dependencies on libpbbam, version build
+ dependency on libpbbam-dev to ensure a proper dependency
+ is generated.
+
+ -- Adrian Bunk <b...@debian.org> Wed, 06 Feb 2019 09:02:44 +0200
+
pbseqlib (5.3.1+dfsg-2) unstable; urgency=medium
* Team upload.
diff -Nru pbseqlib-5.3.1+dfsg/debian/control pbseqlib-5.3.1+dfsg/debian/control
--- pbseqlib-5.3.1+dfsg/debian/control 2019-01-28 12:27:41.000000000 +0200
+++ pbseqlib-5.3.1+dfsg/debian/control 2019-02-06 09:02:44.000000000 +0200
@@ -9,7 +9,7 @@
zlib1g-dev,
libhdf5-dev,
libboost-dev,
- libpbbam-dev,
+ libpbbam-dev (>= 0.18.0+dfsg-1~),
libhts-dev,
libgtest-dev <!nocheck>
Standards-Version: 4.3.0
@@ -62,8 +62,7 @@
Architecture: any
Multi-Arch: same
Depends: ${shlibs:Depends},
- ${misc:Depends},
- libpbbam
+ ${misc:Depends}
Description: tools for handling PacBio sequences
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
@@ -91,8 +90,7 @@
Multi-Arch: same
Depends: ${shlibs:Depends},
${misc:Depends},
- libpbdata (= ${binary:Version}),
- libpbbam
+ libpbdata (= ${binary:Version})
Description: tools for handling PacBio hdf5 files
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
@@ -121,8 +119,7 @@
Depends: ${shlibs:Depends},
${misc:Depends},
libpbdata (= ${binary:Version}),
- libpbihdf (= ${binary:Version}),
- libpbbam
+ libpbihdf (= ${binary:Version})
Description: tools for aligning PacBio reads to target sequences
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
diff -Nru unanimity-3.3.0+dfsg/debian/changelog
unanimity-3.3.0+dfsg/debian/changelog
--- unanimity-3.3.0+dfsg/debian/changelog 2019-02-01 13:45:08.000000000
+0200
+++ unanimity-3.3.0+dfsg/debian/changelog 2019-02-06 09:11:14.000000000
+0200
@@ -1,3 +1,12 @@
+unanimity (3.3.0+dfsg-2.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Remove manual dependencies on libpbbam, version build
+ dependency on libpbbam-dev to ensure a proper dependency
+ is generated.
+
+ -- Adrian Bunk <b...@debian.org> Wed, 06 Feb 2019 09:11:14 +0200
+
unanimity (3.3.0+dfsg-2) unstable; urgency=medium
[ Steve Langasek ]
diff -Nru unanimity-3.3.0+dfsg/debian/control
unanimity-3.3.0+dfsg/debian/control
--- unanimity-3.3.0+dfsg/debian/control 2019-02-01 13:45:08.000000000 +0200
+++ unanimity-3.3.0+dfsg/debian/control 2019-02-06 09:11:14.000000000 +0200
@@ -14,7 +14,7 @@
python-numpy,
libboost-dev,
libhts-dev,
- libpbbam-dev,
+ libpbbam-dev (>= 0.18.0+dfsg-1~),
libpbcopper-dev,
libseqan2-dev,
pandoc
@@ -27,8 +27,7 @@
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- ${python:Depends},
- libpbbam
+ ${python:Depends}
Description: generate and process accurate consensus nucleotide sequences
Unanimity provides a set of tools for consensus sequences from Pacific
Biosciences sequencing data:
diff -Nru pbdagcon-0.3+git20161121.0000000+ds/debian/changelog
pbdagcon-0.3+git20161121.0000000+ds/debian/changelog
--- pbdagcon-0.3+git20161121.0000000+ds/debian/changelog 2019-02-04
16:36:14.000000000 +0200
+++ pbdagcon-0.3+git20161121.0000000+ds/debian/changelog 2019-02-06
09:20:03.000000000 +0200
@@ -1,3 +1,12 @@
+pbdagcon (0.3+git20161121.0000000+ds-1.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Remove manual dependencies on libpbbam, version build
+ dependency on libpbbam-dev to ensure a proper dependency
+ is generated.
+
+ -- Adrian Bunk <b...@debian.org> Wed, 06 Feb 2019 09:20:03 +0200
+
pbdagcon (0.3+git20161121.0000000+ds-1) unstable; urgency=low
* Team upload
diff -Nru pbdagcon-0.3+git20161121.0000000+ds/debian/control
pbdagcon-0.3+git20161121.0000000+ds/debian/control
--- pbdagcon-0.3+git20161121.0000000+ds/debian/control 2019-02-04
16:36:14.000000000 +0200
+++ pbdagcon-0.3+git20161121.0000000+ds/debian/control 2019-02-06
09:20:03.000000000 +0200
@@ -10,7 +10,7 @@
libboost-dev,
libtclap-dev,
libpbseq-dev,
- libpbbam-dev,
+ libpbbam-dev (>= 0.18.0+dfsg-1~),
libpbdata-dev,
# Test-Depends:
googletest
@@ -23,8 +23,7 @@
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libpbseq,
- libpbbam
+ libpbseq
Suggests: blasr
Description: sequence consensus using directed acyclic graphs
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)
diff -Nru blasr-5.3.2+dfsg/debian/changelog blasr-5.3.2+dfsg/debian/changelog
--- blasr-5.3.2+dfsg/debian/changelog 2019-01-28 17:10:36.000000000 +0200
+++ blasr-5.3.2+dfsg/debian/changelog 2019-02-06 09:24:24.000000000 +0200
@@ -1,3 +1,11 @@
+blasr (5.3.2+dfsg-1.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Remove manual dependency on libpbbam, a proper one is already
+ being generated.
+
+ -- Adrian Bunk <b...@debian.org> Wed, 06 Feb 2019 09:24:24 +0200
+
blasr (5.3.2+dfsg-1) unstable; urgency=medium
* Team upload
diff -Nru blasr-5.3.2+dfsg/debian/control blasr-5.3.2+dfsg/debian/control
--- blasr-5.3.2+dfsg/debian/control 2019-01-28 17:10:36.000000000 +0200
+++ blasr-5.3.2+dfsg/debian/control 2019-02-06 09:24:24.000000000 +0200
@@ -24,8 +24,7 @@
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libpbseq (>= 0~20160912),
- libpbbam
+ libpbseq (>= 0~20160912)
Description: mapping single-molecule sequencing reads
Basic local alignment with successive refinement (BLASR) is a method
for mapping single-molecule sequencing reads against a reference genome.
