[med-svn] r22296 - in trunk/packages/idba/trunk/debian: . patches
Gert Wollny
gert-guest at moszumanska.debian.org
Fri Jul 1 12:09:12 UTC 2016
Author: gert-guest
Date: 2016-07-01 12:09:11 +0000 (Fri, 01 Jul 2016)
New Revision: 22296
Added:
trunk/packages/idba/trunk/debian/patches/gcc-6.patch
trunk/packages/idba/trunk/debian/patches/run_tests.patch
Modified:
trunk/packages/idba/trunk/debian/changelog
trunk/packages/idba/trunk/debian/control
trunk/packages/idba/trunk/debian/patches/series
trunk/packages/idba/trunk/debian/rules
Log:
Add patches to build with g++-6 and to run test suite
Also update the standards version
Modified: trunk/packages/idba/trunk/debian/changelog
===================================================================
--- trunk/packages/idba/trunk/debian/changelog 2016-07-01 09:07:04 UTC (rev 22295)
+++ trunk/packages/idba/trunk/debian/changelog 2016-07-01 12:09:11 UTC (rev 22296)
@@ -1,7 +1,14 @@
idba (1.1.2-2) UNRELEASED; urgency=medium
+ [Andreas Tille]
* Fix source code location
+ [Gert Wollny]
+ * d/p/gcc-6: Add patch to compile with g++-6, Closes: #811644
+ * d/p/run_tests, d/rules, d/control: Run the test suite during
+ package build
+ * Update standards version to 3.9.8
+
-- Andreas Tille <tille at debian.org> Wed, 20 Jan 2016 09:40:51 +0100
idba (1.1.2-1) unstable; urgency=medium
Modified: trunk/packages/idba/trunk/debian/control
===================================================================
--- trunk/packages/idba/trunk/debian/control 2016-07-01 09:07:04 UTC (rev 22295)
+++ trunk/packages/idba/trunk/debian/control 2016-07-01 12:09:11 UTC (rev 22296)
@@ -1,10 +1,11 @@
Source: idba
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.5
+Build-Depends: debhelper (>= 9),
+ dh-autoreconf
+Standards-Version: 3.9.8
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/idba/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/idba/trunk/
Homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_tran/
Added: trunk/packages/idba/trunk/debian/patches/gcc-6.patch
===================================================================
--- trunk/packages/idba/trunk/debian/patches/gcc-6.patch (rev 0)
+++ trunk/packages/idba/trunk/debian/patches/gcc-6.patch 2016-07-01 12:09:11 UTC (rev 22296)
@@ -0,0 +1,63 @@
+Description: compile with gcc-6
+Forwarded: no
+Bug-Debian: http://bugs.debian.org/811644
+Author: Gert Wollny <gw.fossdev at gmail.com>
+Last-Update: Fri, 1 Jul 2016
+
+--- a/src/sequence/sequence_reader.cpp
++++ b/src/sequence/sequence_reader.cpp
+@@ -47,11 +47,11 @@
+
+ bool FastaReader::ReadRecord(Sequence &seq, string &comment, string &quality)
+ {
+- return ReadFasta(*is_, seq, comment);
++ return !ReadFasta(*is_, seq, comment).fail();
+ }
+
+ bool FastqReader::ReadRecord(Sequence &seq, string &comment, string &quality)
+ {
+- return ReadFastq(*is_, seq, comment, quality);
++ return !ReadFastq(*is_, seq, comment, quality).fail();
+ }
+
+--- a/src/sequence/sequence_writer.cpp
++++ b/src/sequence/sequence_writer.cpp
+@@ -46,11 +46,11 @@
+
+ bool FastaWriter::WriteRecord(const Sequence &seq, const string &comment, const string &quality)
+ {
+- return WriteFasta(*os_, seq, comment);
++ return !WriteFasta(*os_, seq, comment).fail();
+ }
+
+ bool FastqWriter::WriteRecord(const Sequence &seq, const string &comment, const string &quality)
+ {
+- return WriteFastq(*os_, seq, comment, quality);
++ return !WriteFastq(*os_, seq, comment, quality).fail();
+ }
+
+--- a/src/graph/hash_graph.h
++++ b/src/graph/hash_graph.h
+@@ -188,8 +188,13 @@
+ void clear() { vertex_table_.clear(); num_edges_ = 0; }
+
+ private:
++#if __cplusplus >= 201103L
++ HashGraph(const HashGraph &) = delete;
++ const HashGraph &operator =(const HashGraph &) = delete;
++#else
+ HashGraph(const HashGraph &);
+ const HashGraph &operator =(const HashGraph &);
++#endif
+
+ bool GetNextVertexAdaptor(const HashGraphVertexAdaptor ¤t, HashGraphVertexAdaptor &next)
+ {
+@@ -428,7 +433,7 @@
+
+ namespace std
+ {
+-template <> inline void swap(HashGraph &x, HashGraph &y)
++inline void swap(HashGraph &x, HashGraph &y)
+ { x.swap(y); }
+ }
+
Added: trunk/packages/idba/trunk/debian/patches/run_tests.patch
===================================================================
--- trunk/packages/idba/trunk/debian/patches/run_tests.patch (rev 0)
+++ trunk/packages/idba/trunk/debian/patches/run_tests.patch 2016-07-01 12:09:11 UTC (rev 22296)
@@ -0,0 +1,21 @@
+Description: run test suite during package build
+Forwarded: no
+Author: Gert Wollny <gw.fossdev at gmail.com>
+Last-Update: Fri, 1 Jul 2016
+
+--- a/test/Makefile.am
++++ b/test/Makefile.am
+@@ -16,7 +16,7 @@
+ short_sequence_unittest_SOURCES = $(top_srcdir)/src/test/short_sequence_unittest.cpp
+ hash_map_unittest_SOURCES = $(top_srcdir)/src/test/hash_map_unittest.cpp
+
+-noinst_PROGRAMS = \
++check_PROGRAMS = \
+ compact_sequence_unittest \
+ hash_table_unittest \
+ bit_edges_unittest \
+@@ -30,3 +30,4 @@
+ short_sequence_unittest \
+ hash_map_unittest
+
++TESTS=$(check_PROGRAMS)
Modified: trunk/packages/idba/trunk/debian/patches/series
===================================================================
--- trunk/packages/idba/trunk/debian/patches/series 2016-07-01 09:07:04 UTC (rev 22295)
+++ trunk/packages/idba/trunk/debian/patches/series 2016-07-01 12:09:11 UTC (rev 22296)
@@ -1,2 +1,4 @@
use-atomic-for-mips.patch
clang.patch
+gcc-6.patch
+run_tests.patch
Modified: trunk/packages/idba/trunk/debian/rules
===================================================================
--- trunk/packages/idba/trunk/debian/rules 2016-07-01 09:07:04 UTC (rev 22295)
+++ trunk/packages/idba/trunk/debian/rules 2016-07-01 12:09:11 UTC (rev 22296)
@@ -5,7 +5,7 @@
DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
%:
- dh $@
+ dh $@ --with autoreconf
override_dh_auto_configure:
dh_auto_configure -- LDFLAGS="$(LDFLAGS) -Wl,--as-needed" LIBS="$(LIBS) -latomic"
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