[med-svn] [jellyfish1] 07/08: Adapt build to new upstream version

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository jellyfish1.

commit e0b93ab6b615ec7c481823fbb5d2cea289011a9e
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 17 09:28:10 2015 +0100

    Adapt build to new upstream version
---
 debian/control                                     |  4 ++-
 .../a3c491af4b02086cf13269eb5df8266a748e1c7c.patch | 30 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 debian/rules                                       |  2 +-
 4 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/debian/control b/debian/control
index a554dc9..fb66cae 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,9 @@ Uploaders: Shaun Jackman <sjackman at debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               autotools-dev
+               dh-autoreconf,
+               pkg-config,
+               yaggo
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/jellyfish1.git
 Vcs-Git: git://anonscm.debian.org/debian-med/jellyfish1.git
diff --git a/debian/patches/a3c491af4b02086cf13269eb5df8266a748e1c7c.patch b/debian/patches/a3c491af4b02086cf13269eb5df8266a748e1c7c.patch
new file mode 100644
index 0000000..107e4fd
--- /dev/null
+++ b/debian/patches/a3c491af4b02086cf13269eb5df8266a748e1c7c.patch
@@ -0,0 +1,30 @@
+From: Guillaume Marcais <gmarcais at umd.edu>
+Date: Thu, 2 Jul 2015 09:25:02 -0400
+Last-Update: Tue, 17 Nov 2015 09:20:50 +0100
+Subject: [PATCH] Removed kludgy -Dprotected=public flags in testing.
+ Adapted by Andreas Tille for Jellyfish 1.5.5.
+Origin: https://github.com/gmarcais/Jellyfish/commit/a3c491af4b02086cf13269eb5df8266a748e1c7c.patch
+Bug-Debian: #795847
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -191,7 +191,7 @@ bin_test_all_SOURCES = unit_tests/test_m
+ 	               unit_tests/test_stdio_filebuf.cc
+ bin_test_all_SOURCES += jellyfish/backtrace.cc
+ 
+-bin_test_all_CPPFLAGS = -Dprotected=public -Dprivate=public -DJSON_IS_AMALGAMATION=1
++bin_test_all_CPPFLAGS = -DJSON_IS_AMALGAMATION=1
+ bin_test_all_CXXFLAGS = $(AM_CXXFLAGS) -I$(top_srcdir)/unit_tests/gtest/include -I$(top_srcdir)/unit_tests -I$(top_srcdir)/include
+ bin_test_all_LDADD = libgtest.la $(LDADD)
+ YAGGO_SOURCES += unit_tests/test_main_cmdline.hpp
+--- a/unit_tests/test_mer_heap.cc
++++ b/unit_tests/test_mer_heap.cc
+@@ -16,7 +16,7 @@ static const uint16_t mer_len  = 50;
+ static const size_t   nb_mers  = ary_size / 2;
+ 
+ class MerHeapTest : public ::testing::TestWithParam<size_t> {
+-protected:
++public:
+   static void SetUpTestCase() {
+     mer_dna::k(mer_len);
+     shared_ary = new large_array(ary_size, mer_len * 2, 0, 63);
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..d1a3f20
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+a3c491af4b02086cf13269eb5df8266a748e1c7c.patch
diff --git a/debian/rules b/debian/rules
index 4c9a9ae..aa52c7e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,7 +3,7 @@
 export DH_OPTIONS
 
 %:
-	dh $@
+	dh $@ --with autoreconf
 
 override_dh_auto_configure:
 	dh_auto_configure

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/jellyfish1.git