[med-svn] [jellyfish] 01/01: Try to use Debian packaged libjsoncpp but failed

[Andreas Tille]

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

tille pushed a commit to branch libjsoncpp
in repository jellyfish.

commit e7c3e72af5611ecd44cd6edd13e0ce2725e082a1
Author: Andreas Tille <tille at debian.org>
Date:   Tue Oct 7 22:19:32 2014 +0200

    Try to use Debian packaged libjsoncpp but failed
---
 debian/changelog                |  2 +-
 debian/clean                    |  1 +
 debian/control                  |  3 ++-
 debian/copyright                |  2 ++
 debian/patches/libjsoncpp.patch | 55 +++++++++++++++++++++++++++++++++++++++++
 debian/patches/series           |  1 +
 debian/watch                    |  3 ++-
 7 files changed, 64 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ddc9fe9..f2912db 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-jellyfish (2.1.4-1) UNRELEASED; urgency=medium
+jellyfish (2.1.4+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version
   * d/watch: point to new location on Github
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..5da17f8
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+config.log
diff --git a/debian/control b/debian/control
index 7fc530f..e32888d 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,8 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
                dh-autoreconf,
-               yaggo
+               yaggo,
+               libjsoncpp-dev
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/jellyfish.git
 Vcs-Git: git://anonscm.debian.org/debian-med/jellyfish.git
diff --git a/debian/copyright b/debian/copyright
index 7da9ef5..24c76cd 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,6 +2,8 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: JELLYFISH
 Upstream-Contact: Guillaume Marçais <gmarcais at umd.edu>
 Source: http://www.cbcb.umd.edu/software/jellyfish/
+Files-Excluded: lib/jsoncpp.cpp
+                include/jellyfish/json.h
 
 Files: *
 Copyright: Copyright 2011 Guillaume Marçais1, Carl Kingsford
diff --git a/debian/patches/libjsoncpp.patch b/debian/patches/libjsoncpp.patch
new file mode 100644
index 0000000..f34546d
--- /dev/null
+++ b/debian/patches/libjsoncpp.patch
@@ -0,0 +1,55 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -26,6 +26,12 @@ AS_IF([test "x$MD5" = "x"], AC_MSG_ERROR
+ AC_ARG_VAR([YAGGO], [Yaggo switch parser generator])
+ AS_IF([test "x$YAGGO" = "x"], [AC_PATH_PROG([YAGGO], [yaggo], [false])])
+ 
++#check for jsoncpp
++AC_CHECK_LIB(jsoncpp,[_ZNK4Json5Value4sizeEv],[
++	JSONCPP_LIB="-ljsoncpp"
++	AC_SUBST(JSONCPP_LIB)
++],AC_MSG_ERROR(Unable to find the libjsoncpp), )
++
+ dnl define([concat], $1$2$3)dnl
+ define([PC_FILE], jellyfish-2.0.pc)
+ AC_CONFIG_FILES([
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -5,7 +5,7 @@ man1_MANS = doc/jellyfish.man
+ pkgconfigdir = $(libdir)/pkgconfig
+ pkgconfig_DATA = jellyfish-2.0.pc
+ 
+-AM_LDFLAGS = -lpthread # $(VALGRIND_LIBS)
++AM_LDFLAGS = -lpthread $(JSONCPP_LIB) # $(VALGRIND_LIBS)
+ AM_CPPFLAGS = -Wall -Wnon-virtual-dtor -I$(top_srcdir) -I$(top_srcdir)/include -g -O3 $(VALGRIND_CFLAGS)
+ AM_CXXFLAGS = $(ALL_CXXFLAGS) -g -O3
+ 
+@@ -69,7 +69,7 @@ libjellyfish_2_0_la_SOURCES = lib/rectan
+                               lib/mer_dna.cc lib/storage.cc		\
+                               lib/allocators_mmap.cc lib/misc.cc	\
+                               lib/int128.cc lib/thread_exec.cc		\
+-                              lib/jsoncpp.cpp lib/time.cc	\
++                              lib/time.cc	\
+                               lib/generator_manager.cc
+ 
+ 
+@@ -101,7 +101,7 @@ library_include_HEADERS = $(JFI)/allocat
+                           $(JFI)/locks_pthread.hpp			\
+                           $(JFI)/file_header.hpp			\
+                           $(JFI)/generic_file_header.hpp		\
+-                          $(JFI)/json.h $(JFI)/hash_counter.hpp		\
++                          $(JFI)/hash_counter.hpp		\
+                           $(JFI)/mapped_file.hpp			\
+                           $(JFI)/mer_dna_bloom_counter.hpp		\
+                           $(JFI)/bloom_common.hpp			\
+--- a/include/jellyfish/generic_file_header.hpp
++++ b/include/jellyfish/generic_file_header.hpp
+@@ -36,7 +36,7 @@
+ #include <iomanip>
+ #include <sstream>
+ 
+-#include <jellyfish/json.h>
++#include <jsoncpp/json/json.h>
+ 
+ namespace jellyfish {
+ /// Generic file header. It contains by default the hostname, the
diff --git a/debian/patches/series b/debian/patches/series
index a640172..0a64000 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 fix_yaggo_syntax.patch
+libjsoncpp.patch
diff --git a/debian/watch b/debian/watch
index 43df025..12a18c4 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,3 @@
 version=3
-https://github.com/gmarcais/Jellyfish/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+opts="uversionmangle=s/$/+dfsg/" \
+  https://github.com/gmarcais/Jellyfish/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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