[Debian-med-packaging] [SCM] The European Molecular Biology Open Software Suite. branch, master, updated. upstream/6.3.0-26-g0ab985d

[Charles Plessy]

The following commit has been merged in the master branch:
commit 0ab985d68db6e1f5a1dc59e426745b975f167dfe
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Jul 16 13:46:03 2010 +0900

    Build against Debian's zlib and expat libraries.

diff --git a/debian/README.source b/debian/README.source
index c2cd5f0..ae044ba 100644
--- a/debian/README.source
+++ b/debian/README.source
@@ -1,2 +1,8 @@
 This packages uses a patch system. Please read
 /usr/share/doc/quilt/README.source for more informations.
+
+The binary packages are built against the zlib and expat library distributed in
+Debian, not the conveniences copies co-distributed with EMBOSS. This is done by:
+
+ - passing ‘--enable-systemlibs’ to the configure command.
+ - passing ‘LDFLAGS="-lexpat"’ to the make command.
diff --git a/debian/control b/debian/control
index 5936aa6..eed99bc 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>, Nelson A. de Oliveira <naoliv at debian.org>
-Build-Depends: debhelper (>= 7), quilt, libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev, libpcre3-dev, antiword, sharutils, autotools-dev, tcsh | csh | c-shell
+Build-Depends: debhelper (>= 7), quilt, libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev, libpcre3-dev, libexpat1-dev, antiword, sharutils, autotools-dev, tcsh | csh | c-shell
 Build-Depends-Indep: openjdk-6-jdk
 Vcs-Browser: http://git.debian.org/?p=debian-med/emboss.git
 Vcs-Git: git://git.debian.org/git/debian-med/emboss.git
diff --git a/debian/libajax6.lintian-overrides b/debian/libajax6.lintian-overrides
deleted file mode 100644
index 43838fc..0000000
--- a/debian/libajax6.lintian-overrides
+++ /dev/null
@@ -1,5 +0,0 @@
-# I have contacted upstream to ask if EMBOSS can be built against the latest zlib.
-# http://lists.open-bio.org/pipermail/emboss/2010-May/003915.html
-# Fedora's patch will be applied as soon as I get Upstream's approval
-# -- Charles Plessy <plessy at debian.org>  Thu, 27 May 2010 13:31:29 +0900
-libajax6: embedded-zlib ./usr/lib/libezlib.so.1.1.0
diff --git a/debian/rules b/debian/rules
index 716a391..dfc6662 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,7 +11,9 @@ EMBOSS-TEST = $(CURDIR)/debian/emboss-test
 AJAX        = $(CURDIR)/debian/libajax6
 NUCLEUS     = $(CURDIR)/debian/libnucleus6
 
-CONFFLAGS   = --prefix=/usr --bindir=/usr/lib/emboss
+CONFFLAGS   = --prefix=/usr
+CONFFLAGS   += --bindir=/usr/lib/emboss
+CONFFLAGS   += --enable-systemlibs
 
 # If openjdk-6-jdk is not installed don't tell configure to use it.
 # This allows binary-arch builds to be performed without openjdk
@@ -32,7 +34,7 @@ include /usr/share/quilt/quilt.make
 build: config.status patch debian/copyright build-stamp
 build-stamp:
 	dh_testdir
-	$(MAKE) AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\"
+	$(MAKE) AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" LDFLAGS="-lexpat"
 	touch build-stamp
 
 # In order to use this rule you must install libemboss-acd-perl, xsltproc, docbook-xml and docbook-xsl

-- 
The European Molecular Biology Open Software Suite.