Package: emboss
Version: 6.3.1-6
Severity: normal
Tags: patch
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu precise ubuntu-patch
*** /tmp/tmpuDRGQ2/bug_body
In Ubuntu, the attached patch was applied to achieve the following:
Without this patch, mysql is not linked to emboss-lib in Ubuntu, I
think this is because of --as-needed.
* d/patches/fix-mysql-macro.patch: use LIBS rather than LDFLAGS
so mysql libraries are detected properly.
* d/control,d/rules: use dh_autoreconf to enact mysql changes
* d/rules: remove git cleanup as it breaks clean on non-git
managed builds.
* d/rules: patch before configure to pick up m4 changes
Thanks for considering the patch.
-- System Information:
Debian Release: wheezy/sid
APT prefers precise-updates
APT policy: (500, 'precise-updates'), (500, 'precise-security'), (500,
'precise')
Architecture: amd64 (x86_64)
Kernel: Linux 3.0.0-12-generic (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
diff -u emboss-6.3.1/debian/changelog emboss-6.3.1/debian/changelog
diff -u emboss-6.3.1/debian/control emboss-6.3.1/debian/control
--- emboss-6.3.1/debian/control
+++ emboss-6.3.1/debian/control
@@ -1,12 +1,14 @@
Source: emboss
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <ple...@debian.org>, Nelson A. de Oliveira <nao...@debian.org>
Build-Depends: debhelper (>= 7), quilt, libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev, libexpat1-dev, libhpdf-dev, libmysqlclient-dev, libpq-dev, antiword, sharutils, autotools-dev, tcsh | csh | c-shell,
# Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031
- default-jdk
+ default-jdk,
+ dh-autoreconf
#Build-Depends-Indep: default-jdk
Vcs-Browser: http://git.debian.org/?p=debian-med/emboss.git
Vcs-Git: git://git.debian.org/git/debian-med/emboss.git
diff -u emboss-6.3.1/debian/rules emboss-6.3.1/debian/rules
--- emboss-6.3.1/debian/rules
+++ emboss-6.3.1/debian/rules
@@ -24,15 +24,16 @@
DEB_LDFLAGS += -lpq
#DEB_LDFLAGS += $(shell pg_config | grep LIBS | cut -f2 -d=)
-config.status:
+config.status: patch
dh_testdir
+ dh_autoreconf
ln -sf /usr/share/misc/config.sub .
ln -sf /usr/share/misc/config.guess .
./configure $(CONFFLAGS)
include /usr/share/quilt/quilt.make
-build: config.status patch debian/copyright build-stamp
+build: config.status debian/copyright build-stamp
build-stamp:
dh_testdir
$(MAKE) AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" LDFLAGS="$(DEB_LDFLAGS)"
@@ -57,8 +58,8 @@
find jemboss/ -type f -name "*.class" | xargs -r rm -f
rm --force --recursive debian/emboss_tmp
$(RM) config.status install-stamp
+ dh_autoreconf_clean
dh_clean debian/copyright config.sub config.guess test-stamp
- [ ! -f /usr/bin/git ] || git checkout config.sub config.guess
install: build install-stamp
install-stamp:
diff -u emboss-6.3.1/debian/patches/series emboss-6.3.1/debian/patches/series
--- emboss-6.3.1/debian/patches/series
+++ emboss-6.3.1/debian/patches/series
@@ -3,0 +4 @@
+fix-mysql-macro.patch
only in patch2:
unchanged:
--- emboss-6.3.1.orig/debian/patches/fix-mysql-macro.patch
+++ emboss-6.3.1/debian/patches/fix-mysql-macro.patch
@@ -0,0 +1,25 @@
+Index: emboss-6.3.1/m4/mysql.m4
+===================================================================
+--- emboss-6.3.1.orig/m4/mysql.m4 2010-05-18 15:12:06.000000000 -0700
++++ emboss-6.3.1/m4/mysql.m4 2011-11-27 17:06:21.622474403 -0800
+@@ -95,9 +95,9 @@
+ dnl not be installed
+
+ EMBCFLAGS=$CFLAGS
+- EMBLDFLAGS=$LDFLAGS
++ EMBLIBS=$LIBS
+ CFLAGS=$MYSQL_CFLAGS
+- LDFLAGS=$MYSQL_LDFLAGS
++ LIBS=$MYSQL_LDFLAGS
+
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
+ #include "mysql.h"]],
+@@ -106,7 +106,7 @@
+ [havemysql=no])
+
+ CFLAGS=$EMBCFLAGS
+- LDFLAGS=$EMBLDFLAGS
++ LIBS=$EMBLIBS
+
+ if test "$havemysql" = yes; then
+ AC_DEFINE([HAVE_MYSQL], [1],
