[Debian-med-packaging] Bug#650237: emboss: Fails to link mysqlclient with linker set for --as-needed

[Andreas Tille]

Hi Charles,

any reason to not apply this patch and fix the bug?

Kind regards

       Andreas.

On Sun, Nov 27, 2011 at 05:35:30PM -0800, Clint Byrum wrote:
> Package: emboss
> Version: 6.3.1-6
> Severity: normal
> Tags: patch
> User: ubuntu-devel at 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-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, 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],

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