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-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],
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