Your message dated Fri, 10 Aug 2012 08:48:10 +0000
with message-id <[email protected]>
and subject line Bug#650237: fixed in emboss 6.4.0-3
has caused the Debian Bug report #650237,
regarding emboss: Fails to link mysqlclient with linker set for --as-needed
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
650237: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650237
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: emboss
Version: 6.3.1-6
Severity: normal
Tags: patch
User: [email protected]
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 <[email protected]>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <[email protected]>, Nelson A. de Oliveira <[email protected]>
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],
--- End Message ---
--- Begin Message ---
Source: emboss
Source-Version: 6.4.0-3
We believe that the bug you reported is fixed in the latest version of
emboss, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated emboss package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Thu, 09 Aug 2012 16:01:07 +0200
Source: emboss
Binary: emboss emboss-data emboss-doc emboss-test emboss-lib jemboss
Architecture: source i386 all
Version: 6.4.0-3
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
emboss - european molecular biology open software suite
emboss-data - data files for the EMBOSS package
emboss-doc - documentation for EMBOSS
emboss-lib - EMBOSS Libraries
emboss-test - test files for the EMBOSS package
jemboss - graphical user interface to EMBOSS
Closes: 650237 683190
Changes:
emboss (6.4.0-3) unstable; urgency=low
.
* Import patches prepared by Felix Geyer <[email protected]> to cope
with the --as-needed issue when linking against database clients
(thanks to Felix)
Closes: #650237
* Fix typo to build emboss including PostgreSQL support (Thanks to
Felix Geyer <[email protected]> for the patch)
Closes: #683190
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