[Debian-med-packaging] [micahg at ubuntu.com: Bug#651802: exonerate: Fix build with --as-needed]

[Andreas Tille]

Hi Guy,

I just applied the patch mentioned below to the Debian packaging of
exonerate.  When doing so I realised that the package does not build on
a current Debian unstable system because of relying on to old automake
tools.  By simply using `autoreconf` I created a patch which fixes this
issue.  Moreover I followed the Debian tool lintian to fix some minor
bugs in the manpages inside exonerate but did not finished because of
time constrainst.  However, I dropped a note inside the patch how to
simply fight the remaining issues.

You can find all patches at

    http://anonscm.debian.org/viewvc/debian-med/trunk/packages/exonerate/trunk/debian/patches/

Feel free to apply them in your next upstream release.

Kind regards and thanks for providing exonerate as Free Software

     Andreas.

----- Forwarded message from Micah Gersten <micahg at ubuntu.com> -----

Date: Mon, 12 Dec 2011 03:12:38 -0600
From: Micah Gersten <micahg at ubuntu.com>
To: Debian Bug Tracking System <submit at bugs.debian.org>
Subject: Bug#651802: exonerate: Fix build with
	--as-needed

Package: exonerate
Version: 2.2.0-2
Severity: normal
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu precise ubuntu-patch



*** /tmp/tmpIx70yM
In Ubuntu, the attached patch was applied to achieve the following:


  * Add -pthread to LIBS instead of LDFLAGS; fixes FTBFS with --as-needed
    - update configure.in


Thanks for considering the patch.


-- System Information:
Debian Release: wheezy/sid
  APT prefers oneiric-updates
  APT policy: (500, 'oneiric-updates'), (500, 'oneiric-security'), (500, 'oneiric-proposed'), (500, 'oneiric'), (100, 'oneiric-backports')
Architecture: amd64 (x86_64)

Kernel: Linux 3.0.0-13-generic (SMP w/8 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

only in patch2:
unchanged:
--- exonerate-2.2.0.orig/configure.in
+++ exonerate-2.2.0/configure.in
@@ -289,7 +289,7 @@
 if test "$enable_pthreads" = yes; then
     echo "Using PTHREADS"
     CFLAGS="$CFLAGS -DUSE_PTHREADS"
-    LDFLAGS="$LDFLAGS -lpthread"
+    LIBS="$LIBS -lpthread"
 elif test "$enable_pthreads" = no; then
     echo "Not using pthreads"
 else

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----- End forwarded message -----

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