[Debian-med-packaging] Bug#687968: New upstream version

Mon Sep 17 20:26:07 UTC 2012

Hi Carlos,

could you merge this with your changes in Git?

Kind regards

        Andreas.

----- Forwarded message from Alessandro -oggei- Ogier <alessandro.ogier at ieo.eu> -----

Date: Mon, 17 Sep 2012 13:42:59 +0200
From: Alessandro -oggei- Ogier <alessandro.ogier at ieo.eu>
To: Debian Bug Tracking System <submit at bugs.debian.org>
Subject: Bug#687968: New upstream version
X-Debian-PR-Message: report 687968
X-Debian-PR-Package: cufflinks
X-Debian-PR-Keywords: patch
X-Debian-PR-Source: cufflinks
X-Spam_score: -2.8

Package: cufflinks
Version: 1.3.0-2
Severity: wishlist
Tags: patch

Hi team,

    here at European Institute of Oncology we managed to upgrade
cufflinks packaging to 2.0.2 version (current stable), starting
from your good work.
Here is the changelog:

 * New upstream release
 * Adding libeigen3-dev to Build-Depends
 * Hardened build
 * Fixed autoconf stuff (eigen-related)
 * Parallel compile

We attach the relevant patch, we would be glad if you could
consider to adopt and release new version in debian.

Bests,

ale

-- System Information:
Debian Release: wheezy/sid
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'unstable'), (500, 'testing'), (500, 'stable'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 3.2.0-3-amd64 (SMP w/4 CPU cores)
Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages cufflinks depends on:
ii  dpkg                   1.16.8
ii  libboost-thread1.49.0  1.49.0-3.1
ii  libc6                  2.13-35
ii  libgcc1                1:4.7.1-8
ii  libstdc++6             4.7.1-8
ii  python                 2.7.3-2
ii  zlib1g                 1:1.2.7.dfsg-13

cufflinks recommends no packages.

cufflinks suggests no packages.

-- no debconf information

Index: packages/cufflinks/trunk/debian/control
===================================================================

--- packages/cufflinks/trunk/debian/control	(revision 38)
+++ packages/cufflinks/trunk/debian/control	(revision 43)
@@ -8,5 +8,6 @@
  Charles Plessy <plessy at debian.org>
 Build-Depends: debhelper (>= 8), autotools-dev, libboost-dev (>=1.38.0),
- libboost-thread-dev, libbam-dev (>=0.1.16), zlib1g-dev, dh-autoreconf, python (>=2.6.6-3~)
+ libboost-thread-dev, libbam-dev (>=0.1.16), zlib1g-dev, dh-autoreconf, python (>=2.6.6-3~),
+ hardening-wrapper, libeigen3-dev
 Standards-Version: 3.9.3
 Homepage: http://cufflinks.cbcb.umd.edu/
Index: packages/cufflinks/trunk/debian/changelog
===================================================================
--- packages/cufflinks/trunk/debian/changelog	(revision 38)
+++ packages/cufflinks/trunk/debian/changelog	(revision 43)
@@ -1,2 +1,13 @@
+cufflinks (2.0.2-0ieo1) unstable; urgency=low
+
+  [ Alessandro -oggei- Ogier ]
+  * New upstream release
+  * Adding libeigen3-dev to Build-Depends
+  * Hardened build
+  * Fixed autoconf stuff (eigen-related)
+  * Parallel compile
+
+ -- oggei <oggei at oggei.ieo>  Mon, 17 Sep 2012 13:31:47 +0200
+
 cufflinks (1.3.0-2) unstable; urgency=low
 
Index: packages/cufflinks/trunk/debian/patches/series
===================================================================
--- packages/cufflinks/trunk/debian/patches/series	(revision 38)
+++ packages/cufflinks/trunk/debian/patches/series	(revision 43)
@@ -3,2 +3,3 @@
 0003-fix_includes_path.patch
 gcc-4.7.patch
+wrong-assumptions
Index: packages/cufflinks/trunk/debian/patches/wrong-assumptions
===================================================================
--- packages/cufflinks/trunk/debian/patches/wrong-assumptions	(revision 43)
+++ packages/cufflinks/trunk/debian/patches/wrong-assumptions	(revision 43)
@@ -0,0 +1,32 @@
+Description: wrong assumptions on user intelligence
+ If I describe my eigen path to $dir, i don't really mean $dir/include
+ .
+ cufflinks (2.0.2-1) UNRELEASED; urgency=low
+ .
+   * New upstream release
+Author: oggei <oggei at oggei.ieo>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- cufflinks-2.0.2.orig/ax_check_eigen.m4
++++ cufflinks-2.0.2/ax_check_eigen.m4
+@@ -50,7 +50,7 @@ succeeded=no
+ 
+ dnl first we check the system location for eigen libraries
+ if test "$ac_eigen_path" != ""; then
+-EIGEN_CPPFLAGS="-I$ac_eigen_path/include"
++EIGEN_CPPFLAGS="-I$ac_eigen_path"
+ else
+ for ac_eigen_path_tmp in /usr /usr/local /opt /opt/local ; do
+ if test -d "$ac_eigen_path_tmp/include/eigen" && test -r "$ac_eigen_path_tmp/include/eigen"; then
Index: packages/cufflinks/trunk/debian/rules
===================================================================
--- packages/cufflinks/trunk/debian/rules	(revision 38)
+++ packages/cufflinks/trunk/debian/rules	(revision 43)
@@ -4,6 +4,16 @@
 #export DH_VERBOSE=1
 
+export DEB_BUILD_HARDENING=1
+export DEB_BUILD_HARDENING_FORMAT=0
+export DEB_BUILD_OPTIONS="parallel=$(shell getconf _NPROCESSORS_ONLN)"
+
 %:
 	dh $@ --with autoreconf
+
+override_dh_auto_configure:
+	dh_auto_configure -- --with-eigen=/usr/include/eigen3/
+
+override_dh_auto_build:
+	dh_auto_build -- -j$(shell getconf _NPROCESSORS_ONLN)
 
 override_dh_auto_clean:

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