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

Mon Sep 17 21:12:50 UTC 2012

Sure I'll work on this today.

On Mon, Sep 17, 2012 at 4:26 PM, Andreas Tille <andreas at an3as.eu> wrote:
> 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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