[med-svn] r16044 - in trunk/packages/spades/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Fri Feb 14 12:22:03 UTC 2014 

Author: tille
Date: 2014-02-14 12:22:03 +0000 (Fri, 14 Feb 2014)
New Revision: 16044

Added:
   trunk/packages/spades/trunk/debian/patches/use_debian-packaged_boost.patch
Modified:
   trunk/packages/spades/trunk/debian/changelog
   trunk/packages/spades/trunk/debian/control
   trunk/packages/spades/trunk/debian/copyright
   trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch
   trunk/packages/spades/trunk/debian/patches/series
   trunk/packages/spades/trunk/debian/rules
   trunk/packages/spades/trunk/debian/watch
Log:
Deal with some code copies, document others (more to come)


Modified: trunk/packages/spades/trunk/debian/changelog
===================================================================
--- trunk/packages/spades/trunk/debian/changelog	2014-02-14 10:47:49 UTC (rev 16043)
+++ trunk/packages/spades/trunk/debian/changelog	2014-02-14 12:22:03 UTC (rev 16044)
@@ -1,4 +1,4 @@
-spades (3.0.0-1) UNRELEASED; urgency=low
+spades (3.0.0+dfsg-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #<bug>)
 

Modified: trunk/packages/spades/trunk/debian/control
===================================================================
--- trunk/packages/spades/trunk/debian/control	2014-02-14 10:47:49 UTC (rev 16043)
+++ trunk/packages/spades/trunk/debian/control	2014-02-14 12:22:03 UTC (rev 16044)
@@ -7,6 +7,7 @@
                cmake,
                python-all-dev,
                zlib1g-dev,
+               libboost-dev,
                lynx
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/spades/trunk/

Modified: trunk/packages/spades/trunk/debian/copyright
===================================================================
--- trunk/packages/spades/trunk/debian/copyright	2014-02-14 10:47:49 UTC (rev 16043)
+++ trunk/packages/spades/trunk/debian/copyright	2014-02-14 12:22:03 UTC (rev 16044)
@@ -1,13 +1,60 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: SPAdes
 Source: http://spades.bioinf.spbau.ru/
+Files-Excluded:
+    ext/include/boost
+    ext/src/python_libs
 
 Files: *
-Copyright: © 2011-2013 Saint-Petersburg Academic University
+Copyright: 2011-2013 Saint-Petersburg Academic University
 License: GPLv2+
 
+Files: ext/include/ConsensusCore/*
+Copyright: 2011-2013, Pacific Biosciences of California, Inc.
+License: BSDlike
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted (subject to the limitations in the
+ disclaimer below) provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided
+   with the distribution.
+ .
+ * Neither the name of Pacific Biosciences nor the names of its
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+ .
+ NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+ GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+ BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+Comment: This is a code copy from
+    https://github.com/PacificBiosciences/ConsensusCore
+  It might make sense to package this for Debian separately since it is
+  in the field of Debian Med
+
+Files: ext/include/otkpp/*
+Copyright: pulkkins at gmail.com
+License: GPLv3+
+Comment: This is a code copy from
+    http://code.google.com/p/otkpp/
+
 Files: debian/*
-Copyright: © 2014 Andreas Tille <tille at debian.org>
+Copyright: 2014 Andreas Tille <tille at debian.org>
 License: GPLv2+
 
 License: GPLv2+
@@ -27,3 +74,21 @@
  .
  On Debian systems you can find the full test of the GNU General Public
  License version 2 at /usr/share/common-licenses/GPL-2.
+
+License: GPLv3+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or
+    (at your option) any later version.
+ .
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+ .
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ On Debian systems you can find the full test of the GNU General Public
+ License version 3 at /usr/share/common-licenses/GPL-3.

Modified: trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch	2014-02-14 10:47:49 UTC (rev 16043)
+++ trunk/packages/spades/trunk/debian/patches/do_not_install_third_party_libs.patch	2014-02-14 12:22:03 UTC (rev 16044)
@@ -1,3 +1,10 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Wed, 05 Feb 2014 15:12:36 +0100
+Description: SPAdes originally contained code copies of
+ python-yaml and python-joblib.  These code copies are removed
+ and this patch is just fixing the cmake input file
+
+
 --- a/ext/src/CMakeLists.txt
 +++ b/ext/src/CMakeLists.txt
 @@ -2,9 +2,5 @@

Modified: trunk/packages/spades/trunk/debian/patches/series
===================================================================
--- trunk/packages/spades/trunk/debian/patches/series	2014-02-14 10:47:49 UTC (rev 16043)
+++ trunk/packages/spades/trunk/debian/patches/series	2014-02-14 12:22:03 UTC (rev 16044)
@@ -1,3 +1,4 @@
 do_not_install_third_party_libs.patch
 adapt_to_debian_pathes.patch
 use_debian_packaged_python-yaml.patch
+use_debian-packaged_boost.patch

Added: trunk/packages/spades/trunk/debian/patches/use_debian-packaged_boost.patch
===================================================================
--- trunk/packages/spades/trunk/debian/patches/use_debian-packaged_boost.patch	                        (rev 0)
+++ trunk/packages/spades/trunk/debian/patches/use_debian-packaged_boost.patch	2014-02-14 12:22:03 UTC (rev 16044)
@@ -0,0 +1,22 @@
+uthor: Andreas Tille <tille at debian.org>
+Last-Changed: Wed, 05 Feb 2014 15:12:36 +0100
+Description: SPAdes originally contained code copies of boost
+  header files.  The code copy was removed and this patch forces
+  cmake to use the correct include dir of boost
+
+--- a/src/cmake/deps.cmake
++++ b/src/cmake/deps.cmake
+@@ -19,11 +19,7 @@ find_package(Readline QUIET)
+ set(CURSES_NEED_NCURSES TRUE)
+ find_package(Curses QUIET)
+ 
+-# Use included boost unless explicitly specified
+-if (NOT SPADES_BOOST_ROOT)
+-  set(BOOST_ROOT "${EXT_DIR}/include")
+-else()
+-  set(BOOST_ROOT SPADES_BOOST_ROOT)
+-endif()
++# Use Debian packaged boost
++set(BOOST_ROOT "/usr/include")
+ set(Boost_USE_MULTITHREADED ON)
+ find_package(Boost REQUIRED)

Modified: trunk/packages/spades/trunk/debian/rules
===================================================================
--- trunk/packages/spades/trunk/debian/rules	2014-02-14 10:47:49 UTC (rev 16043)
+++ trunk/packages/spades/trunk/debian/rules	2014-02-14 12:22:03 UTC (rev 16044)
@@ -9,6 +9,16 @@
 PREFIX:=/usr
 BUILD_DIR:=build_spades
 
+DEB_CMAKE_EXTRA_FLAGS = \
+              -DCMAKE_INSTALL_PREFIX:PATH=/usr \
+              -DCMAKE_BUILD_TYPE:STRING=Release \
+              -DCMAKE_CXX_FLAGS="-Wno-deprecated $(CXXFLAGS)" \
+              -DCMAKE_VERBOSE_MAKEFILE=$(DH_VERBOSE) \
+              -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--as-needed $(LDFLAGS)" \
+              -DCMAKE_EXE_LINKER_FLAGS="-Wl,--as-needed $(LDFLAGS)" \
+              -DCMAKE_SKIP_RPATH:BOOL=ON \
+
+
 %:
 	dh $@  --with python2 --sourcedirectory=src --buildsystem=cmake
 

Modified: trunk/packages/spades/trunk/debian/watch
===================================================================
--- trunk/packages/spades/trunk/debian/watch	2014-02-14 10:47:49 UTC (rev 16043)
+++ trunk/packages/spades/trunk/debian/watch	2014-02-14 12:22:03 UTC (rev 16044)
@@ -1,3 +1,3 @@
 version=3
-opts="downloadurlmangle=s{release([\d.]+)/}{release${1}/SPAdes-${1}.tar.gz},filenamemangle=s{release([\d.]+)/}{SPAdes-${1}.tar.gz}" \
+opts="downloadurlmangle=s{release([\d.]+)/}{release${1}/SPAdes-${1}.tar.gz},filenamemangle=s{release([\d.]+)/}{SPAdes-${1}.tar.gz},dversionmangle=s/\+dfsg//" \
   http://spades.bioinf.spbau.ru/ release([\d.]+)/

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