debian/changelog

@@ -13,6 +13,7 @@ ugene (1.31.1+dfsg-1) UNRELEASED; urgency=medium
   * More Files-Excluded
   * debhelper 12
   * Point Vcs fields to salsa.debian.org
+  * Drop unused lintian-overrides
 
  -- Andreas Tille <tille@debian.org>  Sun, 03 Dec 2017 19:10:03 +0100
 

debian/copyright

@@ -168,44 +168,6 @@ License: BSD-3-clause
     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
     OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-Files: src/plugins_3rdparty/hmm3/src/hmmer3/*
-Copyright: © 2000-2009 Howard Hughes Medical Institute (and others)
-License: GPL-3+
-
-Files: src/plugins_3rdparty/hmm3/src/hmmer3/easel/*
-Copyright: © 2006-2009 Howard Hughes Medical Institute (and others)
-License: JaneliaFarm
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are
- met:
- .
- 1. Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
- .
- 2. 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.
- .
- 3. Neither the name of the Howard Hughes Medical Institute nor the
-    names of its contributors may be used to endorse or promote
-    products derived from this software without specific prior written
-    permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,
- NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR 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;
- REASONABLE ROYALTIES; 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.
-
 Files: src/plugins/biostruct3d_view/src/gl2ps/*
 Copyright: © 1999-2006 Christophe Geuzaine <geuz@geuz.org>
 License: GPL-2+
@@ -263,7 +225,7 @@ License: BSD+Khronos
  TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
  MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
 
-Files: src/corelibs/U2Private/src/StackWalker.*
+Files: src/corelibs/U2Private/src/crash_handler/StackWalker.*
 Copyright: © 2005-2011 Jochen Kalmbach
 License: BSD-2-clause
  Redistribution and use in source and binary forms, with or without modification, 

debian/patches/add_missing_header.patch

 Author:  Andreas Tille <tille@debian.org>
-Last-Update: Sun, 03 Dec 2017 19:10:03 +0100
+Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
 Description: Fix build issue by adding missing headers
 
 --- a/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp

debian/patches/debian_packaged_libs.patch

 Author:  Andreas Tille <tille@debian.org>
-Last-Update: Sun, 03 Dec 2017 19:10:03 +0100
+Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
 Description: Replace zlib and sqlite3 by Debian packaged libs
 
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -35,8 +35,6 @@ set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS
- # 3rd party libs
- add_subdirectory(src/libs_3rdparty/breakpad)
- add_subdirectory(src/libs_3rdparty/samtools)
--add_subdirectory(src/libs_3rdparty/sqlite3)
--add_subdirectory(src/libs_3rdparty/zlib)
- 
- # Core libs
- add_subdirectory(src/corelibs/U2Core)
 --- a/src/libs_3rdparty/samtools/src/samtools/bam.h
 +++ b/src/libs_3rdparty/samtools/src/samtools/bam.h
 @@ -61,7 +61,7 @@ typedef BGZF *bamFile;

debian/patches/do_not_build_phylip.patch

 Author:  Andreas Tille <tille@debian.org>
-Last-Update: Sun, 03 Dec 2017 19:10:03 +0100
+Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
 Description: Do not build phylip plugin which is removed since
  the code copy of the old version has no free license
 

debian/patches/fix_desktop_file.patch

+Author:  Andreas Tille <tille@debian.org>
+Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
+Description: Add exec code for mime in desktop file
+
+--- a/installer/_common_data/ugene.desktop
++++ b/installer/_common_data/ugene.desktop
+@@ -5,6 +5,6 @@ GenericName=Unipro UGENE
+ Terminal=false
+ Icon=ugene
+ Type=Application
+-Exec=ugene -ui
++Exec=ugene -ui %f
+ Categories=Education;Science;
+ MimeType=application/x-ugene-fa;application/x-ugene-uprj;application/x-ugene-uwl;application/x-ugene-uql;application/x-ugene-abi;application/x-ugene-aln;application/x-ugene-embl;application/x-ugene-sw;application/x-ugene-fastq;application/x-ugene-gb;application/x-ugene-gff;application/x-ugene-msf;application/x-ugene-newick;application/x-ugene-pdb;application/x-ugene-sam-bam;application/x-ugene-srfa;application/x-ugene-sto;application/x-ugene-db;application/x-ugene-scf;application/x-ugene-mmdb;application/x-ugene-hmm;

debian/patches/series

@@ -3,3 +3,4 @@ hardening.patch
 debian_packaged_libs.patch
 add_missing_header.patch
 do_not_build_phylip.patch
+fix_desktop_file.patch

debian/ugene-data.lintian-overrides

-# Suppress false positives since the package contains byte identical files taken over from upstream tarball
-ugene-data: package-contains-timestamped-gzip usr/share/ugene/data/sitecon_models/*/*.sitecon.gz
-ugene-data: package-contains-timestamped-gzip usr/share/ugene/data/enzymes/2013_08_01.bairoch.gz
-ugene-data: package-contains-timestamped-gzip usr/share/ugene/data/samples/CLUSTALW/ty3.aln.gz

debian/ugene.install

@@ -3,3 +3,4 @@ usr/lib/ugene
 usr/share/applications
 usr/share/pixmaps
 usr/share/mime
+usr/share/icons