Andreas Tille pushed to branch master at Debian Med / ugene
Commits: 9c892061 by Andreas Tille at 2019-01-31T18:15:31Z Install icon - - - - - 12b89f9d by Andreas Tille at 2019-01-31T20:12:27Z Drop unused lintian-overrides - - - - - 3addfa78 by Andreas Tille at 2019-01-31T20:16:46Z Add exec code for mime in desktop file - - - - - 2fb0ac5d by Andreas Tille at 2019-01-31T20:25:45Z Fix PATHes in d/copyright - - - - - 9 changed files: - debian/changelog - debian/copyright - debian/patches/add_missing_header.patch - debian/patches/debian_packaged_libs.patch - debian/patches/do_not_build_phylip.patch - + debian/patches/fix_desktop_file.patch - debian/patches/series - − debian/ugene-data.lintian-overrides - debian/ugene.install Changes: ===================================== 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 <[email protected]> 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 <[email protected]> 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 ===================================== @@ -1,5 +1,5 @@ Author: Andreas Tille <[email protected]> -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 ===================================== @@ -1,18 +1,7 @@ Author: Andreas Tille <[email protected]> -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 ===================================== @@ -1,5 +1,5 @@ Author: Andreas Tille <[email protected]> -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 ===================================== @@ -0,0 +1,14 @@ +Author: Andreas Tille <[email protected]> +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 deleted ===================================== @@ -1,4 +0,0 @@ -# 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 View it on GitLab: https://salsa.debian.org/med-team/ugene/compare/d0b128d7d258166e2176a756c611281c491195fb...2fb0ac5dd244cf1832f7f02a929826c6b6818739 -- View it on GitLab: https://salsa.debian.org/med-team/ugene/compare/d0b128d7d258166e2176a756c611281c491195fb...2fb0ac5dd244cf1832f7f02a929826c6b6818739 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
