[med-svn] [Git][med-team/ugene][master] 12 commits: Restore "Use UGENE_USE_BUNDLED_ZLIB=0" change
Andreas Tille
gitlab at salsa.debian.org
Thu Jan 9 15:17:03 GMT 2020
Andreas Tille pushed to branch master at Debian Med / ugene
Commits:
6fdae67d by Andreas Tille at 2020-01-09T14:51:11+01:00
Restore "Use UGENE_USE_BUNDLED_ZLIB=0" change
- - - - -
7e5daa26 by Andreas Tille at 2020-01-09T14:54:27+01:00
Make more sensible changelog by moving items from unreleased paragraph to the released version
- - - - -
8459f61d by Andreas Tille at 2020-01-09T15:02:55+01:00
Since last upload was not accepted merge changelog entries
- - - - -
4f6dd854 by Andreas Tille at 2020-01-09T15:03:46+01:00
routine-update: debhelper-compat 12
- - - - -
3f7c4b1a by Andreas Tille at 2020-01-09T15:03:53+01:00
R-U: Trailing whitespace in debian/changelog
- - - - -
43814bfd by Andreas Tille at 2020-01-09T15:03:53+01:00
R-U: Trailing whitespace in debian/control
- - - - -
ecfd6e79 by Andreas Tille at 2020-01-09T15:03:54+01:00
R-U: Trailing whitespace in debian/copyright
- - - - -
49935fdf by Andreas Tille at 2020-01-09T15:04:12+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit.
- - - - -
93785021 by Andreas Tille at 2020-01-09T15:07:07+01:00
Moved TODO in d/changelog to README.source - otherwise these items might be vanish from sight
- - - - -
b4819efc by Andreas Tille at 2020-01-09T15:09:16+01:00
Close bugs, try again building with UGENE_USE_BUNDLED_ZLIB=0
- - - - -
29677a7b by Andreas Tille at 2020-01-09T15:10:44+01:00
Merge my own changes to one section
- - - - -
92b248fd by Andreas Tille at 2020-01-09T16:16:42+01:00
Upload to unstable
- - - - -
7 changed files:
- + debian/README.source
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/README.source
=====================================
@@ -0,0 +1,11 @@
+TODO:
+
+The package builds nicely but should experience some additional love
+and testing. To mind come:
+ - reduce size of binaries by link-time optimization
+ - be nice and reduce the one or other compile time warning, some of which
+ are apparently in the Qt code?!?
+ - add runtime tests
+ - add a Debian Wiki page for the package
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 14 Dec 2019 12:56:14 +0100
=====================================
debian/changelog
=====================================
@@ -1,33 +1,29 @@
ugene (33.0+dfsg-1) unstable; urgency=medium
+ [ Steffen Moeller ]
* New upstream version.
- * Standards-Version: 4.3.0 (no changes required)
+ Closes: #933334, #943514
+ * Standards-Version: 4.4.1 (no changes required)
* Adjusted patches
- Upstream now builds against regular sqlite almost by default
- - UGENE_USE_BUNDLED_ZLIB=0 has remaining problems - changed default
- to system sqlite by a patch
+ - changed default to system sqlite by a patch
- Adjusted paths for dh_shlibdeps
- * TODO: The package builds nicely but should experience some additional love
- and testing. To mind come:
- - reduce size of binaries by link-time optimization
- - be nice and reduce the one or other compile time warning, some of which
- are apparently in the Qt code?!?
- - add runtime tests
- - add a Debian Wiki page for the package
-
- -- Steffen Moeller <moeller at debian.org> Sat, 14 Dec 2019 12:56:14 +0100
-ugene (1.31.1+dfsg1-1) UNRELEASED; urgency=medium
-
- * Use UGENE_USE_BUNDLED_ZLIB=0
+ [ Andreas Tille ]
* Remove psipred from upstream source - it is excluded from build anyway
* d/watch: dversionmangle=auto (to accept +dfsg[0-9])
* Add external plugins to Recommends as far as these are packaged
* Clarification of license makes the whole code free
* Drop Ivan Efremov <iefremov at unipro.ru> from Uploaders (thanks for your
previous work on this package, Ivan)
+ * Use UGENE_USE_BUNDLED_ZLIB=0
+ * debhelper-compat 12
+ * Remove trailing whitespace in debian/changelog
+ * Remove trailing whitespace in debian/control
+ * Remove trailing whitespace in debian/copyright
+ * Set upstream metadata fields: Bug-Database, Bug-Submit.
- -- Andreas Tille <tille at debian.org> Fri, 01 Feb 2019 09:14:17 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 09 Jan 2020 15:11:09 +0100
ugene (1.31.1+dfsg-1) unstable; urgency=medium
@@ -114,7 +110,7 @@ ugene (1.19.0+dfsg-1) unstable; urgency=medium
* DEP5 fixes
[Gert Wollny]
- * Update to build with QT5 (thanks to Gianfranco Costamagna for the initial
+ * Update to build with QT5 (thanks to Gianfranco Costamagna for the initial
transition and pointing out some quirks)
* update d/p/use_system_sqlite.patch
@@ -169,7 +165,7 @@ ugene (1.9.5+repack-0ubuntu1~natty) natty; urgency=low
ugene (1.9.4+repack-0ubuntu1~maverick) maverick; urgency=low
* Latest release maverick build
-
+
-- Alexey Kuznecov <akuznecov at unipro.ru> Thu, 14 Jul 2011 21:15:23 +0700
ugene (1.9.4+repack-0ubuntu1~natty) natty; urgency=low
@@ -287,5 +283,5 @@ ugene (1.3.2+repack-0ubuntu1) jaunty; urgency=low
* Initial packaging (LP: #319917)
* Files unneeded for this package were removed from
the original tarball
-
+
-- Ivan Efremov <iefremov at unipro.ru> Mon, 26 Jan 2009 19:17:51 +0600
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -16,7 +16,7 @@ Build-Depends: qtbase5-dev,
qtchooser,
qttools5-dev,
zlib1g-dev,
- debhelper (>= 12~),
+ debhelper-compat (= 12),
libxtst-dev,
libsqlite3-dev,
libprocps-dev
@@ -61,9 +61,9 @@ Recommends: kraken,
vcftools
Suggests: cufflinks
Description: integrated bioinformatics toolkit
- Unipro UGENE is a cross-platform visual environment for DNA and protein
- sequence analysis. UGENE integrates the most important bioinformatics
- computational algorithms and provides an easy-to-use GUI for performing
+ Unipro UGENE is a cross-platform visual environment for DNA and protein
+ sequence analysis. UGENE integrates the most important bioinformatics
+ computational algorithms and provides an easy-to-use GUI for performing
complex analysis of the genomic data. One of the main features of UGENE
is a designer for custom bioinformatics workflows.
@@ -71,7 +71,7 @@ Package: ugene-data
Architecture: all
Depends: ${misc:Depends}
Description: required data for UGENE - integrated bioinformatics toolkit
- Unipro UGENE is a cross-platform visual environment for DNA and protein
- sequence analysis.
+ Unipro UGENE is a cross-platform visual environment for DNA and protein
+ sequence analysis.
.
- This package contains various data and example files for UGENE.
+ This package contains various data and example files for UGENE.
=====================================
debian/copyright
=====================================
@@ -132,7 +132,7 @@ License: LGPL-2.1
This library 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
- Lesser General Public License for more details.
+ Lesser General Public License for more details.
.
On Debian systems, see /usr/share/common-licenses/LGPL-2.1 for the
full text of the license.
@@ -166,27 +166,27 @@ License: BSD+Khronos
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,
+ Redistribution and use in source and binary forms, with or without modification,
are permitted 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 Jochen Kalmbach nor the names of its contributors may be
- used to endorse or promote products derived from this software without
+ 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 Jochen Kalmbach 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,
- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND 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; 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
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND 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 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; 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/libs_3rdparty/breakpad/src/common/convert_UTF.c src/libs_3rdparty/breakpad/src/common/convert_UTF.h
@@ -200,9 +200,9 @@ License: Unicode
copy, modify, merge, publish, distribute, and/or sell copies of
the Data Files or Software, and to permit persons to whom the Data Files
or Software are furnished to do so, provided that
- (a) this copyright and permission notice appear with all copies
+ (a) this copyright and permission notice appear with all copies
of the Data Files or Software,
- (b) this copyright and permission notice appear in associated
+ (b) this copyright and permission notice appear in associated
documentation, and
(c) there is clear notice in each modified Data File or in the Software
as well as in the documentation associated with the Data File(s) or
=====================================
debian/rules
=====================================
@@ -13,8 +13,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
override_dh_auto_configure:
# exclude non-free plugins
- dh_auto_configure -- QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5
- #UGENE_USE_BUNDLED_ZLIB=0
+ dh_auto_configure -- QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 UGENE_USE_BUNDLED_ZLIB=0
find . -name Makefile.* | xargs -r sed -i '/STRIP/d'
=====================================
debian/upstream/metadata
=====================================
@@ -1,53 +1,54 @@
Reference:
- - Author: >
+- Author: >
Konstantin Okonechnikov and Olga Golosova and Mikhail Fursov
and the UGENE team
- Title: "Unipro UGENE: a unified bioinformatics toolkit"
- Journal: Bioinformatics
- Year: 2012
- Volume: 28
- Number: 8
- Pages: 1166-1167
- DOI: 10.1093/bioinformatics/bts091
- PMID: 22368248
- URL: http://bioinformatics.oxfordjournals.org/content/28/8/1166
- eprint: "http://bioinformatics.oxfordjournals.org/content/\
- 28/8/1166.full.pdf+html"
- - Author: >
+ Title: 'Unipro UGENE: a unified bioinformatics toolkit'
+ Journal: Bioinformatics
+ Year: 2012
+ Volume: 28
+ Number: 8
+ Pages: 1166-1167
+ DOI: 10.1093/bioinformatics/bts091
+ PMID: 22368248
+ URL: http://bioinformatics.oxfordjournals.org/content/28/8/1166
+ eprint: http://bioinformatics.oxfordjournals.org/content/28/8/1166.full.pdf+html
+- Author: >
Olga Golosova1 and Ross Henderson and Yuriy Vaskin and Andrei
Gabrielian and German Grekhov and Vijayaraj Nagarajan and Andrew
J. Oler and Mariam Quiñones and Darrell Hurt and Mikhail Fursov
and Yentram Huyen
- Title: >
+ Title: >
Unipro UGENE NGS pipelines and components for variant calling,
RNA-seq and ChIP-seq data analyses.
- Journal: PeerJ
- Year: 2014
- Volume: 2
- Pages: e644
- DOI: 10.7717/peerj.644
- URL: https://peerj.com/articles/644/
- ePrint: https://peerj.com/articles/644.pdf
- - Author: >
+ Journal: PeerJ
+ Year: 2014
+ Volume: 2
+ Pages: e644
+ DOI: 10.7717/peerj.644
+ URL: https://peerj.com/articles/644/
+ ePrint: https://peerj.com/articles/644.pdf
+- Author: >
Rebecca Rose and Olga Golosova and Dmitrii Sukhomlinov and Aleksey
Tiunov and Mattia Prosperi
- URL: >
+ URL: >
https://doi.org/10.1093/bioinformatics/bty901
- DOI: 10.1093/bioinformatics/bty901
- Title: >
+ DOI: 10.1093/bioinformatics/bty901
+ Title: >
Flexible design of multiple metagenomics classification pipelines
with UGENE.
- Journal: Bioinformatics
- Volume: bty901
- Year: 2018
- Month: 10
- Day: 25
+ Journal: Bioinformatics
+ Volume: bty901
+ Year: 2018
+ Month: 10
+ Day: 25
Registry:
- - Name: OMICtools
- Entry: OMICS_01022
- - Name: bio.tools
- Entry: ugene
- - Name: conda:bioconda
- Entry: NA
- - Name: SciCrunch
- Entry: SCR_005579
+- Name: OMICtools
+ Entry: OMICS_01022
+- Name: bio.tools
+ Entry: ugene
+- Name: conda:bioconda
+ Entry: NA
+- Name: SciCrunch
+ Entry: SCR_005579
+Bug-Database: https://github.com/ugeneunipro/ugene/issues
+Bug-Submit: https://github.com/ugeneunipro/ugene/issues/new
View it on GitLab: https://salsa.debian.org/med-team/ugene/compare/d717b9f62614bb8921bd61e68a58cbb782ca664e...92b248fd9ddb1f567363a7345be4ef08f2ae3a6e
--
View it on GitLab: https://salsa.debian.org/med-team/ugene/compare/d717b9f62614bb8921bd61e68a58cbb782ca664e...92b248fd9ddb1f567363a7345be4ef08f2ae3a6e
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