[med-svn] [Git][med-team/ugene][master] 2 commits: Refresh patches against new upstream version
Tony Mancill
gitlab at salsa.debian.org
Fri Dec 4 20:39:55 GMT 2020
Tony Mancill pushed to branch master at Debian Med / ugene
Commits:
18dfc8c7 by tony mancill at 2020-12-04T11:49:56-08:00
Refresh patches against new upstream version
- - - - -
34aabe2f by tony mancill at 2020-12-04T12:39:00-08:00
interim changelog
- - - - -
5 changed files:
- debian/changelog
- debian/patches/add_missing_header.patch
- debian/patches/do_not_build_phylip.patch
- debian/patches/hardening.patch
- debian/patches/use_debian_sqlite.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,15 @@
ugene (36.0+dfsg-1) UNRELEASED; urgency=medium
[ Steffen Moeller ]
- * New upstream version
+ * New upstream version (Closes: #974075)
* TODO: package new runtime dependencies: clark, wevote
[ Andreas Tille ]
* debhelper-compat 13 (routine-update)
+ [ tony mancill ]
+ * Refresh patches for new upstream version
+
-- Andreas Tille <tille at debian.org> Tue, 10 Nov 2020 09:12:24 +0100
ugene (34.0+dfsg-1) unstable; urgency=medium
=====================================
debian/patches/add_missing_header.patch
=====================================
@@ -2,15 +2,13 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
Description: Fix build issue by adding missing headers
-Index: ugene/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
-===================================================================
---- ugene.orig/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
-+++ ugene/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
-@@ -20,6 +20,7 @@
- */
+--- a/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
++++ b/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
+@@ -22,6 +22,7 @@
+ #include "SlidingWindowStep.h"
#include <U2Core/U2SafePoints.h>
+#include <QIntValidator>
#include "trimmomatic/util/LineEditHighlighter.h"
- #include "SlidingWindowStep.h"
+
=====================================
debian/patches/do_not_build_phylip.patch
=====================================
@@ -5,7 +5,7 @@ Description: Do not build phylip plugin which is removed since
--- a/ugene.pro
+++ b/ugene.pro
-@@ -45,7 +45,6 @@ SUBDIRS += \
+@@ -34,7 +34,6 @@
src/plugins_3rdparty/gor4 \
src/plugins_3rdparty/psipred \
src/plugins_3rdparty/primer3 \
=====================================
debian/patches/hardening.patch
=====================================
@@ -8,13 +8,11 @@ Description: add QMAKE flags to add hardening
Last-Updated: 2015-12-10
Forwarded: no
-Index: ugene/src/ugene_globals.pri
-===================================================================
---- ugene.orig/src/ugene_globals.pri
-+++ ugene/src/ugene_globals.pri
-@@ -9,6 +9,11 @@ DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MI
-
- CONFIG += c++11
+--- a/src/ugene_globals.pri
++++ b/src/ugene_globals.pri
+@@ -14,6 +14,11 @@
+ # use -Wl,-rpath to locate dependencies for own libraries.
+ unix:!macx: CONFIG += unversioned_libname unversioned_soname
+CFLAGS += $(CFLAGS)
+CXXFLAGS += $(CXXFLAGS)
@@ -24,7 +22,7 @@ Index: ugene/src/ugene_globals.pri
# NGS package
_UGENE_NGS = $$(UGENE_NGS)
contains(_UGENE_NGS, 1) : DEFINES += UGENE_NGS
-@@ -55,6 +60,10 @@ linux-g++ {
+@@ -79,6 +84,10 @@
}
}
=====================================
debian/patches/use_debian_sqlite.patch
=====================================
@@ -4,10 +4,8 @@ Description: Tried to use Debian packages sqlite3
but failed because package does not build that way
Forwarded: no
Last-Updated: 2013-11-30
-Index: ugene/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
-===================================================================
---- ugene.orig/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
-+++ ugene/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
+--- a/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
++++ b/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
@@ -19,7 +19,7 @@
* MA 02110-1301, USA.
*/
@@ -17,23 +15,19 @@ Index: ugene/src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.cpp
#include <U2Core/Log.h>
#include <U2Core/U2SafePoints.h>
-Index: ugene/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
-===================================================================
---- ugene.orig/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
-+++ ugene/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
-@@ -25,7 +25,7 @@
- #include <U2Core/U2DbiUtils.h>
- #include <U2Core/U2SafePoints.h>
+--- a/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
++++ b/src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp
+@@ -20,7 +20,7 @@
+ */
+ #include "U2SqlHelpers.h"
-#include <3rdparty/sqlite3/sqlite3.h>
+#include <sqlite3.h>
- namespace U2 {
-
-Index: ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
-===================================================================
---- ugene.orig/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
-+++ ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
+ #include <U2Core/Log.h>
+ #include <U2Core/U2DbiUtils.h>
+--- a/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
++++ b/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
@@ -19,7 +19,7 @@
* MA 02110-1301, USA.
*/
@@ -43,10 +37,8 @@ Index: ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobInputStream.cpp
#include <U2Core/U2DbiUtils.h>
#include <U2Core/U2SafePoints.h>
-Index: ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
-===================================================================
---- ugene.orig/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
-+++ ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
+--- a/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
++++ b/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
@@ -19,7 +19,7 @@
* MA 02110-1301, USA.
*/
@@ -56,37 +48,31 @@ Index: ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteBlobOutputStream.cpp
#include <U2Core/U2SafePoints.h>
#include <U2Core/UdrSchema.h>
-Index: ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
-===================================================================
---- ugene.orig/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
-+++ ugene/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
-@@ -41,7 +41,7 @@
-
- #include <QFile>
+--- a/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
++++ b/src/corelibs/U2Formats/src/sqlite_dbi/SQLiteDbi.cpp
+@@ -20,7 +20,7 @@
+ */
+ #include "SQLiteDbi.h"
-#include <3rdparty/sqlite3/sqlite3.h>
+#include <sqlite3.h>
- namespace U2 {
+ #include <QFile>
-Index: ugene/src/plugins/dbi_bam/src/Dbi.cpp
-===================================================================
---- ugene.orig/src/plugins/dbi_bam/src/Dbi.cpp
-+++ ugene/src/plugins/dbi_bam/src/Dbi.cpp
-@@ -33,7 +33,7 @@
- #include <U2Core/U2OpStatusUtils.h>
- #include <U2Core/IOAdapterUtils.h>
+--- a/src/plugins/dbi_bam/src/Dbi.cpp
++++ b/src/plugins/dbi_bam/src/Dbi.cpp
+@@ -20,7 +20,7 @@
+ */
+ #include "Dbi.h"
-#include <3rdparty/sqlite3/sqlite3.h>
+#include <sqlite3.h>
- namespace U2 {
- namespace BAM {
-Index: ugene/src/ugene_globals.pri
-===================================================================
---- ugene.orig/src/ugene_globals.pri
-+++ ugene/src/ugene_globals.pri
-@@ -197,8 +197,8 @@ defineReplace(add_z_lib) {
+ #include <QDir>
+
+--- a/src/ugene_globals.pri
++++ b/src/ugene_globals.pri
+@@ -213,8 +213,8 @@
# To use locally installed sqlite library use UGENE_USE_BUNDLED_SQLITE = 0
defineTest( use_bundled_sqlite ) {
View it on GitLab: https://salsa.debian.org/med-team/ugene/-/compare/900e1aa53d6373f9b8a30dd1b98273749face948...34aabe2f227eeb7d9da016cc93f6c056530cb183
--
View it on GitLab: https://salsa.debian.org/med-team/ugene/-/compare/900e1aa53d6373f9b8a30dd1b98273749face948...34aabe2f227eeb7d9da016cc93f6c056530cb183
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201204/a64d57b7/attachment-0001.html>
More information about the debian-med-commit
mailing list