[med-svn] [Git][med-team/biobambam2][master] 8 commits: routine-update: New upstream version

Sun Jan 1 21:30:51 GMT 2023


Étienne Mollier pushed to branch master at Debian Med / biobambam2


Commits:
6795d436 by Étienne Mollier at 2023-01-01T17:29:56+01:00
routine-update: New upstream version

- - - - -
3393d89e by Étienne Mollier at 2023-01-01T17:30:06+01:00
New upstream version 2.0.185+ds
- - - - -
0d1f1e02 by Étienne Mollier at 2023-01-01T17:30:07+01:00
Update upstream source from tag 'upstream/2.0.185+ds'

Update to upstream version '2.0.185+ds'
with Debian dir 52f2da88bd516dc08908e35dab50f984ec5aa533
- - - - -
9f0998e1 by Étienne Mollier at 2023-01-01T17:30:07+01:00
routine-update: Standards-Version: 4.6.2

- - - - -
1db7d4ef by Étienne Mollier at 2023-01-01T17:30:15+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit.

Changes-By: lintian-brush

- - - - -
f727e134 by Étienne Mollier at 2023-01-01T17:52:40+01:00
d/copyright: update copyright year.

- - - - -
daeec686 by Étienne Mollier at 2023-01-01T22:28:27+01:00
d/control: build depend on libxerces-c-dev.

This provides the blastnxmltobam program.

- - - - -
d140e627 by Étienne Mollier at 2023-01-01T22:30:17+01:00
ready to upload to unstable.

- - - - -


10 changed files:

- ChangeLog
- config.h.in
- configure.ac
- debian/changelog
- debian/control
- debian/copyright
- debian/upstream/metadata
- src/biobambam2/Licensing.hpp
- src/biobambam2/ReadHeader.hpp
- src/biobambam2/UpdateNumericalIndex.hpp


Changes:

=====================================
ChangeLog
=====================================
@@ -1,3 +1,9 @@
+biobambam2 (2.0.185-1) unstable; urgency=medium
+
+  * Add missing include directives for gcc13
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de>  Sun, 11 Dec 2022 13:21:00 +0100
+
 biobambam2 (2.0.184-1) unstable; urgency=medium
 
   * Add tagonly sort option in bamsort


=====================================
config.h.in
=====================================
@@ -6,12 +6,12 @@
 /* Define to 1 if you have the <inttypes.h> header file. */
 #undef HAVE_INTTYPES_H
 
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
 /* Define to 1 if you have the <stdint.h> header file. */
 #undef HAVE_STDINT_H
 
+/* Define to 1 if you have the <stdio.h> header file. */
+#undef HAVE_STDIO_H
+
 /* Define to 1 if you have the <stdlib.h> header file. */
 #undef HAVE_STDLIB_H
 
@@ -54,7 +54,9 @@
 /* Define to the version of this package. */
 #undef PACKAGE_VERSION
 
-/* Define to 1 if you have the ANSI C header files. */
+/* Define to 1 if all of the C90 standard headers exist (not just the ones
+   required in a freestanding environment). This macro is provided for
+   backward compatibility; new code need not use it. */
 #undef STDC_HEADERS
 
 /* Version number of package */


=====================================
configure.ac
=====================================
@@ -1,4 +1,4 @@
-AC_INIT(biobambam2,2.0.184,[germant at miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])
+AC_INIT(biobambam2,2.0.185,[germant at miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])
 AC_CANONICAL_SYSTEM
 AC_PROG_LIBTOOL
 


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+biobambam2 (2.0.185+ds-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.6.2 (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
+  * d/copyright: update copyright year.
+  * d/control: build depend on libxerces-c-dev; provide blastnxmltobam.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 01 Jan 2023 22:29:25 +0100
+
 biobambam2 (2.0.184+ds-1) unstable; urgency=medium
 
   * d/t/run-unit-test: skip bamsormadup test on i386; allows substancial


=====================================
debian/control
=====================================
@@ -6,8 +6,9 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                pkg-config,
-               libmaus2-dev (>= 2.0.800)
-Standards-Version: 4.6.1
+               libmaus2-dev (>= 2.0.800),
+               libxerces-c-dev
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/biobambam2
 Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git
 Homepage: https://gitlab.com/german.tischler/biobambam2


=====================================
debian/copyright
=====================================
@@ -27,7 +27,7 @@ Files-Excluded:
 
 
 Files: *
-Copyright: 2013-2019 German Tischler <tischler at mpi-cbg.de>
+Copyright: 2013-2022 German Tischler <tischler at mpi-cbg.de>
            2011-2016 Genome Research Limited
 License: GPL-3+
 
@@ -69,6 +69,7 @@ License: GPL-3+
 
 Files: debian/*
 Copyright: 2019 Andreas Tille <tille at debian.org>
+           2020-2023 Étienne Mollier <emollier at debian.org>
 License: GPL-3+
 
 License: GPL-3+


=====================================
debian/upstream/metadata
=====================================
@@ -1,5 +1,5 @@
-Bug-Database: https://gitlab.com/german.tischler/biobambam2/issues
-Bug-Submit: https://gitlab.com/german.tischler/biobambam2/issues/new
+Bug-Database: https://gitlab.com/german.tischler/biobambam2/-/issues
+Bug-Submit: https://gitlab.com/german.tischler/biobambam2/-/issues/new
 Repository: https://gitlab.com/german.tischler/biobambam2.git
 Repository-Browse: https://gitlab.com/german.tischler/biobambam2/ 
 Reference:


=====================================
src/biobambam2/Licensing.hpp
=====================================
@@ -19,6 +19,7 @@
 #if ! defined(LICENSEMESSAGE_HPP)
 #define LICENSEMESSAGE_HPP
 
+#include <cstdint>
 #include <string>
 #include <vector>
 #include <map>


=====================================
src/biobambam2/ReadHeader.hpp
=====================================
@@ -18,6 +18,7 @@
 #if ! defined(BIOBAMBAM2_READHER_HPP)
 #define BIOBAMBAM2_READHER_HPP
 
+#include <cstdint>
 #include <utility>
 #include <string>
 


=====================================
src/biobambam2/UpdateNumericalIndex.hpp
=====================================
@@ -20,6 +20,7 @@
 
 #include <string>
 #include <utility>
+#include <cstdint>
 
 namespace biobambam2
 {



View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/41211d249a26c176a5d54a89b9471bf146229d16...d140e62716c6cb4e4ad507b7f48b6bce8d549c2d

-- 
View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/41211d249a26c176a5d54a89b9471bf146229d16...d140e62716c6cb4e4ad507b7f48b6bce8d549c2d
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