[med-svn] [Git][med-team/fast5][master] 8 commits: initialize changelog

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / fast5


Commits:
5f75f5e1 by Étienne Mollier at 2022-06-26T14:03:20+02:00
initialize changelog

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b9a7fa7c by Étienne Mollier at 2022-06-26T14:03:49+02:00
d/control: add myself to uploaders.

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4100f65c by Étienne Mollier at 2022-06-26T14:28:54+02:00
Add gcc-12.patch: fix ftbfs with gcc-12.

Closes: #1012919

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c77149ee by Étienne Mollier at 2022-06-26T14:30:20+02:00
update changelog

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94e6a72b by Étienne Mollier at 2022-06-26T14:30:38+02:00
routine-update: Standards-Version: 4.6.1

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ae498238 by Étienne Mollier at 2022-06-26T14:40:15+02:00
Add build-flags.patch: propagate standard debian build flags.

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2a7e1910 by Étienne Mollier at 2022-06-26T14:40:42+02:00
d/rules: remove redundant build flag setting.

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2e5bc1dc by Étienne Mollier at 2022-06-26T14:43:24+02:00
ready to upload to unstable

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6 changed files:

- debian/changelog
- debian/control
- + debian/patches/build-flags.patch
- + debian/patches/gcc-12.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+fast5 (0.6.5-7) unstable; urgency=medium
+
+  * d/control: add myself to uploaders.
+  * Add gcc-12.patch: fix ftbfs with gcc-12. (Closes: #1012919)
+  * Standards-Version: 4.6.1 (routine-update)
+  * Add build-flags.patch: propagate standard debian build flags.
+  * d/rules: remove redundant build flag setting.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 26 Jun 2022 14:41:32 +0200
+
 fast5 (0.6.5-6) unstable; urgency=medium
 
   * Really fix watch file


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: fast5
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
@@ -11,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-setuptools,
                cython3,
                debhelper
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/fast5
 Vcs-Git: https://salsa.debian.org/med-team/fast5.git
 Homepage: https://github.com/mateidavid/fast5


=====================================
debian/patches/build-flags.patch
=====================================
@@ -0,0 +1,22 @@
+Description: propagate debian build flags.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-06-26
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- fast5.orig/src/Makefile
++++ fast5/src/Makefile
+@@ -23,10 +23,10 @@
+ EXTRA_TARGETS = f5dump f5pack
+ HPP_FILES := $(addprefix ${FAST5_DIR}/, fast5.hpp fast5/hdf5_tools.hpp fast5/Huffman_Packer.hpp fast5/Bit_Packer.hpp)
+ 
+-CXXFLAGS := -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic
+-CPPFLAGS := -isystem ${HDF5_INCLUDE_DIR} -I $(FAST5_DIR)
++CXXFLAGS += -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic
++CPPFLAGS += -isystem ${HDF5_INCLUDE_DIR} -I $(FAST5_DIR)
+ EXTRA_CPPFLAGS := -isystem ${TCLAP_DIR}/include -I ${HPPTOOLS_DIR}/include
+-LDFLAGS := -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl
++LDFLAGS += -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl
+ 
+ default: ${TARGETS}
+ 


=====================================
debian/patches/gcc-12.patch
=====================================
@@ -0,0 +1,17 @@
+Description: fix ftbfs with gcc-12
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012919
+Forwarded: https://github.com/mateidavid/fast5/pull/28
+Last-Update: 2022-06-26
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- fast5.orig/include/fast5/hdf5_tools.hpp
++++ fast5/include/fast5/hdf5_tools.hpp
+@@ -8,6 +8,7 @@
+ #ifndef __HDF5_TOOLS_HPP
+ #define __HDF5_TOOLS_HPP
+ 
++#include <array>
+ #include <cassert>
+ #include <cstring>
+ #include <exception>


=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
 rpath.patch
+gcc-12.patch
+build-flags.patch


=====================================
debian/rules
=====================================
@@ -10,8 +10,6 @@ export HDF5_INCLUDE_DIR=/usr/include/hdf5/serial
 export HDF5_LIB_DIR=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
 export BOOST_LIB_DIR=/usr/lib/$(DEB_HOST_MULTIARCH)
 
-export CXXFLAGS += -std=c++11
-
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:



View it on GitLab: https://salsa.debian.org/med-team/fast5/-/compare/faf3cc08dc727e4bd5bc0be2544d2e80afebf115...2e5bc1dc2625effa23f6f4da58ff19af25339430

-- 
View it on GitLab: https://salsa.debian.org/med-team/fast5/-/compare/faf3cc08dc727e4bd5bc0be2544d2e80afebf115...2e5bc1dc2625effa23f6f4da58ff19af25339430
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