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commit 2c566bf8538703db2d869f726e86f7aa4b276200 Author: Andreas Tille <ti...@debian.org> Date: Sun Sep 17 07:24:30 2017 +0200 DEP3; removed unused patches --- debian/changelog | 1 + debian/patches/examples.patch | 70 ------------------------------------- debian/patches/functional.patch | 10 +++--- debian/patches/hdf5include.patch | 10 +++--- debian/patches/relative-paths.patch | 17 --------- debian/patches/rpath.patch | 6 ++-- debian/patches/series | 2 -- 7 files changed, 15 insertions(+), 101 deletions(-) diff --git a/debian/changelog b/debian/changelog index 199761d..4ed7bd6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -4,6 +4,7 @@ fast5 (0.6.2-5) UNRELEASED; urgency=medium * Fix clean target * Create dir before moving files Closes: #875991 + * DEP3 -- Andreas Tille <ti...@debian.org> Sun, 17 Sep 2017 07:15:13 +0200 diff --git a/debian/patches/examples.patch b/debian/patches/examples.patch deleted file mode 100644 index 0b07aa9..0000000 --- a/debian/patches/examples.patch +++ /dev/null @@ -1,70 +0,0 @@ -Description: Adapt examples for Debian package - The location of the fast5 hdf header file is slightly different and - the HDF library/header locations are different. -Author: Afif Elghraoui <a...@debian.org> -Forwarded: not-needed -Last-Update: 2016-10-20 ---- fast5.orig/src/Makefile -+++ fast5/src/Makefile -@@ -4,12 +4,12 @@ - .DELETE_ON_ERROR: - .PHONY: all help list clean check_hdf5 - --HDF5_DIR = /usr/local --HDF5_INCLUDE_DIR = ${HDF5_DIR}/include --HDF5_LIB_DIR = ${HDF5_DIR}/lib -+HDF5_DIR = /usr -+HDF5_INCLUDE_DIR ?= ${HDF5_DIR}/include/hdf5/serial -+HDF5_LIB_DIR ?= $(wildcard ${HDF5_DIR}/lib/*/hdf5/serial) - HDF5_LIB = hdf5 --TCLAP_DIR = tclap --HPPTOOLS_DIR = hpptools -+TCLAP_DIR ?= tclap -+HPPTOOLS_DIR ?= hpptools - - TARGETS = f5ls f5ls-full hdf5-mod f5-mod - -@@ -37,8 +37,8 @@ - check_hpptools: - @[ -f "${HPPTOOLS_DIR}/include/alg.hpp" ] || { echo "HPPTOOLS not found; get it from https://github.com/mateidavid/hpptools.git" >&2; exit 1; } - --%: %.cpp fast5.hpp hdf5_tools.hpp | check_hdf5 -- ${CXX} -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem ${HDF5_INCLUDE_DIR} -o $@ $< -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl -+%: %.cpp | check_hdf5 -+ ${CXX} ${CPPFLAGS} ${CXXFLAGS} -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem ${HDF5_INCLUDE_DIR} -o $@ $< -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl - - f5dump: f5dump.cpp fast5.hpp hdf5_tools.hpp | check_hdf5 check_tclap check_hpptools - ${CXX} -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem ${HDF5_INCLUDE_DIR} -isystem ${TCLAP_DIR}/include -I ${HPPTOOLS_DIR}/include -o $@ $< -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl ---- fast5.orig/src/hdf5-mod.cpp -+++ fast5/src/hdf5-mod.cpp -@@ -2,7 +2,7 @@ - #include <iostream> - #include <string> - --#include "hdf5_tools.hpp" -+#include <fast5/hdf5_tools.hpp> - - using namespace std; - using namespace hdf5; ---- fast5.orig/src/f5dump.cpp -+++ fast5/src/f5dump.cpp -@@ -6,7 +6,7 @@ - #include <tclap/CmdLine.h> - #include "alg.hpp" - --#include "fast5.hpp" -+#include <fast5.hpp> - - using namespace std; - ---- fast5.orig/src/f5ls-full.cpp -+++ fast5/src/f5ls-full.cpp -@@ -2,7 +2,7 @@ - #include <iostream> - #include <string> - --#include "fast5.hpp" -+#include <fast5.hpp> - - using namespace std; - diff --git a/debian/patches/functional.patch b/debian/patches/functional.patch index bca2b63..11b2d86 100644 --- a/debian/patches/functional.patch +++ b/debian/patches/functional.patch @@ -1,7 +1,9 @@ -Index: fast5/src/logger.hpp -=================================================================== ---- fast5.orig/src/logger.hpp -+++ fast5/src/logger.hpp +Author: Steffen Moeller +Last-Update: 2017-09-15 14:17:53 +0200 +Description: Add missing header + +--- a/src/logger.hpp ++++ b/src/logger.hpp @@ -72,6 +72,7 @@ #include <iostream> #include <mutex> diff --git a/debian/patches/hdf5include.patch b/debian/patches/hdf5include.patch index 6dd31ea..9b2f86a 100644 --- a/debian/patches/hdf5include.patch +++ b/debian/patches/hdf5include.patch @@ -1,7 +1,9 @@ -Index: fast5/src/hdf5_tools.hpp -=================================================================== ---- fast5.orig/src/hdf5_tools.hpp -+++ fast5/src/hdf5_tools.hpp +Author: Steffen Moeller +Last-Update: 2017-09-15 14:17:53 +0200 +Description: Adapt hdf5 header files to Debian location + +--- a/src/hdf5_tools.hpp ++++ b/src/hdf5_tools.hpp @@ -27,7 +27,7 @@ namespace hdf5 diff --git a/debian/patches/relative-paths.patch b/debian/patches/relative-paths.patch deleted file mode 100644 index e990a89..0000000 --- a/debian/patches/relative-paths.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: Adjust include statement for relocation of auxiliary header - Moving the auxiliary header file to a subdirectory of usr/include - requires modifying the include statement in fast5.hpp. -Author: Afif Elghraoui <a...@ghraoui.name> -Forwarded: not-needed -Last-Update: 2016-01-19 ---- fast5.orig/src/fast5.hpp -+++ fast5/src/fast5.hpp -@@ -14,7 +14,7 @@ - #include <set> - #include <map> - --#include "hdf5_tools.hpp" -+#include <fast5/hdf5_tools.hpp> - #define MAX_K_LEN 8 - - namespace diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch index 0bd2438..b0c6612 100644 --- a/debian/patches/rpath.patch +++ b/debian/patches/rpath.patch @@ -2,10 +2,8 @@ Description: Don't set RPATH for compiled Python extensions Author: Afif Elghraoui <a...@debian.org> Forwarded: not-needed Last-Update: 2016-10-20 -Index: fast5/python/setup.py -=================================================================== ---- fast5.orig/python/setup.py -+++ fast5/python/setup.py +--- a/python/setup.py ++++ b/python/setup.py @@ -53,7 +53,7 @@ extensions = [ sources=['fast5/fast5.' + ['cpp', 'pyx'][use_cython]], include_dirs=[fast5_src_dir], diff --git a/debian/patches/series b/debian/patches/series index 2f38c1c..4398c1d 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,5 +1,3 @@ -#relative-paths.patch -#examples.patch rpath.patch functional.patch hdf5include.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fast5.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit