[med-svn] [fast5] 01/02: DEP3; removed unused patches
Andreas Tille
tille at debian.org
Sun Sep 17 05:32:30 UTC 2017
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tille pushed a commit to branch master
in repository fast5.
commit 2c566bf8538703db2d869f726e86f7aa4b276200
Author: Andreas Tille <tille at 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 <tille at 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 <afif at 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 <afif at 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 <afif at 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
--
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