[med-svn] [nanopolish] 06/09: Drop patches applied upstream

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository nanopolish.

commit 4a135b3269ec2a7446750057d30254fbfec48cc0
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Feb 4 16:10:27 2018 -0500

    Drop patches applied upstream
---
 debian/patches/compiler-flags.patch        | 27 ---------------------
 debian/patches/external-dependencies.patch | 38 ------------------------------
 debian/patches/series                      |  2 --
 3 files changed, 67 deletions(-)

diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch
deleted file mode 100644
index f5c0dc4..0000000
--- a/debian/patches/compiler-flags.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Description: Allow adding settings to standard compiler flags
- * Use CPPFLAGS for C source compilation
- * Use LDFLAGS
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: https://github.com/jts/nanopolish/pull/262
-Last-Update: 2017-11-10
---- nanopolish.orig/Makefile
-+++ nanopolish/Makefile
-@@ -116,15 +116,15 @@
- 	$(CXX) -o $@ -c $(CXXFLAGS) $(CPPFLAGS) -fPIC $<
- 
- .c.o:
--	$(CC) -o $@ -c $(CFLAGS) $(H5_INCLUDE) -fPIC $<
-+	$(CC) -o $@ -c $(CFLAGS) $(CPPFLAGS) $(H5_INCLUDE) -fPIC $<
- 
- # Link main executable
- $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(EIGEN_CHECK)
--	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS)
-+	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS)
- 
- # Link test executable
- $(TEST_PROGRAM): src/test/nanopolish_test.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB)
--	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS)
-+	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS)
- 
- test: $(TEST_PROGRAM)
- 	./$(TEST_PROGRAM)
diff --git a/debian/patches/external-dependencies.patch b/debian/patches/external-dependencies.patch
deleted file mode 100644
index eaac2f5..0000000
--- a/debian/patches/external-dependencies.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-Description: Allow for easily using externally-installed dependencies
- Allow for disabling builds of convenience copies without having to
- edit the Makefile to set options.
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: https://github.com/jts/nanopolish/pull/262
-Last-Update: 2017-11-10
---- nanopolish.orig/Makefile
-+++ nanopolish/Makefile
-@@ -16,8 +16,9 @@
- CC ?= gcc
- 
- # Change the value of HDF5 or EIGEN below to any value to disable compilation of bundled HDF5 code
--HDF5=install
--EIGEN=install
-+HDF5?=install
-+EIGEN?=install
-+HTS?=install
- 
- # Check operating system, OSX doesn't have -lrt
- UNAME_S := $(shell uname -s)
-@@ -45,9 +46,14 @@
-     EIGEN_CHECK=
- endif
- 
--# Build and link the libhts submodule
--HTS_LIB=./htslib/libhts.a
--HTS_INCLUDE=-I./htslib
-+# Default to build and link the libhts submodule
-+ifeq ($(HTS), install)
-+    HTS_LIB=./htslib/libhts.a
-+    HTS_INCLUDE=-I./htslib
-+else
-+    # Use system-wide htslib
-+    HTS_LIB=-lhts
-+endif
- 
- # Include the header-only fast5 library
- FAST5_INCLUDE=-I./fast5/include
diff --git a/debian/patches/series b/debian/patches/series
index 1c30f60..d2144c0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,3 @@
-compiler-flags.patch
-external-dependencies.patch
 add-shebang-to-script.patch
 reproducible.patch
 write_return_values_ignored.patch

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