[med-svn] [libvcflib] 01/04: Keep R files in source tree which are removed in upstream build otherwise

[Andreas Tille]

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tille pushed a commit to branch master
in repository libvcflib.

commit 7171eb9d1b1859542affec57eb5ff0432bdb8839
Author: Andreas Tille <tille at debian.org>
Date:   Fri Sep 16 09:18:27 2016 +0200

    Keep R files in source tree which are removed in upstream build otherwise
---
 debian/patches/keep_R_files.patch | 35 +++++++++++++++++++++++++++++++++++
 debian/patches/series             |  1 +
 2 files changed, 36 insertions(+)

diff --git a/debian/patches/keep_R_files.patch b/debian/patches/keep_R_files.patch
new file mode 100644
index 0000000..7a8c1b1
--- /dev/null
+++ b/debian/patches/keep_R_files.patch
@@ -0,0 +1,35 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 15 Sep 2016 22:26:26 +0200
+Description: There is a dir bin/ containing some R files which
+ is removed in clean target.  Just use a different output dir
+ that can be cleaned without problems
+
+--- a/Makefile
++++ b/Makefile
+@@ -15,7 +15,7 @@ SOURCES = src/Variant.cpp \
+ OBJECTS= $(SOURCES:.cpp=.o)
+ 
+ VCF_LIB_LOCAL:=$(shell pwd)
+-BIN_DIR:=bin
++BIN_DIR:=binaries
+ LIB_DIR:=lib
+ SRC_DIR=src
+ INC_DIR:=include
+@@ -111,7 +111,7 @@ BIN_SOURCES = src/vcfecho.cpp \
+ # src/vcfsom.cpp
+ 
+ #BINS = $(BIN_SOURCES:.cpp=)
+-BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
++BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
+ SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
+ 
+ # TABIX = tabixpp/tabix.o
+@@ -177,7 +177,7 @@ $(FILEVERCMP): pre
+ 	ln -sf ../filevercmp/filevercmp.h $(VCF_LIB_LOCAL)/$(INC_DIR)/filevercmp.h
+ 
+ $(SHORTBINS): pre
+-	$(MAKE) bin/$@
++	$(MAKE) $(BIN_DIR)/$@
+ 
+ $(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
+ 	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
diff --git a/debian/patches/series b/debian/patches/series
index e734ebe..d178342 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ filevercmp.h.patch
 use_debian_packaged_fastahack.patch
 intervaltree.patch
 shared_lib.patch
+keep_R_files.patch

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