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|
Fix building and don't use bundled uchime.
--- a/Makefile
+++ b/Makefile
@@ -104,12 +104,19 @@ endif
# INCLUDE directories for mothur
#
#
- VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
+ VPATH=source:source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
+ source := source
skipUchime := source/uchime_src/
+ skipTestMothur := source/TestMothur/
+ skipSeqnoise := seqnoise.cpp
subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))
+ subdirs := $(filter-out $(skipTestMothur), $(subdirs))
subDirIncludes = $(patsubst %, -I %, $(subdirs))
+ subDirIncludes += $(patsubst %, -I %, $(source))
subDirLinking = $(patsubst %, -L%, $(subdirs))
- CXXFLAGS += -I. $(subDirIncludes)
+ subDirLinking += $(patsubst %, -L%, $(source))
+ subdirs := $(dir source) $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))
+ CXXFLAGS += -Isource -I. $(subDirIncludes)
LDFLAGS += $(subDirLinking)
@@ -118,15 +125,14 @@ endif
#
OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
+ OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.cpp)))
+ OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.c)))
OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
-mothur : $(OBJECTS) uchime
+mothur : $(OBJECTS)
$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
-uchime :
- cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd ..
-
install : mothur
ifeq ($(strip $(INSTALL_DIR)),"\"Enter_your_mothur_install_path_here\"")
--- a/makefile-internal
+++ b/makefile-internal
@@ -115,7 +115,6 @@ endif
mothur : $(OBJECTS)
$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
- strip mothur
%.o : %.c %.h
$(COMPILE.c) $(OUTPUT_OPTION) $<
--- a/source/uchime_src/makefile
+++ b/source/uchime_src/makefile
@@ -1,4 +1,4 @@
-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
+CXXFLAGS = -std=c++11 -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
LDFLAGS = -g
#
@@ -26,4 +26,4 @@ install : uchime
clean :
@rm -f $(OBJECTS)
-
\ No newline at end of file
+
--- a/source/writer.h
+++ b/source/writer.h
@@ -9,6 +9,7 @@
#ifndef writer_h
#define writer_h
+#include <memory>
#include "sharedwriter.hpp"
/***********************************************************************/
|
