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--- kraken2-2.1.3.orig/src/Makefile 2023-06-07 05:55:37.000000000 +0530
+++ kraken2-2.1.3.new/src/Makefile 2023-06-07 15:11:05.404521211 +0530
@@ -1,6 +1,6 @@
CXX = g++
KRAKEN2_SKIP_FOPENMP ?= -fopenmp
-CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3
+CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O2
CXXFLAGS += -DLINEAR_PROBING
.PHONY: all clean install
@@ -10,7 +10,7 @@
all: $(PROGS)
install: $(PROGS)
- cp $(PROGS) "$(KRAKEN2_DIR)/"
+ cp $(PROGS) $(DESTDIR)$(KRAKEN2_DIR)/
clean:
rm -f *.o $(PROGS)
@@ -34,19 +34,19 @@
k2mask.o: k2mask.cc gzstream.h threadpool.h
build_db: build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ $^
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
classify: classify.o reports.o hyperloglogplus.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ $^
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
estimate_capacity: estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ $^
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
dump_table: dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
- $(CXX) $(CXXFLAGS) -o $@ $^
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
lookup_accession_numbers: lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ $^
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
k2mask: k2mask.o seqreader.o
- $(CXX) $(CXXFLAGS) -o $@ $^ -lz -pthread
+ $(CXX) $(CXXFLAGS) -o $@ $^ -lz -pthread $(LDFLAGS)
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