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258 lines
10 KiB
258 lines
10 KiB
--- a/kmer/configure.sh
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+++ b/kmer/configure.sh
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@@ -254,13 +254,13 @@
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# -*- makefile -*-
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# Linux, optimized
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CC := $CC
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-SHLIB_FLAGS := -shared
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-CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
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-CLDFLAGS := -L/usr/local/lib
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+SHLIB_FLAGS := -shared ${LDFLAGS}
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+CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
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+CLDFLAGS :=
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CLIBS := -pthread -ldl
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CXX := $CXX
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-CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
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-CXXLDFLAGS := -L/usr/local/lib
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+CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
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+CXXLDFLAGS :=
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CXXLIBS := -pthread -ldl
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ARFLAGS := ruvs
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INSTALL/ := $target/
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@@ -272,13 +272,13 @@
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# -*- makefile -*-
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# Linux64, optimized
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CC := $CC
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-SHLIB_FLAGS := -shared
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-CFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
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-CLDFLAGS := -L/usr/local/lib
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+SHLIB_FLAGS := -shared ${LDFLAGS}
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+CFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
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+CLDFLAGS :=
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CLIBS := -pthread -ldl
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CXX := $CXX
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-CXXFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
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-CXXLDFLAGS := -L/usr/local/lib
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+CXXFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
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+CXXLDFLAGS :=
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CXXLIBS := -pthread -ldl
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ARFLAGS := ruvs
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INSTALL/ := $target/
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@@ -401,8 +401,8 @@
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.O := .o
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CLD := \${CC}
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CXXLD := \${CXX}
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-CCDEP := gcc -MM -MG
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-CXXDEP := g++ -MM -MG
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+CCDEP := \$(CC) -MM -MG
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+CXXDEP := \$(CXX) -MM -MG
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CLIBS += -lm -lbz2
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CXXLIBS += -lm -lbz2
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PYTHON := $PYTHON
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--- a/kmer/Make.rules
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+++ b/kmer/Make.rules
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@@ -139,12 +139,12 @@
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## EXE targets
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ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}}))
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${ALL_C_EXES}:
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- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS}
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+ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS}
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__SUBGOALS__+=$${${1:.=.C_EXES}}
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ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}}))
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${ALL_CXX_EXES}:
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- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS}
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+ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS}
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__SUBGOALS__+=$${${1:.=.CXX_EXES}}
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define .RULE-install-copy-C-CXX-EXES
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--- a/src/c_make.as
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+++ b/src/c_make.as
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@@ -64,27 +64,27 @@
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ifeq ($(OSTYPE), Linux)
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ifeq ($(MACHINETYPE), i686)
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- ARCH_LDFLAGS += -pthread -lm
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- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
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+ LINK_LIBS += -pthread -lm
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+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
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ARCH_LIB = /usr/X11R6/lib
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endif
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ifeq ($(MACHINETYPE), amd64)
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- ARCH_LDFLAGS += -pthread -lm
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- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
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+ LINK_LIBS += -pthread -lm
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+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
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ARCH_LIB = /usr/lib64 /usr/X11R6/lib64
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endif
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ifeq ($(MACHINETYPE), ia64)
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- ARCH_LDFLAGS += -pthread -lm
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- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
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+ LINK_LIBS += -pthread -lm
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+ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
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ARCH_LIB = /usr/X11R6/lib
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endif
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ifeq ($(BUILDDEBUG), 1)
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- ARCH_CFLAGS += -g
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- ARCH_LDFLAGS +=
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+ ARCH_CFLAGS +=
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+ LINK_LIBS +=
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else
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- ARCH_CFLAGS += -O2
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- ARCH_LDFLAGS += -Wl,-O1
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+ ARCH_CFLAGS +=
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+ LINK_LIBS +=
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endif
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endif
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@@ -94,19 +94,19 @@
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ifeq ($(OSTYPE), FreeBSD)
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ifeq ($(MACHINETYPE), i386)
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- ARCH_LDFLAGS += -pthread -lthr -lm
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- ARCH_CFLAGS = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
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- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
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+ LINK_LIBS += -pthread -lthr -lm
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+ ARCH_CFLAGS = -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
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+ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
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endif
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ifeq ($(MACHINETYPE), amd64)
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- ARCH_LDFLAGS += -pthread -lthr -lm
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- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
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- ARCH_CFLAGS = -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
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+ LINK_LIBS += -pthread -lthr -lm
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+ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
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+ ARCH_CFLAGS = -pthread -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
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endif
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ifeq ($(BUILDCOVERAGE), 1)
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ARCH_CFLAGS += -g -fprofile-arcs -ftest-coverage
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- ARCH_LDFLAGS += -lgcov
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+ LINK_LIBS += -lgcov
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else
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ifeq ($(BUILDDEBUG), 1)
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ARCH_CFLAGS += -g
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@@ -126,8 +126,6 @@
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ifeq ($(OSTYPE), Darwin)
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- CC = gcc
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- CXX = g++
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ARCH_CFLAGS = -D_THREAD_SAFE
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ifeq ($(MACHINETYPE), ppc)
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@@ -140,14 +138,14 @@
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ifeq ($(MACHINETYPE), i386)
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ifeq ($(BUILDDEBUG), 1)
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- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
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- ARCH_LDFLAGS += -m64 -lm
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+ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
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+ LINK_LIBS += -m64 -lm
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else
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# Wow, -Wshorten-64-to-32 is tough
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- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
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+ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
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# ARCH_CFLAGS += -Wextra
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# ARCH_CFLAGS += -pedantic (see above about pedantic)
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- ARCH_LDFLAGS += -m64 -lm
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+ LINK_LIBS += -m64 -lm
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endif
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endif
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@@ -161,23 +159,23 @@
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ifeq ($(OSTYPE), SunOS)
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ifeq ($(MACHINETYPE), i86pc)
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ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
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- ARCH_LDFLAGS += -lm
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+ LINK_LIBS += -lm
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endif
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ifeq ($(MACHINETYPE), sparc32)
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ARCH_CFLAGS = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
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- ARCH_LDFLAGS += -lm -lnsl -lsocket
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+ LINK_LIBS += -lm -lnsl -lsocket
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endif
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ifeq ($(MACHINETYPE), sparc64)
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ARCH_CFLAGS = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
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- ARCH_LDFLAGS += -m64 -lm -lnsl -lsocket
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+ LINK_LIBS += -lm -lnsl -lsocket
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endif
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ifeq ($(BUILDDEBUG), 1)
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- ARCH_CFLAGS += -g
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+ ARCH_CFLAGS +=
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else
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- ARCH_CFLAGS += -O
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+ ARCH_CFLAGS +=
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endif
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endif
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@@ -186,14 +184,14 @@
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ifeq ($(BUILDPROFILE), 1)
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ARCH_CFLAGS += -pg
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- ARCH_LDFLAGS += -pg
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+ LINK_LIBS += -pg
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endif
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# One can argue that CXXFLAGS should be separate. For now, we only
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# add to the flags.
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CFLAGS += $(ARCH_CFLAGS)
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-CXXFLAGS += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS)
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+CXXFLAGS += $(ARCH_CXXFLAGS)
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LDFLAGS += $(ARCH_LDFLAGS)
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INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
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@@ -205,7 +203,7 @@
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OBJ_SEARCH_PATH = $(LOCAL_OBJ)
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ifeq ($(SITE_NAME), JCVI)
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- LDFLAGS += -lcurl
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+ LINK_LIBS += -lcurl
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endif
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# The order of compilation here is very carefully chosen to be the
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--- a/src/c_make.gen
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+++ b/src/c_make.gen
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@@ -248,10 +248,6 @@
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#### Do not redefine if (a) passed in on command line, or (b)
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#### defined in an environment variable.
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-ifneq "$(origin CC)" "environment"
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-CC=gcc
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-endif
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-
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ifneq "$(origin CPPFLAGS)" "environment"
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CPPFLAGS=
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endif
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@@ -264,10 +260,6 @@
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CDEFS=
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endif
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-ifneq "$(origin CXX)" "environment"
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-CXX=g++
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-endif
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-
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ifneq "$(origin CXXFLAGS)" "environment"
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CXXFLAGS=
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endif
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@@ -396,12 +388,12 @@
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$(C_PROGS):
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@ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
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cd $(LOCAL_OBJ); \
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- $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
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+ $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
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$(CXX_PROGS):
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@ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
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cd $(LOCAL_OBJ); \
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- $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
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+ $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
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$(SCRIPT_PROGS): %.sh:
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@echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
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