bio-velvet_underground 0.0.1
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- checksums.yaml +7 -0
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- data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
- data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
- data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
- data/lib/bio-velvet_underground.rb +12 -0
- data/lib/bio-velvet_underground/external/VERSION +1 -0
- data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
- data/spec/binary_sequence_store_spec.rb +27 -0
- data/spec/data/1/CnyUnifiedSeq +0 -0
- data/spec/spec_helper.rb +31 -0
- metadata +456 -0
@@ -0,0 +1,107 @@
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# Makefile for zlib
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# Borland C++ for Win32
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#
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# Updated for zlib 1.2.x by Cosmin Truta, 11-Mar-2003
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# Last updated: 28-Aug-2003
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#
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# Usage:
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# make -f win32/Makefile.bor
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# make -f win32/Makefile.bor LOCAL_ZLIB=-DASMV OBJA=match.obj OBJPA=+match.obj
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# ------------ Borland C++ ------------
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# Optional nonstandard preprocessor flags (e.g. -DMAX_MEM_LEVEL=7)
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# should be added to the environment via "set LOCAL_ZLIB=-DFOO" or
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# added to the declaration of LOC here:
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LOC = $(LOCAL_ZLIB)
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CC = bcc32
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AS = bcc32
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LD = bcc32
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AR = tlib
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CFLAGS = -a -d -k- -O2 $(LOC)
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ASFLAGS = $(LOC)
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LDFLAGS = $(LOC)
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# variables
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ZLIB_LIB = zlib.lib
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OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzio.obj infback.obj
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OBJ2 = inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
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#OBJA =
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OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzio.obj+infback.obj
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OBJP2 = +inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
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#OBJPA=
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# targets
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all: $(ZLIB_LIB) example.exe minigzip.exe
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.c.obj:
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$(CC) -c $(CFLAGS) $<
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.asm.obj:
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$(AS) -c $(ASFLAGS) $<
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adler32.obj: adler32.c zlib.h zconf.h
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compress.obj: compress.c zlib.h zconf.h
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crc32.obj: crc32.c zlib.h zconf.h crc32.h
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deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
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gzio.obj: gzio.c zutil.h zlib.h zconf.h
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infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
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inffast.h inffixed.h
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inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
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inffast.h
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inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
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inffast.h inffixed.h
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inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
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trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
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uncompr.obj: uncompr.c zlib.h zconf.h
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zutil.obj: zutil.c zutil.h zlib.h zconf.h
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example.obj: example.c zlib.h zconf.h
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minigzip.obj: minigzip.c zlib.h zconf.h
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# For the sake of the old Borland make,
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# the command line is cut to fit in the MS-DOS 128 byte limit:
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$(ZLIB_LIB): $(OBJ1) $(OBJ2) $(OBJA)
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-del $(ZLIB_LIB)
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$(AR) $(ZLIB_LIB) $(OBJP1)
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$(AR) $(ZLIB_LIB) $(OBJP2)
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$(AR) $(ZLIB_LIB) $(OBJPA)
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# testing
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test: example.exe minigzip.exe
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example
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echo hello world | minigzip | minigzip -d
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example.exe: example.obj $(ZLIB_LIB)
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$(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
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minigzip.exe: minigzip.obj $(ZLIB_LIB)
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$(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
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# cleanup
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clean:
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-del *.obj
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-del *.lib
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-del *.exe
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-del *.tds
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-del zlib.bak
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-del foo.gz
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# Makefile for zlib. Modified for emx/rsxnt by Chr. Spieler, 6/16/98.
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# Copyright (C) 1995-1998 Jean-loup Gailly.
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# For conditions of distribution and use, see copyright notice in zlib.h
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# To compile, or to compile and test, type:
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#
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# make -fmakefile.emx; make test -fmakefile.emx
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#
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CC=gcc -Zwin32
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#CFLAGS=-MMD -O
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#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
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#CFLAGS=-MMD -g -DDEBUG
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CFLAGS=-MMD -O3 $(BUTT) -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
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-Wstrict-prototypes -Wmissing-prototypes
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# If cp.exe is available, replace "copy /Y" with "cp -fp" .
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CP=copy /Y
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# If gnu install.exe is available, replace $(CP) with ginstall.
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INSTALL=$(CP)
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# The default value of RM is "rm -f." If "rm.exe" is found, comment out:
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RM=del
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LDLIBS=-L. -lzlib
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LD=$(CC) -s -o
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LDSHARED=$(CC)
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INCL=zlib.h zconf.h
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LIBS=zlib.a
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AR=ar rcs
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prefix=/usr/local
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exec_prefix = $(prefix)
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OBJS = adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o \
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zutil.o inflate.o infback.o inftrees.o inffast.o
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TEST_OBJS = example.o minigzip.o
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all: example.exe minigzip.exe
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test: all
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./example
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echo hello world | .\minigzip | .\minigzip -d
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%.o : %.c
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$(CC) $(CFLAGS) -c $< -o $@
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zlib.a: $(OBJS)
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$(AR) $@ $(OBJS)
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%.exe : %.o $(LIBS)
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$(LD) $@ $< $(LDLIBS)
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.PHONY : clean
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clean:
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$(RM) *.d
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$(RM) *.o
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$(RM) *.exe
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$(RM) zlib.a
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$(RM) foo.gz
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DEPS := $(wildcard *.d)
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ifneq ($(DEPS),)
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include $(DEPS)
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endif
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# Makefile for zlib, derived from Makefile.dj2.
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# Modified for mingw32 by C. Spieler, 6/16/98.
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# Updated for zlib 1.2.x by Christian Spieler and Cosmin Truta, Mar-2003.
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# Last updated: 1-Aug-2003.
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# Tested under Cygwin and MinGW.
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# Copyright (C) 1995-2003 Jean-loup Gailly.
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# For conditions of distribution and use, see copyright notice in zlib.h
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# To compile, or to compile and test, type:
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#
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# make -fmakefile.gcc; make test testdll -fmakefile.gcc
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#
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# To use the asm code, type:
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# cp contrib/asm?86/match.S ./match.S
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# make LOC=-DASMV OBJA=match.o -fmakefile.gcc
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#
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# To install libz.a, zconf.h and zlib.h in the system directories, type:
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#
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# make install -fmakefile.gcc
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# Note:
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# If the platform is *not* MinGW (e.g. it is Cygwin or UWIN),
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# the DLL name should be changed from "zlib1.dll".
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STATICLIB = libz.a
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SHAREDLIB = zlib1.dll
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IMPLIB = libzdll.a
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#LOC = -DASMV
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#LOC = -DDEBUG -g
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CC = gcc
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CFLAGS = $(LOC) -O3 -Wall
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AS = $(CC)
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ASFLAGS = $(LOC) -Wall
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LD = $(CC)
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LDFLAGS = $(LOC) -s
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AR = ar
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ARFLAGS = rcs
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RC = windres
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RCFLAGS = --define GCC_WINDRES
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CP = cp -fp
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# If GNU install is available, replace $(CP) with install.
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INSTALL = $(CP)
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RM = rm -f
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prefix = /usr/local
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exec_prefix = $(prefix)
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OBJS = adler32.o compress.o crc32.o deflate.o gzio.o infback.o \
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inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
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OBJA =
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all: $(STATICLIB) $(SHAREDLIB) $(IMPLIB) example minigzip example_d minigzip_d
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test: example minigzip
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./example
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echo hello world | ./minigzip | ./minigzip -d
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testdll: example_d minigzip_d
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./example_d
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echo hello world | ./minigzip_d | ./minigzip_d -d
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.c.o:
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$(CC) $(CFLAGS) -c -o $@ $<
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.S.o:
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$(AS) $(ASFLAGS) -c -o $@ $<
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$(STATICLIB): $(OBJS) $(OBJA)
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$(AR) $(ARFLAGS) $@ $(OBJS) $(OBJA)
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$(IMPLIB): $(SHAREDLIB)
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$(SHAREDLIB): win32/zlib.def $(OBJS) $(OBJA) zlibrc.o
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dllwrap --driver-name $(CC) --def win32/zlib.def \
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--implib $(IMPLIB) -o $@ $(OBJS) $(OBJA) zlibrc.o
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strip $@
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example: example.o $(STATICLIB)
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$(LD) $(LDFLAGS) -o $@ example.o $(STATICLIB)
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minigzip: minigzip.o $(STATICLIB)
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$(LD) $(LDFLAGS) -o $@ minigzip.o $(STATICLIB)
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example_d: example.o $(IMPLIB)
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$(LD) $(LDFLAGS) -o $@ example.o $(IMPLIB)
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minigzip_d: minigzip.o $(IMPLIB)
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$(LD) $(LDFLAGS) -o $@ minigzip.o $(IMPLIB)
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zlibrc.o: win32/zlib1.rc
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$(RC) $(RCFLAGS) -o $@ win32/zlib1.rc
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# INCLUDE_PATH and LIBRARY_PATH must be set.
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.PHONY: install uninstall clean
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install: zlib.h zconf.h $(LIB)
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-@if not exist $(INCLUDE_PATH)/nul mkdir $(INCLUDE_PATH)
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-@if not exist $(LIBRARY_PATH)/nul mkdir $(LIBRARY_PATH)
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-$(INSTALL) zlib.h $(INCLUDE_PATH)
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-$(INSTALL) zconf.h $(INCLUDE_PATH)
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-$(INSTALL) $(STATICLIB) $(LIBRARY_PATH)
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-$(INSTALL) $(IMPLIB) $(LIBRARY_PATH)
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uninstall:
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-$(RM) $(INCLUDE_PATH)/zlib.h
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-$(RM) $(INCLUDE_PATH)/zconf.h
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-$(RM) $(LIBRARY_PATH)/$(STATICLIB)
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-$(RM) $(LIBRARY_PATH)/$(IMPLIB)
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clean:
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-$(RM) $(STATICLIB)
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-$(RM) $(SHAREDLIB)
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-$(RM) $(IMPLIB)
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-$(RM) *.o
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-$(RM) *.exe
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-$(RM) foo.gz
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adler32.o: zlib.h zconf.h
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compress.o: zlib.h zconf.h
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crc32.o: crc32.h zlib.h zconf.h
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deflate.o: deflate.h zutil.h zlib.h zconf.h
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example.o: zlib.h zconf.h
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gzio.o: zutil.h zlib.h zconf.h
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inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
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inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
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infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
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inftrees.o: zutil.h zlib.h zconf.h inftrees.h
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minigzip.o: zlib.h zconf.h
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trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
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uncompr.o: zlib.h zconf.h
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141
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zutil.o: zutil.h zlib.h zconf.h
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@@ -0,0 +1,126 @@
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# Makefile for zlib -- Microsoft (Visual) C
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2
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#
|
3
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# Authors:
|
4
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# Cosmin Truta, 11-Mar-2003
|
5
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# Christian Spieler, 19-Mar-2003
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#
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# Last updated:
|
8
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# Cosmin Truta, 27-Aug-2003
|
9
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#
|
10
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# Usage:
|
11
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# nmake -f win32/Makefile.msc (standard build)
|
12
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# nmake -f win32/Makefile.msc LOC=-DFOO (nonstandard build)
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13
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# nmake -f win32/Makefile.msc LOC=-DASMV OBJA=match.obj (use ASM code)
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# optional build flags
|
17
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+
LOC =
|
18
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+
|
19
|
+
|
20
|
+
# variables
|
21
|
+
STATICLIB = zlib.lib
|
22
|
+
SHAREDLIB = zlib1.dll
|
23
|
+
IMPLIB = zdll.lib
|
24
|
+
|
25
|
+
CC = cl
|
26
|
+
AS = ml
|
27
|
+
LD = link
|
28
|
+
AR = lib
|
29
|
+
RC = rc
|
30
|
+
CFLAGS = -nologo -MD -O2 $(LOC)
|
31
|
+
ASFLAGS = -coff
|
32
|
+
LDFLAGS = -nologo -release
|
33
|
+
ARFLAGS = -nologo
|
34
|
+
RCFLAGS = /dWIN32 /r
|
35
|
+
|
36
|
+
OBJS = adler32.obj compress.obj crc32.obj deflate.obj gzio.obj infback.obj \
|
37
|
+
inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
|
38
|
+
OBJA =
|
39
|
+
|
40
|
+
|
41
|
+
# targets
|
42
|
+
all: $(STATICLIB) $(SHAREDLIB) $(IMPLIB) \
|
43
|
+
example.exe minigzip.exe example_d.exe minigzip_d.exe
|
44
|
+
|
45
|
+
$(STATICLIB): $(OBJS) $(OBJA)
|
46
|
+
$(AR) $(ARFLAGS) -out:$@ $(OBJS) $(OBJA)
|
47
|
+
|
48
|
+
$(IMPLIB): $(SHAREDLIB)
|
49
|
+
|
50
|
+
$(SHAREDLIB): win32/zlib.def $(OBJS) $(OBJA) zlib1.res
|
51
|
+
$(LD) $(LDFLAGS) -def:win32/zlib.def -dll -implib:$(IMPLIB) \
|
52
|
+
-out:$@ $(OBJS) $(OBJA) zlib1.res
|
53
|
+
|
54
|
+
example.exe: example.obj $(STATICLIB)
|
55
|
+
$(LD) $(LDFLAGS) example.obj $(STATICLIB)
|
56
|
+
|
57
|
+
minigzip.exe: minigzip.obj $(STATICLIB)
|
58
|
+
$(LD) $(LDFLAGS) minigzip.obj $(STATICLIB)
|
59
|
+
|
60
|
+
example_d.exe: example.obj $(IMPLIB)
|
61
|
+
$(LD) $(LDFLAGS) -out:$@ example.obj $(IMPLIB)
|
62
|
+
|
63
|
+
minigzip_d.exe: minigzip.obj $(IMPLIB)
|
64
|
+
$(LD) $(LDFLAGS) -out:$@ minigzip.obj $(IMPLIB)
|
65
|
+
|
66
|
+
.c.obj:
|
67
|
+
$(CC) -c $(CFLAGS) $<
|
68
|
+
|
69
|
+
.asm.obj:
|
70
|
+
$(AS) -c $(ASFLAGS) $<
|
71
|
+
|
72
|
+
adler32.obj: adler32.c zlib.h zconf.h
|
73
|
+
|
74
|
+
compress.obj: compress.c zlib.h zconf.h
|
75
|
+
|
76
|
+
crc32.obj: crc32.c zlib.h zconf.h crc32.h
|
77
|
+
|
78
|
+
deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
|
79
|
+
|
80
|
+
gzio.obj: gzio.c zutil.h zlib.h zconf.h
|
81
|
+
|
82
|
+
infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
|
83
|
+
inffast.h inffixed.h
|
84
|
+
|
85
|
+
inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
|
86
|
+
inffast.h
|
87
|
+
|
88
|
+
inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
|
89
|
+
inffast.h inffixed.h
|
90
|
+
|
91
|
+
inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
|
92
|
+
|
93
|
+
trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
|
94
|
+
|
95
|
+
uncompr.obj: uncompr.c zlib.h zconf.h
|
96
|
+
|
97
|
+
zutil.obj: zutil.c zutil.h zlib.h zconf.h
|
98
|
+
|
99
|
+
example.obj: example.c zlib.h zconf.h
|
100
|
+
|
101
|
+
minigzip.obj: minigzip.c zlib.h zconf.h
|
102
|
+
|
103
|
+
zlib1.res: win32/zlib1.rc
|
104
|
+
$(RC) $(RCFLAGS) /fo$@ win32/zlib1.rc
|
105
|
+
|
106
|
+
|
107
|
+
# testing
|
108
|
+
test: example.exe minigzip.exe
|
109
|
+
example
|
110
|
+
echo hello world | minigzip | minigzip -d
|
111
|
+
|
112
|
+
testdll: example_d.exe minigzip_d.exe
|
113
|
+
example_d
|
114
|
+
echo hello world | minigzip_d | minigzip_d -d
|
115
|
+
|
116
|
+
|
117
|
+
# cleanup
|
118
|
+
clean:
|
119
|
+
-del $(STATICLIB)
|
120
|
+
-del $(SHAREDLIB)
|
121
|
+
-del $(IMPLIB)
|
122
|
+
-del *.obj
|
123
|
+
-del *.res
|
124
|
+
-del *.exp
|
125
|
+
-del *.exe
|
126
|
+
-del foo.gz
|