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 +1,69 @@
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# Makefile for zlib. Modified for emx 0.9c by Chr. Spieler, 6/17/98.
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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
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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
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# Microsoft C 5.1 or later
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# Last updated: 19-Mar-2003
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# To use, do "make makefile.msc"
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# To compile in small model, set below: MODEL=S
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# If you wish to reduce the memory requirements (default 256K for big
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# objects plus a few K), you can add to the LOC macro below:
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# -DMAX_MEM_LEVEL=7 -DMAX_WBITS=14
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# See zconf.h for details about the memory requirements.
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# ------------- Microsoft C 5.1 and later -------------
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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 added
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# to the declaration of LOC here:
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LOC = $(LOCAL_ZLIB)
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# Type for CPU required: 0: 8086, 1: 80186, 2: 80286, 3: 80386, etc.
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CPU_TYP = 0
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# Memory model: one of S, M, C, L (small, medium, compact, large)
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MODEL=L
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CC=cl
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CFLAGS=-nologo -A$(MODEL) -G$(CPU_TYP) -W3 -Oait -Gs $(LOC)
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#-Ox generates bad code with MSC 5.1
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LIB_CFLAGS=-Zl $(CFLAGS)
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LD=link
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LDFLAGS=/noi/e/st:0x1500/noe/farcall/packcode
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# "/farcall/packcode" are only useful for `large code' memory models
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# but should be a "no-op" for small code models.
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# variables
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ZLIB_LIB = zlib_$(MODEL).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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# targets
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all: $(ZLIB_LIB) example.exe minigzip.exe
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.c.obj:
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$(CC) -c $(LIB_CFLAGS) $*.c
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adler32.obj: adler32.c zlib.h zconf.h
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compress.obj: compress.c zlib.h zconf.h
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crc32.obj: crc32.c zlib.h zconf.h crc32.h
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deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
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gzio.obj: gzio.c zutil.h zlib.h zconf.h
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infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
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inffast.h inffixed.h
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inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
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inffast.h
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inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
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inffast.h inffixed.h
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inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
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trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
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uncompr.obj: uncompr.c zlib.h zconf.h
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zutil.obj: zutil.c zutil.h zlib.h zconf.h
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example.obj: example.c zlib.h zconf.h
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$(CC) -c $(CFLAGS) $*.c
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minigzip.obj: minigzip.c zlib.h zconf.h
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$(CC) -c $(CFLAGS) $*.c
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# the command line is cut to fit in the MS-DOS 128 byte limit:
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$(ZLIB_LIB): $(OBJ1) $(OBJ2)
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if exist $(ZLIB_LIB) del $(ZLIB_LIB)
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lib $(ZLIB_LIB) $(OBJ1);
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lib $(ZLIB_LIB) $(OBJ2);
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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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test: example.exe minigzip.exe
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example
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echo hello world | minigzip | minigzip -d
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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 *.map
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-del zlib_*.bak
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-del foo.gz
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@@ -0,0 +1,94 @@
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# Makefile for zlib
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# Turbo C 2.01, Turbo C++ 1.01
|
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# Last updated: 15-Mar-2003
|
4
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|
5
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# To use, do "make -fmakefile.tc"
|
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# To compile in small model, set below: MODEL=s
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8
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# WARNING: the small model is supported but only for small values of
|
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# MAX_WBITS and MAX_MEM_LEVEL. For example:
|
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# -DMAX_WBITS=11 -DMAX_MEM_LEVEL=3
|
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# If you wish to reduce the memory requirements (default 256K for big
|
12
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# objects plus a few K), you can add to CFLAGS below:
|
13
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# -DMAX_MEM_LEVEL=7 -DMAX_WBITS=14
|
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# See zconf.h for details about the memory requirements.
|
15
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# ------------ Turbo C 2.01, Turbo C++ 1.01 ------------
|
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MODEL=l
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CC=tcc
|
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LD=tcc
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AR=tlib
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# CFLAGS=-O2 -G -Z -m$(MODEL) -DMAX_WBITS=11 -DMAX_MEM_LEVEL=3
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CFLAGS=-O2 -G -Z -m$(MODEL)
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LDFLAGS=-m$(MODEL) -f-
|
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|
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# variables
|
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ZLIB_LIB = zlib_$(MODEL).lib
|
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|
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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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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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# targets
|
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all: $(ZLIB_LIB) example.exe minigzip.exe
|
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|
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.c.obj:
|
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$(CC) -c $(CFLAGS) $*.c
|
40
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|
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adler32.obj: adler32.c zlib.h zconf.h
|
42
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|
43
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compress.obj: compress.c zlib.h zconf.h
|
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|
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crc32.obj: crc32.c zlib.h zconf.h crc32.h
|
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|
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deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
|
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+
|
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gzio.obj: gzio.c zutil.h zlib.h zconf.h
|
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|
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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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|
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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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|
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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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|
60
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inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
|
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|
62
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trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
|
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|
64
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uncompr.obj: uncompr.c zlib.h zconf.h
|
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|
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zutil.obj: zutil.c zutil.h zlib.h zconf.h
|
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|
68
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example.obj: example.c zlib.h zconf.h
|
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|
70
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minigzip.obj: minigzip.c zlib.h zconf.h
|
71
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|
72
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|
73
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# the command line is cut to fit in the MS-DOS 128 byte limit:
|
74
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$(ZLIB_LIB): $(OBJ1) $(OBJ2)
|
75
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-del $(ZLIB_LIB)
|
76
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$(AR) $(ZLIB_LIB) $(OBJP1)
|
77
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$(AR) $(ZLIB_LIB) $(OBJP2)
|
78
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+
|
79
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example.exe: example.obj $(ZLIB_LIB)
|
80
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$(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
|
81
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|
82
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minigzip.exe: minigzip.obj $(ZLIB_LIB)
|
83
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$(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
|
84
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+
|
85
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test: example.exe minigzip.exe
|
86
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example
|
87
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echo hello world | minigzip | minigzip -d
|
88
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|
89
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clean:
|
90
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-del *.obj
|
91
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-del *.lib
|
92
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-del *.exe
|
93
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-del zlib_*.bak
|
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-del foo.gz
|
@@ -0,0 +1,151 @@
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# Project: zlib_1_03
|
2
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# Patched for zlib 1.1.2 rw@shadow.org.uk 19980430
|
3
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# test works out-of-the-box, installs `somewhere' on demand
|
4
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|
5
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# Toolflags:
|
6
|
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CCflags = -c -depend !Depend -IC: -g -throwback -DRISCOS -fah
|
7
|
+
C++flags = -c -depend !Depend -IC: -throwback
|
8
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+
Linkflags = -aif -c++ -o $@
|
9
|
+
ObjAsmflags = -throwback -NoCache -depend !Depend
|
10
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+
CMHGflags =
|
11
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LibFileflags = -c -l -o $@
|
12
|
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Squeezeflags = -o $@
|
13
|
+
|
14
|
+
# change the line below to where _you_ want the library installed.
|
15
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+
libdest = lib:zlib
|
16
|
+
|
17
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+
# Final targets:
|
18
|
+
@.lib: @.o.adler32 @.o.compress @.o.crc32 @.o.deflate @.o.gzio \
|
19
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@.o.infblock @.o.infcodes @.o.inffast @.o.inflate @.o.inftrees @.o.infutil @.o.trees \
|
20
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@.o.uncompr @.o.zutil
|
21
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LibFile $(LibFileflags) @.o.adler32 @.o.compress @.o.crc32 @.o.deflate \
|
22
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@.o.gzio @.o.infblock @.o.infcodes @.o.inffast @.o.inflate @.o.inftrees @.o.infutil \
|
23
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@.o.trees @.o.uncompr @.o.zutil
|
24
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test: @.minigzip @.example @.lib
|
25
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@copy @.lib @.libc A~C~DF~L~N~P~Q~RS~TV
|
26
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@echo running tests: hang on.
|
27
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@/@.minigzip -f -9 libc
|
28
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@/@.minigzip -d libc-gz
|
29
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@/@.minigzip -f -1 libc
|
30
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@/@.minigzip -d libc-gz
|
31
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@/@.minigzip -h -9 libc
|
32
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@/@.minigzip -d libc-gz
|
33
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@/@.minigzip -h -1 libc
|
34
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@/@.minigzip -d libc-gz
|
35
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@/@.minigzip -9 libc
|
36
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@/@.minigzip -d libc-gz
|
37
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@/@.minigzip -1 libc
|
38
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@/@.minigzip -d libc-gz
|
39
|
+
@diff @.lib @.libc
|
40
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+
@echo that should have reported '@.lib and @.libc identical' if you have diff.
|
41
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+
@/@.example @.fred @.fred
|
42
|
+
@echo that will have given lots of hello!'s.
|
43
|
+
|
44
|
+
@.minigzip: @.o.minigzip @.lib C:o.Stubs
|
45
|
+
Link $(Linkflags) @.o.minigzip @.lib C:o.Stubs
|
46
|
+
@.example: @.o.example @.lib C:o.Stubs
|
47
|
+
Link $(Linkflags) @.o.example @.lib C:o.Stubs
|
48
|
+
|
49
|
+
install: @.lib
|
50
|
+
cdir $(libdest)
|
51
|
+
cdir $(libdest).h
|
52
|
+
@copy @.h.zlib $(libdest).h.zlib A~C~DF~L~N~P~Q~RS~TV
|
53
|
+
@copy @.h.zconf $(libdest).h.zconf A~C~DF~L~N~P~Q~RS~TV
|
54
|
+
@copy @.lib $(libdest).lib A~C~DF~L~N~P~Q~RS~TV
|
55
|
+
@echo okay, installed zlib in $(libdest)
|
56
|
+
|
57
|
+
clean:; remove @.minigzip
|
58
|
+
remove @.example
|
59
|
+
remove @.libc
|
60
|
+
-wipe @.o.* F~r~cV
|
61
|
+
remove @.fred
|
62
|
+
|
63
|
+
# User-editable dependencies:
|
64
|
+
.c.o:
|
65
|
+
cc $(ccflags) -o $@ $<
|
66
|
+
|
67
|
+
# Static dependencies:
|
68
|
+
|
69
|
+
# Dynamic dependencies:
|
70
|
+
o.example: c.example
|
71
|
+
o.example: h.zlib
|
72
|
+
o.example: h.zconf
|
73
|
+
o.minigzip: c.minigzip
|
74
|
+
o.minigzip: h.zlib
|
75
|
+
o.minigzip: h.zconf
|
76
|
+
o.adler32: c.adler32
|
77
|
+
o.adler32: h.zlib
|
78
|
+
o.adler32: h.zconf
|
79
|
+
o.compress: c.compress
|
80
|
+
o.compress: h.zlib
|
81
|
+
o.compress: h.zconf
|
82
|
+
o.crc32: c.crc32
|
83
|
+
o.crc32: h.zlib
|
84
|
+
o.crc32: h.zconf
|
85
|
+
o.deflate: c.deflate
|
86
|
+
o.deflate: h.deflate
|
87
|
+
o.deflate: h.zutil
|
88
|
+
o.deflate: h.zlib
|
89
|
+
o.deflate: h.zconf
|
90
|
+
o.gzio: c.gzio
|
91
|
+
o.gzio: h.zutil
|
92
|
+
o.gzio: h.zlib
|
93
|
+
o.gzio: h.zconf
|
94
|
+
o.infblock: c.infblock
|
95
|
+
o.infblock: h.zutil
|
96
|
+
o.infblock: h.zlib
|
97
|
+
o.infblock: h.zconf
|
98
|
+
o.infblock: h.infblock
|
99
|
+
o.infblock: h.inftrees
|
100
|
+
o.infblock: h.infcodes
|
101
|
+
o.infblock: h.infutil
|
102
|
+
o.infcodes: c.infcodes
|
103
|
+
o.infcodes: h.zutil
|
104
|
+
o.infcodes: h.zlib
|
105
|
+
o.infcodes: h.zconf
|
106
|
+
o.infcodes: h.inftrees
|
107
|
+
o.infcodes: h.infblock
|
108
|
+
o.infcodes: h.infcodes
|
109
|
+
o.infcodes: h.infutil
|
110
|
+
o.infcodes: h.inffast
|
111
|
+
o.inffast: c.inffast
|
112
|
+
o.inffast: h.zutil
|
113
|
+
o.inffast: h.zlib
|
114
|
+
o.inffast: h.zconf
|
115
|
+
o.inffast: h.inftrees
|
116
|
+
o.inffast: h.infblock
|
117
|
+
o.inffast: h.infcodes
|
118
|
+
o.inffast: h.infutil
|
119
|
+
o.inffast: h.inffast
|
120
|
+
o.inflate: c.inflate
|
121
|
+
o.inflate: h.zutil
|
122
|
+
o.inflate: h.zlib
|
123
|
+
o.inflate: h.zconf
|
124
|
+
o.inflate: h.infblock
|
125
|
+
o.inftrees: c.inftrees
|
126
|
+
o.inftrees: h.zutil
|
127
|
+
o.inftrees: h.zlib
|
128
|
+
o.inftrees: h.zconf
|
129
|
+
o.inftrees: h.inftrees
|
130
|
+
o.inftrees: h.inffixed
|
131
|
+
o.infutil: c.infutil
|
132
|
+
o.infutil: h.zutil
|
133
|
+
o.infutil: h.zlib
|
134
|
+
o.infutil: h.zconf
|
135
|
+
o.infutil: h.infblock
|
136
|
+
o.infutil: h.inftrees
|
137
|
+
o.infutil: h.infcodes
|
138
|
+
o.infutil: h.infutil
|
139
|
+
o.trees: c.trees
|
140
|
+
o.trees: h.deflate
|
141
|
+
o.trees: h.zutil
|
142
|
+
o.trees: h.zlib
|
143
|
+
o.trees: h.zconf
|
144
|
+
o.trees: h.trees
|
145
|
+
o.uncompr: c.uncompr
|
146
|
+
o.uncompr: h.zlib
|
147
|
+
o.uncompr: h.zconf
|
148
|
+
o.zutil: c.zutil
|
149
|
+
o.zutil: h.zutil
|
150
|
+
o.zutil: h.zlib
|
151
|
+
o.zutil: h.zconf
|
@@ -0,0 +1,48 @@
|
|
1
|
+
# descrip.mms: MMS description file for building zlib on VMS
|
2
|
+
# written by Martin P.J. Zinser <m.zinser@gsi.de>
|
3
|
+
|
4
|
+
cc_defs =
|
5
|
+
c_deb =
|
6
|
+
|
7
|
+
.ifdef __DECC__
|
8
|
+
pref = /prefix=all
|
9
|
+
.endif
|
10
|
+
|
11
|
+
OBJS = adler32.obj, compress.obj, crc32.obj, gzio.obj, uncompr.obj,\
|
12
|
+
deflate.obj, trees.obj, zutil.obj, inflate.obj, infblock.obj,\
|
13
|
+
inftrees.obj, infcodes.obj, infutil.obj, inffast.obj
|
14
|
+
|
15
|
+
CFLAGS= $(C_DEB) $(CC_DEFS) $(PREF)
|
16
|
+
|
17
|
+
all : example.exe minigzip.exe
|
18
|
+
@ write sys$output " Example applications available"
|
19
|
+
libz.olb : libz.olb($(OBJS))
|
20
|
+
@ write sys$output " libz available"
|
21
|
+
|
22
|
+
example.exe : example.obj libz.olb
|
23
|
+
link example,libz.olb/lib
|
24
|
+
|
25
|
+
minigzip.exe : minigzip.obj libz.olb
|
26
|
+
link minigzip,libz.olb/lib,x11vms:xvmsutils.olb/lib
|
27
|
+
|
28
|
+
clean :
|
29
|
+
delete *.obj;*,libz.olb;*
|
30
|
+
|
31
|
+
|
32
|
+
# Other dependencies.
|
33
|
+
adler32.obj : zutil.h zlib.h zconf.h
|
34
|
+
compress.obj : zlib.h zconf.h
|
35
|
+
crc32.obj : zutil.h zlib.h zconf.h
|
36
|
+
deflate.obj : deflate.h zutil.h zlib.h zconf.h
|
37
|
+
example.obj : zlib.h zconf.h
|
38
|
+
gzio.obj : zutil.h zlib.h zconf.h
|
39
|
+
infblock.obj : zutil.h zlib.h zconf.h infblock.h inftrees.h infcodes.h infutil.h
|
40
|
+
infcodes.obj : zutil.h zlib.h zconf.h inftrees.h infutil.h infcodes.h inffast.h
|
41
|
+
inffast.obj : zutil.h zlib.h zconf.h inftrees.h infutil.h inffast.h
|
42
|
+
inflate.obj : zutil.h zlib.h zconf.h infblock.h
|
43
|
+
inftrees.obj : zutil.h zlib.h zconf.h inftrees.h
|
44
|
+
infutil.obj : zutil.h zlib.h zconf.h inftrees.h infutil.h
|
45
|
+
minigzip.obj : zlib.h zconf.h
|
46
|
+
trees.obj : deflate.h zutil.h zlib.h zconf.h
|
47
|
+
uncompr.obj : zlib.h zconf.h
|
48
|
+
zutil.obj : zutil.h zlib.h zconf.h
|