makefile

EM算法的改进

# Makefile.in generated by automake 1.6.3 from Makefile.am.
# src/Makefile.  Generated from Makefile.in by configure.

# Copyright 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002
# Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.


SHELL = /bin/sh

srcdir = .
top_srcdir = ..

prefix = /root
exec_prefix = ${prefix}

bindir = ${exec_prefix}/bin
sbindir = ${exec_prefix}/sbin
libexecdir = ${exec_prefix}/libexec
datadir = ${prefix}/share
sysconfdir = ${prefix}/etc
sharedstatedir = ${prefix}/com
localstatedir = ${prefix}/var
libdir = ${exec_prefix}/lib
infodir = ${prefix}/info
mandir = ${prefix}/man
includedir = ${prefix}/include
oldincludedir = /usr/include
pkgdatadir = $(datadir)/meme
pkglibdir = $(libdir)/meme
pkgincludedir = $(includedir)/meme
top_builddir = ..

ACLOCAL = ${SHELL} /mnt/hgfs/linuxshare/meme_3.5.4/config/missing --run aclocal-1.6
AUTOCONF = ${SHELL} /mnt/hgfs/linuxshare/meme_3.5.4/config/missing --run autoconf
AUTOMAKE = ${SHELL} /mnt/hgfs/linuxshare/meme_3.5.4/config/missing --run automake-1.6
AUTOHEADER = ${SHELL} /mnt/hgfs/linuxshare/meme_3.5.4/config/missing --run autoheader

am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
INSTALL = /usr/bin/install -c
INSTALL_PROGRAM = ${INSTALL}
INSTALL_DATA = ${INSTALL} -m 644
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
install_sh_SCRIPT = $(install_sh) -c
INSTALL_SCRIPT = ${INSTALL}
INSTALL_HEADER = $(INSTALL_DATA)
transform = s,x,x,
NORMAL_INSTALL = :
PRE_INSTALL = :
POST_INSTALL = :
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
host_alias = 
host_triplet = i686-pc-linux-gnu

EXEEXT = 
OBJEXT = o
PATH_SEPARATOR = :
AMTAR = ${SHELL} /mnt/hgfs/linuxshare/meme_3.5.4/config/missing --run tar
AWK = gawk
CC = gcc
CONTACT = [e-mail]
DEBUG_FLAGS = 
DEPDIR = .deps
HOSTNAME = localhost.localdomain
INSTALL_STRIP_PROGRAM = ${SHELL} $(install_sh) -c -s
LAMBIN = 
LD = /usr/bin/ld
LIBS = -lm 
MACHID = linux
MAIL = /bin/mail
MAST_PORT = 3013
MAXTIME = 7200
MEME_DB = ${prefix}/db
MEME_DIRECTORY = ${prefix}
MEME_LOGS = ${prefix}/LOGS
MEME_PORT = 3012
MEME_USER = root
MPICC = 
MPIFLAGS = -DPARALLEL -O
MPIINC = 
MPILIBDIR = 
MPITYPE = 
MPI_CMD = 
NPROCS = 2
OPT_FLAGS = -O3
PACKAGE = meme
PERL = /usr/bin/perl
QNAME = 
QSTAT = 
QTYPE = 
RANLIB = ranlib
SED = /bin/sed
SENDMAIL = /usr/sbin/sendmail
SERVER = 
STRIP = 
URL = http://localhost.localdomain/meme
VERSION = 3.5.4
WEBDIR = ${prefix}/web
am__include = include
am__quote = 
install_sh = /mnt/hgfs/linuxshare/meme_3.5.4/config/install-sh

AUTOMAKE_OPTIONS = no-dependencies

ADDDIR = libadd
ADDINC = -I./libadd
READSEQ_ADDSRC = $(ADDDIR)/strlcpy.c

SERVER_PROGS = meme-server mast-server 
#SUBDIRS = . parallel

bin_PROGRAMS = alphtype getsize readseq \
               meme.bin mast.bin meme-client.bin \
               $(SERVER_PROGS) 


SEQ = hash.c hash_alph.c read_seq_file.c background.c
MOTIF = logodds.c motifs.c regress.c

alphtype_SOURCES = alphtype.c hash_alph.c
getsize_SOURCES = getsize.c $(SEQ)
getsize_LDADD = -lm
readseq_SOURCES = readseq.c ureadseq.c $(READSEQ_ADDSRC)
meme_server_SOURCES = meme-server.c readwrite.c
mast_server_SOURCES = mast-server.c readwrite.c
meme_bin_SOURCES = clock.c display.c dpalign.c em.c init.c mast-util.c \
               pssm-distr.c meme.c meme_util.c seq2theta.c starts.c prior.c \
               justlike.c \
               oops.c tcm.c banner.c gamma.c likelihood.c subseq7.c \
               discretize.c mp.c message.c $(MOTIF) $(SEQ) llr.c io.c logs.c

meme_bin_LDADD = -lm
mast_bin_SOURCES = mast.c clock.c diagram.c mast-util.c pssm-distr.c \
               $(MOTIF) $(SEQ) 

mast_bin_LDADD = -lm
meme_client_bin_SOURCES = meme-client.c readwrite.c

INCLUDES = -I./include $(ADDINC) 

EXTRA_DIST = include libadd parallel diagram.y 
subdir = src
mkinstalldirs = $(SHELL) $(top_srcdir)/config/mkinstalldirs
CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
bin_PROGRAMS = alphtype$(EXEEXT) getsize$(EXEEXT) \
	readseq$(EXEEXT) meme.bin$(EXEEXT) \
	mast.bin$(EXEEXT) meme-client.bin$(EXEEXT) \
	meme-server$(EXEEXT) mast-server$(EXEEXT)
#bin_PROGRAMS = alphtype$(EXEEXT) getsize$(EXEEXT) \
#	readseq$(EXEEXT) meme.bin$(EXEEXT) \
#	mast.bin$(EXEEXT) meme-client.bin$(EXEEXT)
PROGRAMS = $(bin_PROGRAMS)

am_alphtype_OBJECTS = alphtype.$(OBJEXT) hash_alph.$(OBJEXT)
alphtype_OBJECTS = $(am_alphtype_OBJECTS)
alphtype_LDADD = $(LDADD)
alphtype_DEPENDENCIES =
alphtype_LDFLAGS =
am__objects_1 = hash.$(OBJEXT) hash_alph.$(OBJEXT) \
	read_seq_file.$(OBJEXT) background.$(OBJEXT)
am_getsize_OBJECTS = getsize.$(OBJEXT) $(am__objects_1)
getsize_OBJECTS = $(am_getsize_OBJECTS)
getsize_DEPENDENCIES =
getsize_LDFLAGS =
am_mast_server_OBJECTS = mast-server.$(OBJEXT) readwrite.$(OBJEXT)
mast_server_OBJECTS = $(am_mast_server_OBJECTS)
mast_server_LDADD = $(LDADD)
mast_server_DEPENDENCIES =
mast_server_LDFLAGS =
am__objects_2 = logodds.$(OBJEXT) motifs.$(OBJEXT) regress.$(OBJEXT)
am_mast_bin_OBJECTS = mast.$(OBJEXT) clock.$(OBJEXT) diagram.$(OBJEXT) \
	mast-util.$(OBJEXT) pssm-distr.$(OBJEXT) $(am__objects_2) \
	$(am__objects_1)
mast_bin_OBJECTS = $(am_mast_bin_OBJECTS)
mast_bin_DEPENDENCIES =
mast_bin_LDFLAGS =
am_meme_client_bin_OBJECTS = meme-client.$(OBJEXT) readwrite.$(OBJEXT)
meme_client_bin_OBJECTS = $(am_meme_client_bin_OBJECTS)
meme_client_bin_LDADD = $(LDADD)
meme_client_bin_DEPENDENCIES =
meme_client_bin_LDFLAGS =
am_meme_server_OBJECTS = meme-server.$(OBJEXT) readwrite.$(OBJEXT)
meme_server_OBJECTS = $(am_meme_server_OBJECTS)
meme_server_LDADD = $(LDADD)
meme_server_DEPENDENCIES =
meme_server_LDFLAGS =
am_meme_bin_OBJECTS = clock.$(OBJEXT) display.$(OBJEXT) \
	dpalign.$(OBJEXT) em.$(OBJEXT) init.$(OBJEXT) \
	mast-util.$(OBJEXT) pssm-distr.$(OBJEXT) meme.$(OBJEXT) \
	meme_util.$(OBJEXT) seq2theta.$(OBJEXT) starts.$(OBJEXT) \
	prior.$(OBJEXT) justlike.$(OBJEXT) oops.$(OBJEXT) tcm.$(OBJEXT) \
	banner.$(OBJEXT) gamma.$(OBJEXT) likelihood.$(OBJEXT) \
	subseq7.$(OBJEXT) discretize.$(OBJEXT) mp.$(OBJEXT) \
	message.$(OBJEXT) $(am__objects_2) $(am__objects_1) \
	llr.$(OBJEXT) io.$(OBJEXT) logs.$(OBJEXT)
meme_bin_OBJECTS = $(am_meme_bin_OBJECTS)
meme_bin_DEPENDENCIES =
meme_bin_LDFLAGS =
am__objects_3 = strlcpy.$(OBJEXT)
am_readseq_OBJECTS = readseq.$(OBJEXT) ureadseq.$(OBJEXT) \
	$(am__objects_3)
readseq_OBJECTS = $(am_readseq_OBJECTS)
readseq_LDADD = $(LDADD)
readseq_DEPENDENCIES =
readseq_LDFLAGS =

DEFS = -DHAVE_CONFIG_H
DEFAULT_INCLUDES =  -I. -I$(srcdir) -I$(top_builddir)
CPPFLAGS = 
LDFLAGS = 
depcomp =
am__depfiles_maybe =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
CFLAGS = -Wall -DUNIX -D__USE_FIXED_PROTOTYPES__  -O3
DIST_SOURCES = $(alphtype_SOURCES) $(getsize_SOURCES) \
	$(mast_server_SOURCES) $(mast_bin_SOURCES) \
	$(meme_client_bin_SOURCES) $(meme_server_SOURCES) \
	$(meme_bin_SOURCES) $(readseq_SOURCES)

RECURSIVE_TARGETS = info-recursive dvi-recursive install-info-recursive \
	uninstall-info-recursive all-recursive install-data-recursive \
	install-exec-recursive installdirs-recursive install-recursive \
	uninstall-recursive check-recursive installcheck-recursive
DIST_COMMON = Makefile.am Makefile.in
DIST_SUBDIRS = . parallel
SOURCES = $(alphtype_SOURCES) $(getsize_SOURCES) $(mast_server_SOURCES) $(mast_bin_SOURCES) $(meme_client_bin_SOURCES) $(meme_server_SOURCES) $(meme_bin_SOURCES) $(readseq_SOURCES)

all: all-recursive

.SUFFIXES:
.SUFFIXES: .c .o .obj
$(srcdir)/Makefile.in:  Makefile.am  $(top_srcdir)/configure.ac $(ACLOCAL_M4)
	cd $(top_srcdir) && \
	  $(AUTOMAKE) --gnu  src/Makefile
Makefile:  $(srcdir)/Makefile.in  $(top_builddir)/config.status
	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)
binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
install-binPROGRAMS: $(bin_PROGRAMS)
	@$(NORMAL_INSTALL)
	$(mkinstalldirs) $(DESTDIR)$(bindir)
	@list='$(bin_PROGRAMS)'; for p in $$list; do \
	  p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
	  if test -f $$p \
	  ; then \
	    f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
	   echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \
	   $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \
	  else :; fi; \
	done

uninstall-binPROGRAMS:
	@$(NORMAL_UNINSTALL)
	@list='$(bin_PROGRAMS)'; for p in $$list; do \
	  f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
	  echo " rm -f $(DESTDIR)$(bindir)/$$f"; \
	  rm -f $(DESTDIR)$(bindir)/$$f; \
	done