squared muscle

Former-commit-id: 54638fc7623ec0485109b0b5879144f8f2514213
Former-commit-id: 23f43cd31169d95df12ae1c207d9fd1c924d26b1

config/default.conf

@@ -118,10 +118,12 @@ INCDIR	 =	$(abspath $(PRTDIR))/include
 # default gmake variable in implicit rules
 # ------------------------------------
 
-CFLAGS 	  := $(CFLAGS)	$(OPTIM) $(MACHDEF) -I$(INCDIR)
+#CFLAGS 	  := $(CFLAGS) $(OPTIM) $(MACHDEF) -I$(INCDIR)
+CFLAGS 	  = $(OPTIM) $(MACHDEF) -I$(INCDIR)
 
-LDFLAGS	  := $(LDFLAGS)    -L$(LIBDIR) -L.
+#LDFLAGS	  := $(LDFLAGS) -L$(LIBDIR) -L.
+LDFLAGS	  = -L$(LIBDIR) -L.
 
-LDLIBS	  =	    $(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
+LDLIBS	  =	$(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
 
-LINTFLAGS = 	$(MACHDEF) -I$(INCDIR)
+LINTFLAGS = $(MACHDEF) -I$(INCDIR)

config/targets/lxbin.targ

@@ -34,7 +34,7 @@ all::	prelib $(PROGS) install
 
 prelib::
 	test -d $(PRTDIR) || mkdir $(PRTDIR)  # because some linker may complain
-	test -d $(LIBDIR) || mkdir $(LIBDIR)  # if -L$(LIBDIR) does not exist
+	test -d $(LIBDIR) || mkdir $(LIBDIR)  # if LIBDIR does not exist
 
 install::
 	test -d $(PRTDIR) || mkdir $(PRTDIR)

config/targets/package.targ

@@ -31,7 +31,6 @@ pkg.expand::
 	test -f $(PKGDIR)/configure || $(TAR) zxf $(PKGTAR) -C $(PKGDIR) --strip-components 1
 
 pkg.make:: pkg.expand
-	echo $(PKG_CONFIG)
 	test -f $(PKGDIR)/Makefile || (export PATH="$(PRTPATH_BIN):$$PATH" && \
 	                               export PKG_CONFIG=$(PKG_CONFIG) && \
 	                               export CC="$(CC)" && \

src/hmmer3/Makefile

@@ -22,7 +22,3 @@ include $(CFGDIR)targets/package.targ
 
 include $(CFGDIR)targets/help.targ
 
-# bug fix
-all::
-	-mkdir $(PKGDIR)/userguide
-

src/kimono/Makefile

@@ -22,9 +22,3 @@ DIRS = lxpack
 include ../../config/targets/propagate.targ
 
 include ../../config/targets/help.targ
-
-all::
-	$(MAKE) ACTION=$@ _action
-
-clean::
-	$(MAKE) -C lxpack portclean

src/muscle/Makefile

@@ -22,9 +22,3 @@ DIRS = muscle3.8.31
 include ../../config/targets/propagate.targ
 
 include ../../config/targets/help.targ
-
-all::
-	$(MAKE) ACTION=$@ _action
-
-clean::
-	$(MAKE) -C lxpack portclean

src/muscle/muscle3.8.31/Makefile

@@ -2,29 +2,24 @@
 # $Id: $
 # ---------------------------------------------------------------
 # @file: Makefile
-# @desc: makefile for lxpack
-#
-# @history:
-# @history:
-# @+	    <Gloup> : Apr 97 : Created
-# @+	    <Gloup> : Mar 02 : Updated for LXxware
-#
-# @note: should be processed with gnu compatible make
-# @note: helixware_compatible
-#
-# @end:
+# @desc: makefile for muscle
 # ---------------------------------------------------------------
 #
 include ../../../config/auto.conf
 
-DIRS = src
+all: muscle install 
 
-include ../../../config/targets/propagate.targ
+muscle:
+	chmod +x ./mk
+	(export CXX=$(CXX) && ./mk)
 
-include ../../../config/targets/help.targ
+test:
 
-all::
-	$(MAKE) ACTION=$@ _action
+install:
+	cp muscle $(BINDIR)
+	
+clean:
+	-\rm -f *.o muscle
 
-clean::
-	$(MAKE) -C lxpack portclean
+portclean: clean
+	-\rm -f $(BINDIR)/muscle