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distrib > Mandriva > current > i586 > media > contrib-release-src > by-pkgid > c67796e82803b3bbf60d267e0709c765 > files > 1

ncbi-6.1.20061015-5mdv2009.0.src.rpm

--- ncbi-tools6-6.1.20061015.orig/make/makeall.unx
+++ ncbi-tools6-6.1.20061015/make/makeall.unx
@@ -1,4 +1,4 @@
-#	makefile for asntool and ncbi core routines,
+#	-*- makefile -*- for asntool and ncbi core routines,
 #
 #	$Id: makeall.unx,v 6.276 2006/09/14 14:20:19 ucko Exp $
 #
@@ -233,7 +233,7 @@
 	dlgutil1.c dlgutil2.c e2trmlst.c e2docsum.c asn2graphic.c \
 	medview.c bspview.c gbfview.c gphview.c gphdraw.c gxydraw.c gtrdraw.c \
 	seqpanel.c ingengraph.c ingenext.c ingenwin.c \
-	biosrc.c cdrgn.c import.c pubdesc.c seqsub.c mapgene.c prtgene.c salogif.c
+	biosrc.c cdrgn.c import.c pubdesc.c seqsub.c mapgene.c prtgene.c
 
 SRC45 = ddvclick.c ddvgraph.c ddvopen.c ddvpanel.c
 
@@ -382,7 +382,7 @@
 	dlgutil1.o dlgutil2.o e2trmlst.o e2docsum.o asn2graphic.o \
 	medview.o bspview.o gbfview.o gphview.o gphdraw.o gxydraw.o gtrdraw.o \
 	seqpanel.o ingengraph.o ingenext.o ingenwin.o \
-	biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o salogif.o
+	biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o
 
 OBJ45 = ddvclick.o ddvgraph.o ddvopen.o ddvpanel.o
 
@@ -477,7 +477,7 @@
 nocopy : sources $(THR_OBJ) $(LIB1) $(LIB2) $(LIB3) $(DLIB4) $(DLIB400) \
 	$(LIB5) $(DLIB20) $(DLIB45) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
 	$(DLIB28) $(DLIB30) $(DLIB3000) \
-	$(DLIB34) $(DLIB37) $(DLIB38) $(LIB50) $(LIB60) $(LIB61) $(NCBI_SHLIBS)
+	$(DLIB34) $(DLIB37) $(DLIB38) $(LIB60) $(LIB61) $(NCBI_SHLIBS)
 
 sources : $(THR_SRC) $(SRC1) $(SRC2) $(SRC3) $(SRC4) $(SRC5) $(SRC20) $(SRC22) \
     $(SRC23) $(SRC28) $(SRC30) $(SRC50) $(SRC60) $(SRC61) $(SRCCOMPADJ)
@@ -485,7 +485,7 @@
 ## To clean out the directory without removing make
 ##
 clean :
-	-rm -f *.[acho]
+	-rm -f *.[acho] *.glo
 
 .NO_PARALLEL:	copy $(ULIB4) $(ULIB30)
 
@@ -643,10 +643,12 @@
 	cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS)
 	rm -f ../shlib/*.a
 
-#
-# Linux shared libs are built the same in the same manner as for SGI
-#
-shlib.lnx : shlib.sgi
+shlib.lnx :
+	-mkdir ../shlib
+	-rm -f ../shlib/*.a
+	ln $(NCBI_LIBDIR)/*.a ../shlib
+	cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so.$(NCBI_VERSION_MAJOR)/"` SH1="$(CC) -o" SH2="-shared *.o"
+	rm -f ../shlib/*.a
 
 shlib.sgi :
 	-mkdir ../shlib
@@ -767,7 +769,7 @@
 	cp -fp ../algo/blast/core/*.h ../include/algo/blast/core
 	- mkdir -p ../include/algo/blast/composition_adjustment
 	$(SRCCOPY) ../algo/blast/composition_adjustment/*.c .
-	$(SRCCOPY) ../algo/blast/composition_adjustment/*.h ../include
+#	$(SRCCOPY) ../algo/blast/composition_adjustment/*.h ../include
 	cp -fp ../algo/blast/composition_adjustment/*.h \
 		../include/algo/blast/composition_adjustment
 	- mkdir -p ../include/algo/blast/api
--- ncbi-tools6-6.1.20061015.orig/make/makedemo.unx
+++ ncbi-tools6-6.1.20061015/make/makedemo.unx
@@ -1,4 +1,4 @@
-#	makefile for demo programs
+#	-*- makefile -*- for demo programs
 #
 #	$Id: makedemo.unx,v 6.85 2005/10/19 20:45:14 ucko Exp $
 #
@@ -215,7 +215,7 @@
 # fa2htgs
 
 fa2htgs : fa2htgs.c
-	$(CC) -o fa2htgs $(LDFLAGS) fa2htgs.c $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
+	$(CC) -o fa2htgs $(LDFLAGS) fa2htgs.c $(LIB2) $(LIB1) $(OTHERLIBS)
 
 # getseq
 
--- ncbi-tools6-6.1.20061015.orig/make/makeshlb.unx
+++ ncbi-tools6-6.1.20061015/make/makeshlb.unx
@@ -1,4 +1,4 @@
-#
+# -*- makefile -*-
 #
 #	$Id: makeshlb.unx,v 6.1 1999/03/18 17:31:11 beloslyu Exp $
 #
@@ -12,7 +12,91 @@
 SH2 = `lorder *.o | tsort` $(NCBI_OTHERLIBS)
 
 %.so: %.a
-	rm -f *.o __*
+	rm -f *.o *.glo __*
 	ar x $<
+	case $< in \
+	    *OGL.a) for f in *.glo; do mv $$f `basename $$f .glo`.o; done ;; \
+	esac
 	$(SH1) $@ $(SH2)
 	rm -f *.o __*
+
+so=so.$(NCBI_VERSION_MAJOR).$(NCBI_VERSION_MINOR)
+
+%.$(so): %.a
+	$(CC) -shared -Wl,-soname=$*.so.$(NCBI_VERSION_MAJOR) -o $@ \
+	    -Wl,--whole-archive $< -Wl,--no-whole-archive \
+	    $($*_deps) $($*_sysdeps)
+
+%.so.$(NCBI_VERSION_MAJOR): %.$(so)
+	ln -s $< $@
+	ln -s $< $*.so
+
+# Make libncbiCacc and libncbiacc pointers to libncbiNacc, since it's
+# the most useful variant in the usual (net-only) case.  Do the same
+# for libnetentr, and link the static version into libncbiNacc.so, due
+# to a circular dependency.
+libnetentr.$(so) libncbiCacc.$(so) libncbiacc.$(so):
+	ln -s libncbiNacc.$(so) $@
+
+# Standardize on the OpenGL-enabled versions of Vibrant, since there's
+# no longer any real penalty in doing so.
+libvibrant.$(so):
+	ln -s libvibrantOGL.$(so) $@
+libncbicn3d.$(so):
+	ln -s libncbicn3dOGL.$(so) $@
+
+libblast_deps    = libblastcompadj.$(so) libncbi.$(so)
+libblastapi_deps = libblast.$(so) libncbitool.$(so)
+libblastcompadj_sysdeps = -lm
+libncbi_sysdeps  = -lm
+# libncbiCacc_deps = libncbicdr.$(so) libnetentr.a libnetcli.$(so)
+libncbiNacc_deps = libncbicdr.$(so) libnetentr.a libnetcli.$(so)
+# libncbiacc_deps  = libncbicdr.$(so)
+libncbicdr_deps  = libncbiobj.$(so)
+libncbiid1_deps  = libncbiobj.$(so) libnetcli.$(so)
+libncbimla_deps  = libncbiobj.$(so) libnetcli.$(so)
+libncbimmdb_deps = libncbiid1.$(so) libncbitool.$(so)
+libncbiobj_deps  = libncbi.$(so)
+libncbitool_deps = libblastcompadj.$(so) libncbiobj.$(so)
+libncbitxc2_deps = libncbitool.$(so) libnetcli.$(so)
+libnetblast_deps = libncbitool.$(so) libnetcli.$(so)
+libnetcli_deps   = libncbi.$(so)
+# libnetentr_deps = libncbiacc.$(so) libnetcli.$(so)
+
+libddvlib_deps        = libncbidesk.$(so)
+libncbicn3d_deps      = libncbiNacc.$(so) libddvlib.$(so)
+libncbicn3dOGL_deps   = $(libncbicn3d_deps) libvibrantOGL.$(so)
+libncbidesk_deps      = libblastapi.$(so) libncbimmdb.$(so) libvibrantOGL.$(so)
+libvibgif_deps        = libncbi.$(so)
+libvibnet_deps        = libncbiNacc.$(so) libncbidesk.$(so)
+# libvibrant_deps     = libncbi.$(so)
+# libvibrant_sysdeps  = $(VIBLIBS)
+# for ddvcolor stuff
+libvibrantOGL_deps    = libncbiobj.$(so)
+libvibrantOGL_sysdeps = $(OGLLIBS) $(VIBLIBS)
+
+# XXX - is there a way to express these programmatically?
+libblast.$(so):    $(libblast_deps)
+libblastapi.$(so): $(libblastapi_deps)
+# libncbiCacc.$(so): $(libncbiCacc_deps)
+libncbiNacc.$(so): $(libncbiNacc_deps)
+# libncbiacc.$(so):  $(libncbiacc_deps)
+libncbicdr.$(so):  $(libncbicdr_deps)
+libncbiid1.$(so):  $(libncbiid1_deps)
+libncbimla.$(so):  $(libncbimla_deps)
+libncbimmdb.$(so): $(libncbimmdb_deps)
+libncbiobj.$(so):  $(libncbiobj_deps)
+libncbitool.$(so): $(libncbitool_deps)
+libncbitxc2.$(so): $(libncbitxc2_deps)
+libnetblast.$(so): $(libnetblast_deps)
+libnetcli.$(so):   $(libnetcli_deps)
+# libnetentr.$(so): $(libnetentr_deps)
+
+libddvlib.$(so):      $(libddvlib_deps)
+# libncbicn3d.$(so):  $(libncbicn3d_deps)
+libncbicn3dOGL.$(so): $(libncbicn3dOGL_deps)
+libncbidesk.$(so):    $(libncbidesk_deps)
+libvibgif.$(so):      $(libvibgif_deps)
+libvibnet.$(so):      $(libvibnet_deps)
+# libvibrant.$(so):   $(libvibrant_deps)
+libvibrantOGL.$(so):  $(libvibrantOGL_deps)
--- ncbi-tools6-6.1.20061015.orig/make/makenet.unx
+++ ncbi-tools6-6.1.20061015/make/makenet.unx
@@ -1,4 +1,4 @@
-#   makefile for network demo programs and network entrez
+#   -*- makefile -*- for network demo programs and network entrez
 #
 #	$Id: makenet.unx,v 6.216 2006/05/03 03:37:42 kans Exp $
 #   test, ignore
@@ -322,6 +322,8 @@
 
 # objects & sources needed for versions of network demo programs
 
+OBJCN3D =       cn3dmain.o
+
 OBJDDV = ddvmain.o
 
 OBJUDV = udvmain.o
@@ -431,10 +433,12 @@
 	cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS)
 	rm -f ../shlib/*.a
 
-#
-# Linux shared libs are built the same in the same manner as for SGI
-#
-shlib.lnx : shlib.sgi
+shlib.lnx :
+	-mkdir ../shlib
+	-rm -f ../shlib/*.a
+	ln $(NCBI_LIBDIR)/*.a ../shlib
+	cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so.$(NCBI_VERSION_MAJOR)/"` SH1="$(CC) -o" SH2="-shared *.o"
+	rm -f ../shlib/*.a
 
 shlib.sgi :
 	-mkdir ../shlib
@@ -908,6 +912,12 @@
 		$(LIB23) $(LIBCOMPADJ) $(LIB3) $(LIB8) $(LIB7) $(NETCLILIB) \
 		$(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
 
+Cn3D : $(OBJCN3D) $(BENTREZLIBS) netentcf $(BLIB36)
+	$(CC) -o Cn3D $(LDFLAGS) $(OBJCN3D) $(LIB31) $(LIB3000) $(LIB20) $(LIB45) \
+		$(LIB22) $(LIB41) $(LIB23) $(LIB8) $(LIB7) $(NETCLILIB) \
+		$(LIB400) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) \
+		$(OGLLIBS)
+
 ddv    : $(OBJDDV)
 	$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
 	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
@@ -1146,11 +1156,11 @@
 
 # 'query' program used as WWW Entrez server
 query : query.c sumutils.c $(BLIB27) $(BLIB25) $(BLIB22)
-	$(CC) -o query $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(LIB5) $(LIB3) $(LIB2) $(LIB1) $(OTHERLIBS)
+	$(CC) -o query $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(LIB41) $(LIB5) $(LIB3) $(LIB2) $(LIB1) $(OTHERLIBS)
 
 # 'query' program used as WWW Entrez server
 Nquery : query.c sumutils.c $(BLIB27) $(BLIB25) $(BLIB22) $(BENTREZLIBS)
-	$(CC) -o Nquery $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
+	$(CC) -o Nquery $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(LIB41) $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
 
 
 # srchnt - pattern match REN search

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