--- 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