Attachment #265945 for bug #358981

View | Details | Raw Unified | Return to bug 358981
Collapse All | Expand All

Lines 5-11 Link Here

(-)old/plugins/Makefile (-1 lines)
5	##	5	##
6	## $Id: Makefile,v 1.125 2011/03/07 20:06:35 johns Exp $	6	## $Id: Makefile,v 1.125 2011/03/07 20:06:35 johns Exp $
7	##	7	##
8	.SILENT:
9		8
10	default: make-arch-help	9	default: make-arch-help
11		10

Lines 4-10 Link Here

(-)old/plugins/Makefile.orig (-1 lines)
4	## Theoretical and Computational Biophysics Group	4	## Theoretical and Computational Biophysics Group
5	##	5	##
6		6
7	.SILENT:
8		7
9	default: make-arch-help	8	default: make-arch-help
10		9

Lines 1-4 Link Here

(-)old/plugins/aligntool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = aligntool.tcl cealign.tcl pkgIndex.tcl	2	VMFILES = aligntool.tcl cealign.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/apbsrun/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = apbsrun.tcl pkgIndex.tcl radii.dat	2	VMFILES = apbsrun.tcl pkgIndex.tcl radii.dat
4	VMVERSION = 1.3	3	VMVERSION = 1.3

Lines 1-4 Link Here

(-)old/plugins/atomedit/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = atomedit.tcl pkgIndex.tcl	2	VMFILES = atomedit.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/autoimd/Makefile (-1 lines)
1	.SILENT:
2		1
3	AUTOIMDFILES = autoimd.tcl autoimd-settings.tcl autoimd-api.tcl autoimd-gui.tcl pkgIndex.tcl autoimd-template.namd doc/ug.pdf namdrun.tcl	2	AUTOIMDFILES = autoimd.tcl autoimd-settings.tcl autoimd-api.tcl autoimd-gui.tcl pkgIndex.tcl autoimd-template.namd doc/ug.pdf namdrun.tcl
4	AUTOIMDVERSION = 1.7	3	AUTOIMDVERSION = 1.7

Lines 1-4 Link Here

(-)old/plugins/autoionize/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = autoionize.tcl autoionizegui.tcl pkgIndex.tcl	2	VMFILES = autoionize.tcl autoionizegui.tcl pkgIndex.tcl
4	VMVERSION = 1.3	3	VMVERSION = 1.3

Lines 1-4 Link Here

(-)old/plugins/bignum/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = bignum.tcl pkgIndex.tcl	2	VMFILES = bignum.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/biocore/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = biocore.tcl biocorechat.tcl biocorelogin.tcl biocorepubsync.tcl pkgIndex.tcl locked.gif unlocked.gif biocoreHelper.tcl biocoreutil.tcl	2	VMFILES = biocore.tcl biocorechat.tcl biocorelogin.tcl biocorepubsync.tcl pkgIndex.tcl locked.gif unlocked.gif biocoreHelper.tcl biocoreutil.tcl
4		3

Lines 1-6 Link Here

(-)old/plugins/catdcd/Makefile (-3 / +2 lines)
1	# Makefile for catdcd	1	# Makefile for catdcd
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5
Lines 45-52 ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${ Link Here
45	LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}	44	LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
46		45
47	# all other platforms	46	# all other platforms
48	${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a	47	${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
49	${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm	48	${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
50		49
51	${ARCHDIR}/hash.o: hash.h hash.c	50	${ARCHDIR}/hash.o: hash.h hash.c
52	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o	51	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o

Lines 1-4 Link Here

(-)old/plugins/cgtools/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = cggui.tcl cgtools.tcl cgnetworking.tcl pkgIndex.tcl \	2	VMFILES = cggui.tcl cgtools.tcl cgnetworking.tcl pkgIndex.tcl \
4	protein.cgc water.cgc rbcg-2007.par rbcg-2007.top	3	protein.cgc water.cgc rbcg-2007.par rbcg-2007.top

Lines 1-4 Link Here

(-)old/plugins/chirality/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = chirality.tcl chirality_gui.tcl pkgIndex.tcl	2	VMFILES = chirality.tcl chirality_gui.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-6 Link Here

(-)old/plugins/cionize/Makefile (-3 / +2 lines)
1	# Makefile for cionize	1	# Makefile for cionize
2		2
3	#.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5
Lines 52-59 ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} $ Link Here
52	LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}	51	LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
53		52
54	# all other platforms	53	# all other platforms
55	${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a	54	${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
56	${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm	55	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
57		56
58	${ARCHDIR}/hash.o: hash.h hash.c	57	${ARCHDIR}/hash.o: hash.h hash.c
59	${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o	58	${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o

Lines 1-6 Link Here

(-)old/plugins/cionize/Makefile.mine (-1 lines)
1	# Makefile for cionize	1	# Makefile for cionize
2		2
3	#.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-6 Link Here

(-)old/plugins/cionize/Makefile.mine.old (-1 lines)
1	# Makefile for cionize	1	# Makefile for cionize
2		2
3	#.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-6 Link Here

(-)old/plugins/cionize/Makefile.specialbuilds (-1 lines)
1	# Makefile for cionize	1	# Makefile for cionize
2		2
3	#.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-6 Link Here

(-)old/plugins/cionize/mcudahacks/Makefile.specialbuilds (-1 lines)
1	# Makefile for cionize	1	# Makefile for cionize
2		2
3	#.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-4 Link Here

(-)old/plugins/cispeptide/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = cispeptide.tcl cispeptide_gui.tcl pkgIndex.tcl	2	VMFILES = cispeptide.tcl cispeptide_gui.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/cliptool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = cliptool.tcl pkgIndex.tcl	2	VMFILES = cliptool.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/clonerep/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = clonerep.tcl pkgIndex.tcl	2	VMFILES = clonerep.tcl pkgIndex.tcl
4	VMVERSION = 1.2	3	VMVERSION = 1.2

Lines 1-6 Link Here

(-)old/plugins/clustalw/Makefile (-2 / +1 lines)
1	# Makefile for clustalw	1	# Makefile for clustalw
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5
Lines 66-72 OBJS = ${ARCHDIR}/alnscore.o \ Link Here
66	${ARCHDIR}/clustalw.exe: ${OBJS}	65	${ARCHDIR}/clustalw.exe: ${OBJS}
67	LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe	66	LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe
68	${ARCHDIR}/clustalw: ${OBJS}	67	${ARCHDIR}/clustalw: ${OBJS}
69	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm	68	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
70		69
71		70
72	# Objects.	71	# Objects.

Lines 1-6 Link Here

(-)old/plugins/cluster/Makefile (-2 / +1 lines)
1	# Makefile for psfgen	1	# Makefile for psfgen
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5
Lines 48-54 ${ARCHDIR}/cluster.exe : ${OBJS} Link Here
48		47
49	# all other platforms	48	# all other platforms
50	${ARCHDIR}/cluster : ${OBJS}	49	${ARCHDIR}/cluster : ${OBJS}
51	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm	50	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
52		51
53	${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c	52	${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c
54	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o	53	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o

Lines 1-4 Link Here

(-)old/plugins/colorscalebar/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = colorscalebar.tcl pkgIndex.tcl	2	VMFILES = colorscalebar.tcl pkgIndex.tcl
4	VMVERSION = 1.3	3	VMVERSION = 1.3

Lines 1-4 Link Here

(-)old/plugins/contactmap/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = contactmap.tcl pkgIndex.tcl	2	VMFILES = contactmap.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/dataimport/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = dataimport.tcl pkgIndex.tcl	2	VMFILES = dataimport.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/demomaster/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = demomaster.tcl pkgIndex.tcl	2	VMFILES = demomaster.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/dipwatch/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = dipwatch.tcl pkgIndex.tcl	2	VMFILES = dipwatch.tcl pkgIndex.tcl
4	VMVERSION = 1.2	3	VMVERSION = 1.2

Lines 1-7 Link Here

(-)old/plugins/doc/Makefile (-1 lines)
1	#	1	#
2	# Plugin documentation Makefile	2	# Plugin documentation Makefile
3	#	3	#
4	.SILENT:
5		4
6	ECHO = echo	5	ECHO = echo
7	DELETEDIR = rm -rf	6	DELETEDIR = rm -rf

Lines 1-4 Link Here

(-)old/plugins/dowser/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = dowser.tcl dowser_gui.tcl pkgIndex.tcl	2	VMFILES = dowser.tcl dowser_gui.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/exectool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = exectool.tcl jobmanager.tcl pkgIndex.tcl	2	VMFILES = exectool.tcl jobmanager.tcl pkgIndex.tcl
4	VMVERSION = 1.2	3	VMVERSION = 1.2

Lines 1-4 Link Here

(-)old/plugins/extendedpdb/Makefile (-1 lines)
1	#.SILENT:
2		1
3	VMFILES = extendedpdb.tcl pkgIndex.tcl	2	VMFILES = extendedpdb.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-6 Link Here

(-)old/plugins/fmtool/Makefile (-1 lines)
1	# Makefile for fmtool	1	# Makefile for fmtool
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-4 Link Here

(-)old/plugins/gofrgui/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = gofrgui.tcl pkgIndex.tcl	2	VMFILES = gofrgui.tcl pkgIndex.tcl
4	VMVERSION = 1.2	3	VMVERSION = 1.2

Lines 1-4 Link Here

(-)old/plugins/hbonds/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = hbonds.tcl pkgIndex.tcl	2	VMFILES = hbonds.tcl pkgIndex.tcl
4	VMVERSION = 1.2	3	VMVERSION = 1.2

Lines 1-4 Link Here

(-)old/plugins/idatm/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = idatm.tcl pkgIndex.tcl	2	VMFILES = idatm.tcl pkgIndex.tcl
4	VMVERSION = 0.1	3	VMVERSION = 0.1

Lines 1-4 Link Here

(-)old/plugins/ilstools/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = ilstools.tcl pkgIndex.tcl oxygen.xyz nitricoxide.xyz \	2	VMFILES = ilstools.tcl pkgIndex.tcl oxygen.xyz nitricoxide.xyz \
4	carbonmonoxide.xyz carbondioxide.xyz ethene.xyz methane.xyz \	3	carbonmonoxide.xyz carbondioxide.xyz ethene.xyz methane.xyz \

Lines 1-4 Link Here

(-)old/plugins/imdmenu/Makefile (-1 lines)
1	.SILENT:
2		1
3	IMDMENUFILES = imdmenu.tcl pkgIndex.tcl	2	IMDMENUFILES = imdmenu.tcl pkgIndex.tcl
4	IMDMENUVERSION = 1.0	3	IMDMENUVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/inorganicbuilder/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = inorganicbuilder.tcl pkgIndex.tcl	2	VMFILES = inorganicbuilder.tcl pkgIndex.tcl
4	VMVERSION = 0.1	3	VMVERSION = 0.1

Lines 1-4 Link Here

(-)old/plugins/irspecgui/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = irspecgui.tcl pkgIndex.tcl	2	VMFILES = irspecgui.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/jmvexport/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = jmvexport.tcl pkgIndex.tcl	2	VMFILES = jmvexport.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0




# Makefile for libbiokit

.SILENT:

.SUFFIXES: 


${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}
	LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe
${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}
	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o


${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}
	LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe
${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}
	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o


${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}
	LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe
${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}
	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o


${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}
	LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe
${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}
	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o


${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}
	LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe
${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}
	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o


${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}
	LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe
${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}
	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp
	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o
    

Lines 1-4 Link Here

(-)old/plugins/mdff/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = mdff.tcl mdff_check.tcl mdff_map.tcl mdff_sim.tcl mdff_correlation.tcl mdff_setup.tcl pkgIndex.tcl mdff_template.namd mdff_tmp.tcl	2	VMFILES = mdff.tcl mdff_check.tcl mdff_map.tcl mdff_sim.tcl mdff_correlation.tcl mdff_setup.tcl pkgIndex.tcl mdff_template.namd mdff_tmp.tcl
4		3

Lines 1-4 Link Here

(-)old/plugins/membrane/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = membrane.tcl pkgIndex.tcl \	2	VMFILES = membrane.tcl pkgIndex.tcl \
4	popc_box.pdb popc_box.psf \	3	popc_box.pdb popc_box.psf \

Lines 1-4 Link Here

(-)old/plugins/mergestructs/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = mergestructs.tcl pkgIndex.tcl	2	VMFILES = mergestructs.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/molefacture/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = molefacture.tcl molefacture_builder.tcl \	2	VMFILES = molefacture.tcl molefacture_builder.tcl \
4	molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \	3	molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \

Lines 1-7 Link Here

(-)old/plugins/molfile_plugin/Makefile (-3 / +2 lines)
1	# Makefile for molecule file readers	1	# Makefile for molecule file readers
2	# $Id: Makefile,v 1.112 2011/03/05 04:27:06 johns Exp $	2	# $Id: Makefile,v 1.112 2011/03/05 04:27:06 johns Exp $
3		3
4	.SILENT:
5		4
6	.SUFFIXES:	5	.SUFFIXES:
7		6
Lines 14-21 INCDIR = -I../include -I${SRCDIR} Link Here
14		13
15	VPATH = src ../include ${ARCHDIR}	14	VPATH = src ../include ${ARCHDIR}
16		15
17	SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"	16	SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN"
18	SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"	17	SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
19		18
20	#	19	#
21	# Rules	20	# Rules

Lines 1-6 Link Here

(-)old/plugins/molfile_plugin/src/cifplugin/Makefile (-2 / +1 lines)
1	# Makefile for molecule file readers	1	# Makefile for molecule file readers
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5
Lines 14-20 INCDIR = -I../include -I${SRCDIR} Link Here
14	VPATH = src ../include ${ARCHDIR}	13	VPATH = src ../include ${ARCHDIR}
15		14
16	SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"	15	SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
17	SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"	16	SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
18		17
19	#	18	#
20	# Rules	19	# Rules

Lines 1-4 Link Here

(-)old/plugins/moltoptools/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = moltoptools.tcl pkgIndex.tcl	2	VMFILES = moltoptools.tcl pkgIndex.tcl
4	VMVERSION = 0.1	3	VMVERSION = 0.1

Lines 1-4 Link Here

(-)old/plugins/multimolanim/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = multimolanim.tcl pkgIndex.tcl	2	VMFILES = multimolanim.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/multiplot/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = multiplot.tcl pkgIndex.tcl	2	VMFILES = multiplot.tcl pkgIndex.tcl
4	VMVERSION = 1.5	3	VMVERSION = 1.5

Lines 1-4 Link Here

(-)old/plugins/multitext/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = multitext.tcl pkgIndex.tcl	2	VMFILES = multitext.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/namdenergy/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = namdenergy.tcl pkgIndex.tcl	2	VMFILES = namdenergy.tcl pkgIndex.tcl
4	VMVERSION = 1.3	3	VMVERSION = 1.3

Lines 1-4 Link Here

(-)old/plugins/namdgui/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = namdgui.tcl namdgui_tclforces.tcl pkgIndex.tcl	2	VMFILES = namdgui.tcl namdgui_tclforces.tcl pkgIndex.tcl
4	VMVERSION = 1.3	3	VMVERSION = 1.3

Lines 1-4 Link Here

(-)old/plugins/namdplot/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = namdplot.tcl pkgIndex.tcl	2	VMFILES = namdplot.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/namdserver/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = namdserver.tcl pkgIndex.tcl	2	VMFILES = namdserver.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/nanotube/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = gui.tcl graphene.tcl nanotube.tcl pkgIndex.tcl	2	VMFILES = gui.tcl graphene.tcl nanotube.tcl pkgIndex.tcl
4	VMVERSION = 1.2	3	VMVERSION = 1.2

Lines 1-4 Link Here

(-)old/plugins/navfly/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = navfly.tcl pkgIndex.tcl	2	VMFILES = navfly.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/navigate/Makefile (-1 lines)
1	.SILENT:
2		1
3	COPYFILES = navigate.tcl pkgIndex.tcl	2	COPYFILES = navigate.tcl pkgIndex.tcl
4	DIR = $(PLUGINDIR)/noarch/tcl/navigate1.0	3	DIR = $(PLUGINDIR)/noarch/tcl/navigate1.0

Lines 1-6 Link Here

(-)old/plugins/nlenergy/Makefile (-1 lines)
1	# Makefile for nlenergy	1	# Makefile for nlenergy
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-4 Link Here

(-)old/plugins/optimization/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = optimization.tcl pkgIndex.tcl	2	VMFILES = optimization.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/palettetool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = palettetool.tcl pkgIndex.tcl	2	VMFILES = palettetool.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/paratool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = paratool.tcl paratool_atomedit.tcl paratool_aux.tcl \	2	VMFILES = paratool.tcl paratool_atomedit.tcl paratool_aux.tcl \
4	paratool_respcharges.tcl paratool_charmmcharges.tcl \	3	paratool_respcharges.tcl paratool_charmmcharges.tcl \

Lines 1-4 Link Here

(-)old/plugins/parsefep/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = parseFEP.tcl pkgIndex.tcl	2	VMFILES = parseFEP.tcl pkgIndex.tcl
4	VMVERSION = 1.4	3	VMVERSION = 1.4

Lines 1-4 Link Here

(-)old/plugins/pbctools/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = pbcbox.tcl pbcgui.tcl pbcjoin.tcl pbcset.tcl pbctools.tcl \	2	VMFILES = pbcbox.tcl pbcgui.tcl pbcjoin.tcl pbcset.tcl pbctools.tcl \
4	pbcunwrap.tcl pbcwrap.tcl pkgIndex.tcl	3	pbcunwrap.tcl pbcwrap.tcl pkgIndex.tcl

Lines 1-4 Link Here

(-)old/plugins/pdbtool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = pdbtool.tcl pkgIndex.tcl	2	VMFILES = pdbtool.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/phylotree/Makefile (-1 lines)
1	.SILENT:
2		1
3	.SUFFIXES:	2	.SUFFIXES:
4		3

Lines 1-4 Link Here

(-)old/plugins/plumed/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = vmdplumed.tcl pkgIndex.tcl	2	VMFILES = vmdplumed.tcl pkgIndex.tcl
4	VMVERSION = 0.9	3	VMVERSION = 0.9

Lines 1-6 Link Here

(-)old/plugins/pmepot/Makefile (-1 lines)
1	# Makefile for PME potential library	1	# Makefile for PME potential library
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-6 Link Here

(-)old/plugins/psfgen/Makefile (-1 lines)
1	# Makefile for psfgen	1	# Makefile for psfgen
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 5-11 Link Here

(-)old/plugins/psfgen/Makefile.pluginio (-1 lines)
5	# them itself, but at the moment this is a good short-term development	5	# them itself, but at the moment this is a good short-term development
6	# path until we write something better.	6	# path until we write something better.
7		7
8	.SILENT:
9		8
10	.SUFFIXES:	9	.SUFFIXES:
11		10

Lines 1-4 Link Here

(-)old/plugins/qmtool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = qmtool.tcl qmtool_analysis.tcl qmtool_atomedit.tcl \	2	VMFILES = qmtool.tcl qmtool_analysis.tcl qmtool_atomedit.tcl \
4	qmtool_aux.tcl qmtool_charges.tcl qmtool_intcoor.tcl \	3	qmtool_aux.tcl qmtool_charges.tcl qmtool_intcoor.tcl \

Lines 1-4 Link Here

(-)old/plugins/ramaplot/Makefile (-1 lines)
1	.SILENT:
2		1
3	FILES = ramaplot.tcl pkgIndex.tcl	2	FILES = ramaplot.tcl pkgIndex.tcl
4	VERSION = 1.1	3	VERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/readcharmmpar/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = readcharmmpar.tcl par_all27_prot_lipid_na.inp pkgIndex.tcl par_amber2charmm.inp par_all36_lipid.prm	2	VMFILES = readcharmmpar.tcl par_all27_prot_lipid_na.inp pkgIndex.tcl par_amber2charmm.inp par_all36_lipid.prm
4	VMVERSION = 1.2	3	VMVERSION = 1.2

Lines 1-4 Link Here

(-)old/plugins/readcharmmtop/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = readcharmmtop.tcl pkgIndex.tcl top_all27_prot_lipid_na.inp top_all27_hybrid.inp top_amber2charmm.inp top_all36_lipid.rtf	2	VMFILES = readcharmmtop.tcl pkgIndex.tcl top_all27_prot_lipid_na.inp top_all27_hybrid.inp top_amber2charmm.inp top_all36_lipid.rtf
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/resptool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = resptool.tcl pkgIndex.tcl	2	VMFILES = resptool.tcl pkgIndex.tcl
4	VMVERSION = 1.2	3	VMVERSION = 1.2

Lines 1-4 Link Here

(-)old/plugins/rmsd/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = rmsd.tcl pkgIndex.tcl	2	VMFILES = rmsd.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/rmsdtt/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = rmsdtt.tcl pkgIndex.tcl	2	VMFILES = rmsdtt.tcl pkgIndex.tcl
4	VMVERSION = 2.0	3	VMVERSION = 2.0

Lines 1-6 Link Here

(-)old/plugins/rnaview/Makefile (-1 lines)
1	# Makefile for rnaview	1	# Makefile for rnaview
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-4 Link Here

(-)old/plugins/ruler/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = ruler.tcl pkgIndex.tcl	2	VMFILES = ruler.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/runante/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = runante.tcl pkgIndex.tcl	2	VMFILES = runante.tcl pkgIndex.tcl
4	VMVERSION = 0.1	3	VMVERSION = 0.1

Lines 1-4 Link Here

(-)old/plugins/runsqm/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = runsqm.tcl pkgIndex.tcl	2	VMFILES = runsqm.tcl pkgIndex.tcl
4	VMVERSION = 0.1	3	VMVERSION = 0.1

Lines 1-4 Link Here

(-)old/plugins/saltbr/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = saltbr.tcl pkgIndex.tcl	2	VMFILES = saltbr.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/solvate/Makefile (-1 lines)
1	.SILENT:
2		1
3	SOLVFILES = wat.top wat.pdb wat.psf solvate.tcl pkgIndex.tcl	2	SOLVFILES = wat.top wat.pdb wat.psf solvate.tcl pkgIndex.tcl
4	SOLVVERSION = 1.4	3	SOLVVERSION = 1.4

Lines 1-4 Link Here

(-)old/plugins/ssrestraints/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = ssrestraints.tcl ssrestraints_stride.tcl pkgIndex.tcl	2	VMFILES = ssrestraints.tcl ssrestraints_stride.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-6 Link Here

(-)old/plugins/stamp/Makefile (-2 / +1 lines)
1	# Makefile for stamp	1	# Makefile for stamp
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5
Lines 101-107 OBJS = ${ARCHDIR}/a3to1.o \ Link Here
101	${ARCHDIR}/stamp.exe: ${OBJS}	100	${ARCHDIR}/stamp.exe: ${OBJS}
102	LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe	101	LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe
103	${ARCHDIR}/stamp: ${OBJS}	102	${ARCHDIR}/stamp: ${OBJS}
104	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm	103	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
105		104
106		105
107	# Objects.	106	# Objects.

Lines 1-4 Link Here

(-)old/plugins/stingtool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = stingtool.tcl pkgIndex.tcl	2	VMFILES = stingtool.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/symmetrytool/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = symmetry.tcl pkgIndex.tcl	2	VMFILES = symmetry.tcl pkgIndex.tcl
4	VMVERSION = 1.3	3	VMVERSION = 1.3

Lines 1-4 Link Here

(-)old/plugins/textview/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = textview.tcl pkgIndex.tcl	2	VMFILES = textview.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1

Lines 1-4 Link Here

(-)old/plugins/timeline/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = timeline.tcl pkgIndex.tcl	2	VMFILES = timeline.tcl pkgIndex.tcl
4	VMVERSION = 2.3	3	VMVERSION = 2.3

Lines 1-4 Link Here

(-)old/plugins/topotools/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = pkgIndex.tcl README topotools.tcl topoatoms.tcl \	2	VMFILES = pkgIndex.tcl README topotools.tcl topoatoms.tcl \
4	topobonds.tcl topoangles.tcl topodihedrals.tcl topoimpropers.tcl \	3	topobonds.tcl topoangles.tcl topodihedrals.tcl topoimpropers.tcl \

Lines 1-4 Link Here

(-)old/plugins/trunctraj/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = trunctraj.tcl pkgIndex.tcl	2	VMFILES = trunctraj.tcl pkgIndex.tcl
4	VMVERSION = 1.5	3	VMVERSION = 1.5

Lines 1-4 Link Here

(-)old/plugins/updater/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = updater.tcl pkgIndex.tcl	2	VMFILES = updater.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/utilities/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = utilities.tcl pkgIndex.tcl	2	VMFILES = utilities.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/vdna/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = vdna.tcl pkgIndex.tcl	2	VMFILES = vdna.tcl pkgIndex.tcl
4	VMVERSION = 2.2	3	VMVERSION = 2.2

Lines 1-4 Link Here

(-)old/plugins/viewchangerender/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = vcr.tcl vcr_gui.tcl pkgIndex.tcl	2	VMFILES = vcr.tcl vcr_gui.tcl pkgIndex.tcl
4	VMVERSION = 1.5	3	VMVERSION = 1.5

Lines 1-4 Link Here

(-)old/plugins/viewmaster/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = viewmaster.tcl pkgIndex.tcl	2	VMFILES = viewmaster.tcl pkgIndex.tcl
4	VMVERSION = 2.4	3	VMVERSION = 2.4

Lines 1-4 Link Here

(-)old/plugins/vmddebug/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = vmddebug.tcl debugatomsel.tcl pkgIndex.tcl	2	VMFILES = vmddebug.tcl debugatomsel.tcl pkgIndex.tcl
4	VMVERSION = 1.0	3	VMVERSION = 1.0

Lines 1-4 Link Here

(-)old/plugins/vmdmovie/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = vmdmovie.tcl pkgIndex.tcl	2	VMFILES = vmdmovie.tcl pkgIndex.tcl
4	VMVERSION = 1.8	3	VMVERSION = 1.8

Lines 1-4 Link Here

(-)old/plugins/vmdtkcon/Makefile (-1 lines)
1	.SILENT:
2		1
3	TKCONFILES = vmdtkcon.tcl tkcon-modified.tcl pkgIndex.tcl tkcon-2.3 README	2	TKCONFILES = vmdtkcon.tcl tkcon-modified.tcl pkgIndex.tcl tkcon-2.3 README
4	DIR = $(PLUGINDIR)/noarch/tcl/vmdtkcon1.1	3	DIR = $(PLUGINDIR)/noarch/tcl/vmdtkcon1.1

Lines 1-4 Link Here

(-)old/plugins/volmapgui/Makefile (-1 lines)
1	.SILENT:
2		1
3	COPYFILES = volmapgui.tcl pkgIndex.tcl	2	COPYFILES = volmapgui.tcl pkgIndex.tcl
4	DIR = $(PLUGINDIR)/noarch/tcl/volmapgui1.1	3	DIR = $(PLUGINDIR)/noarch/tcl/volmapgui1.1

Lines 1-6 Link Here

(-)old/plugins/volutil/Makefile (-1 lines)
1	# Makefile for volutil	1	# Makefile for volutil
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5

Lines 1-4 Link Here

(-)old/plugins/zoomseq/Makefile (-1 lines)
1	.SILENT:
2		1
3	VMFILES = zoomseq.tcl pkgIndex.tcl	2	VMFILES = zoomseq.tcl pkgIndex.tcl
4	VMVERSION = 1.1	3	VMVERSION = 1.1




$install_name = "vmd";

# Directory where VMD startup script is installed, should be in users' paths.
$install_bin_dir="gentoo-bindir";

# Directory where VMD files and executables are installed
$install_library_dir="gentoo-libdir/$install_name";


# optionally override hard-coded defaults above with environment variables

# Configure script code begins here
############################################################################

## Test for existence of a properly compiled plugin tree
if (!(-e "plugins")) {
  print "\n";
  print "VMD plugin directory not found.\n";
  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
  print "into a 'plugins' directory linked or located in this directory.\n";
  print "Be sure your PLUGINDIR environment variable is set before running\n";
  print "'make distrib' in the plugin build area.\n";
  print "\n";
  die "Halting configuration until VMD plugins are built.\n";
} else {
  if (!(-e "plugins/include/vmdplugin.h")) {
    print "\n";
    print "VMD plugin include files or directory not found.\n";
    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
    print "into a 'plugins' directory linked or located in this directory.\n";
    print "Be sure your PLUGINDIR environment variable is set before running\n";
    print "'make distrib' in the plugin build area.\n";
    print "\n";
    die "Halting configuration until VMD plugins are built.\n";
  }
} 

#################### Parse command line options   ###########
# list of allowed architectures
@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'FREEBSDAMD64', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'BLUEWATERS', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');


################ Plugin options
#
$plugin_dir	= "gentoo-plugindir";
$plugin_include = "-I$plugin_dir/include";
$plugin_library = "";
$plugin_libs    = "";

@plugin_extra   = ();

if ($config_staticplugin) {
  $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
  $plugin_include .= " -I$molfile_dir";
  $plugin_library .= " -L$molfile_dir";
  $plugin_libs    .= " -lmolfile_plugin";

################ FLTK GUI
$fltk_defines     = "-DVMDGUI -DVMDFLTK";
$fltk_dir         = "$vmd_library_dir/fltk";
$fltk_include     = "-Igentoo-fltk-include";
$fltk_library     = "-Lgentoo-fltk-libs";
$fltk_libs        = "-lfltk -lX11";
#@fltk_cc          = ('forms_ui.c');
@fltk_cu          = ();

if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
$tcl_library      = "-L$stock_tcl_library_dir";
if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
$tcl_libs         = "-ltcl";  
if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }

@tcl_cc           = ();
@tcl_cu           = ();

#######################
$netcdf_defines     = "";
$netcdf_dir         = "$vmd_library_dir/netcdf";
$netcdf_include     = "-Igentoo-netcdf-include";
$netcdf_library     = "-Lgentoo-netcdf-libs";
$netcdf_libs        = "-lnetcdf";
@netcdf_cc          = ();
@netcdf_cu          = ();

$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";

$python_defines     = "-DVMDPYTHON";
$python_include     = "-Igentoo-python-include -Igentoo-numpy-include";
$python_library     = "-Lgentoo-python-lib";
$python_libs        = "-lgentoo-python-link -lpthread";
@python_h           = ('PythonTextInterp.h',
                       'VMDTkinterMenu.h',
		       'py_commands.h',


    # XFree 4.0 Direct Rendering Interface and GLX 
    $opengl_dir         = "/usr/X11R6";
    $opengl_include     = "-Igentoo-opengl-include";
    $opengl_library     = "-Lgentoo-opengl-libs";
    $opengl_libs        = "-lGL -lGLU"; 
    # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";


      $arch_lopts       .= "-i-static ";
    } else {
      # compling with GCC
      $arch_cc          = "gentoo-gcc";
      $arch_ccpp        = "gentoo-g++";
      $arch_depend_flag = "-MM";
      $arch_shld        = "gentoo-g++ -shared";
      $arch_shlibname   = "so";
      $arch_shcppopts   = "-fPIC";
      $arch_shldopts    = "gentoo-ldflags";
      $arch_opt_flag    = "gentoo-cflags";
      $arch_copts       = "gentoo-cflags";

      if ($config_static) {
        $arch_lopts       = "-static";

      $arch_template_repository = "foobar";
      $arch_shlibname   = "so";
      $arch_shcppopts   = "-fPIC";
      $arch_shldopts    = "gentoo-ldflags";

      if ($config_static) {
        # link everything statically (this won't work due to libGL issues)

DEFINES     = $DEFINES

# compiler and compiler directives 
CC          = gentoo-gcc
CFLAGS      = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags

CCPP	    = gentoo-g++
CPPFLAGS    = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags

NVCC        = $arch_nvcc
NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)

	if [ ! -r ./$arch_template_repository ]; then \\
	  ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\
	fi; \\
	\$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
	\$(COMPILERC) \$(RCFLAGS)

install:

	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
	\$(CD) $vmd_bin_dir ; \\
	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
	if [ -x "/bin/bash" ]; then \\
		\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
		\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
		\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
		\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\

Return to bug 358981

Lines 1-6 Link Here

(-)old/plugins/libbiokit/Makefile (-7 / +6 lines)
1	# Makefile for libbiokit	1	# Makefile for libbiokit
2		2
3	.SILENT:
4		3
5	.SUFFIXES:	4	.SUFFIXES:
6		5
Lines 111-117 ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cp Link Here
111	${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}	110	${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}
112	LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe	111	LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe
113	${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}	112	${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}
114	${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm	113	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
115	${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp	114	${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
116	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o	115	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o
117		116
Lines 119-125 ${ARCHDIR}/percid.o: ${UTILSRCDIR}/perci Link Here
119	${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}	118	${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}
120	LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe	119	LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe
121	${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}	120	${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}
122	${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm	121	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
123	${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp	122	${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
124	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o	123	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o
125		124
Lines 127-133 ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair. Link Here
127	${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}	126	${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}
128	LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe	127	LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe
129	${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}	128	${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}
130	${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm	129	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
131	${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp	130	${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
132	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o	131	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o
133		132
Lines 135-141 ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cp Link Here
135	${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}	134	${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}
136	LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe	135	LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe
137	${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}	136	${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}
138	${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm	137	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
139	${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp	138	${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
140	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o	139	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o
141		140
Lines 143-149 ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp Link Here
143	${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}	142	${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}
144	LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe	143	LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe
145	${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}	144	${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}
146	${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm	145	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
147	${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp	146	${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
148	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o	147	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o
149		148
Lines 151-157 ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr. Link Here
151	${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}	150	${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}
152	LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe	151	LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe
153	${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}	152	${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}
154	${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm	153	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
155	${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp	154	${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp
156	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o	155	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o
157		156

Lines 13-22 Link Here

(-)old/vmd-1.9/configure (-52 / +28 lines)
13	$install_name = "vmd";	13	$install_name = "vmd";
14		14
15	# Directory where VMD startup script is installed, should be in users' paths.	15	# Directory where VMD startup script is installed, should be in users' paths.
16	$install_bin_dir="/usr/local/bin";	16	$install_bin_dir="gentoo-bindir";
17		17
18	# Directory where VMD files and executables are installed	18	# Directory where VMD files and executables are installed
19	$install_library_dir="/usr/local/lib/$install_name";	19	$install_library_dir="gentoo-libdir/$install_name";
20		20
21		21
22	# optionally override hard-coded defaults above with environment variables	22	# optionally override hard-coded defaults above with environment variables
Lines 132-160 if ($ENV{VMDINSTALLLIBRARYDIR}) { Link Here
132	# Configure script code begins here	132	# Configure script code begins here
133	############################################################################	133	############################################################################
134		134
135	## Test for existence of a properly compiled plugin tree
136	if (!(-e "plugins")) {
137	print "\n";
138	print "VMD plugin directory not found.\n";
139	print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
140	print "into a 'plugins' directory linked or located in this directory.\n";
141	print "Be sure your PLUGINDIR environment variable is set before running\n";
142	print "'make distrib' in the plugin build area.\n";
143	print "\n";
144	die "Halting configuration until VMD plugins are built.\n";
145	} else {
146	if (!(-e "plugins/include/vmdplugin.h")) {
147	print "\n";
148	print "VMD plugin include files or directory not found.\n";
149	print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
150	print "into a 'plugins' directory linked or located in this directory.\n";
151	print "Be sure your PLUGINDIR environment variable is set before running\n";
152	print "'make distrib' in the plugin build area.\n";
153	print "\n";
154	die "Halting configuration until VMD plugins are built.\n";
155	}
156	}
157
158	#################### Parse command line options ###########	135	#################### Parse command line options ###########
159	# list of allowed architectures	136	# list of allowed architectures
160	@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'FREEBSDAMD64', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'BLUEWATERS', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');	137	@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'FREEBSDAMD64', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'BLUEWATERS', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
Lines 451-457 chop($arch_no_math_float); Link Here
451		428
452	################ Plugin options	429	################ Plugin options
453	#	430	#
454	$plugin_dir = "../plugins";	431	$plugin_dir = "gentoo-plugindir";
455	$plugin_include = "-I$plugin_dir/include";	432	$plugin_include = "-I$plugin_dir/include";
456	$plugin_library = "";	433	$plugin_library = "";
457	$plugin_libs = "";	434	$plugin_libs = "";
Lines 464-470 $plugin_defines = ""; Link Here
464	@plugin_extra = ();	441	@plugin_extra = ();
465		442
466	if ($config_staticplugin) {	443	if ($config_staticplugin) {
467	$molfile_dir = "$plugin_dir/$config_arch/molfile";	444	$molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
468	$plugin_include .= " -I$molfile_dir";	445	$plugin_include .= " -I$molfile_dir";
469	$plugin_library .= " -L$molfile_dir";	446	$plugin_library .= " -L$molfile_dir";
470	$plugin_libs .= " -lmolfile_plugin";	447	$plugin_libs .= " -lmolfile_plugin";
Lines 564-571 $fltkopengl_defines = "-DVMDOPENGL - Link Here
564	################ FLTK GUI	541	################ FLTK GUI
565	$fltk_defines = "-DVMDGUI -DVMDFLTK";	542	$fltk_defines = "-DVMDGUI -DVMDFLTK";
566	$fltk_dir = "$vmd_library_dir/fltk";	543	$fltk_dir = "$vmd_library_dir/fltk";
567	$fltk_include = "-I$fltk_dir/include";	544	$fltk_include = "-Igentoo-fltk-include";
568	$fltk_library = "-L$fltk_dir/$config_arch";	545	$fltk_library = "-Lgentoo-fltk-libs";
569	$fltk_libs = "-lfltk -lX11";	546	$fltk_libs = "-lfltk -lX11";
570	#@fltk_cc = ('forms_ui.c');	547	#@fltk_cc = ('forms_ui.c');
571	@fltk_cu = ();	548	@fltk_cu = ();
Lines 626-633 $tcl_include = "-I$stock_tcl_includ Link Here
626	if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }	603	if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
627	$tcl_library = "-L$stock_tcl_library_dir";	604	$tcl_library = "-L$stock_tcl_library_dir";
628	if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }	605	if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
629	$tcl_libs = "-ltcl8.5";	606	$tcl_libs = "-ltcl";
630	if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }	607	if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
631		608
632	@tcl_cc = ();	609	@tcl_cc = ();
633	@tcl_cu = ();	610	@tcl_cu = ();
Lines 1004-1011 $mpi_libs = "-L/usr/mpi/gcc/mvapi Link Here
1004	#######################	981	#######################
1005	$netcdf_defines = "";	982	$netcdf_defines = "";
1006	$netcdf_dir = "$vmd_library_dir/netcdf";	983	$netcdf_dir = "$vmd_library_dir/netcdf";
1007	$netcdf_include = "-I$netcdf_dir/include";	984	$netcdf_include = "-Igentoo-netcdf-include";
1008	$netcdf_library = "-L$netcdf_dir/lib_$config_arch";	985	$netcdf_library = "-Lgentoo-netcdf-libs";
1009	$netcdf_libs = "-lnetcdf";	986	$netcdf_libs = "-lnetcdf";
1010	@netcdf_cc = ();	987	@netcdf_cc = ();
1011	@netcdf_cu = ();	988	@netcdf_cu = ();
Lines 1083-1091 $stock_numpy_include_dir=$ENV{"NUMPY_INC Link Here
1083	$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} \|\| "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";	1060	$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} \|\| "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";
1084		1061
1085	$python_defines = "-DVMDPYTHON";	1062	$python_defines = "-DVMDPYTHON";
1086	$python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir";	1063	$python_include = "-Igentoo-python-include -Igentoo-numpy-include";
1087	$python_library = "-L$stock_python_library_dir";	1064	$python_library = "-Lgentoo-python-lib";
1088	$python_libs = "-lpython2.5 -lpthread";	1065	$python_libs = "-lgentoo-python-link -lpthread";
1089	@python_h = ('PythonTextInterp.h',	1066	@python_h = ('PythonTextInterp.h',
1090	'VMDTkinterMenu.h',	1067	'VMDTkinterMenu.h',
1091	'py_commands.h',	1068	'py_commands.h',
Lines 1807-1814 if ($config_arch eq "LINUX") { Link Here
1807		1784
1808	# XFree 4.0 Direct Rendering Interface and GLX	1785	# XFree 4.0 Direct Rendering Interface and GLX
1809	$opengl_dir = "/usr/X11R6";	1786	$opengl_dir = "/usr/X11R6";
1810	$opengl_include = "-I$opengl_dir/include";	1787	$opengl_include = "-Igentoo-opengl-include";
1811	$opengl_library = "-L$opengl_dir/lib";	1788	$opengl_library = "-Lgentoo-opengl-libs";
1812	$opengl_libs = "-lGL -lGLU";	1789	$opengl_libs = "-lGL -lGLU";
1813	# $opengl_libs = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";	1790	# $opengl_libs = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
1814		1791
Lines 1836-1850 if ($config_arch eq "LINUX") { Link Here
1836	$arch_lopts .= "-i-static ";	1813	$arch_lopts .= "-i-static ";
1837	} else {	1814	} else {
1838	# compling with GCC	1815	# compling with GCC
1839	$arch_cc = "gcc";	1816	$arch_cc = "gentoo-gcc";
1840	$arch_ccpp = "g++";	1817	$arch_ccpp = "gentoo-g++";
1841	$arch_depend_flag = "-MM";	1818	$arch_depend_flag = "-MM";
1842	$arch_shld = "g++ -shared";	1819	$arch_shld = "gentoo-g++ -shared";
1843	$arch_shlibname = "so";	1820	$arch_shlibname = "so";
1844	$arch_shcppopts = "-fPIC";	1821	$arch_shcppopts = "-fPIC";
1845	$arch_shldopts = "";	1822	$arch_shldopts = "gentoo-ldflags";
1846	$arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3";	1823	$arch_opt_flag = "gentoo-cflags";
1847	$arch_copts = "-m32 -Wall -O3";	1824	$arch_copts = "gentoo-cflags";
1848		1825
1849	if ($config_static) {	1826	if ($config_static) {
1850	$arch_lopts = "-static";	1827	$arch_lopts = "-static";
Lines 1955-1961 if ($config_arch eq "LINUXAMD64") { Link Here
1955	$arch_template_repository = "foobar";	1932	$arch_template_repository = "foobar";
1956	$arch_shlibname = "so";	1933	$arch_shlibname = "so";
1957	$arch_shcppopts = "-fPIC";	1934	$arch_shcppopts = "-fPIC";
1958	$arch_shldopts = "";	1935	$arch_shldopts = "gentoo-ldflags";
1959		1936
1960	if ($config_static) {	1937	if ($config_static) {
1961	# link everything statically (this won't work due to libGL issues)	1938	# link everything statically (this won't work due to libGL issues)
Lines 2927-2937 LIBDIRS = $LIBDIRS Link Here
2927	DEFINES = $DEFINES	2904	DEFINES = $DEFINES
2928		2905
2929	# compiler and compiler directives	2906	# compiler and compiler directives
2930	CC = $arch_cc	2907	CC = gentoo-gcc
2931	CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags	2908	CFLAGS = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
2932		2909
2933	CCPP = $arch_ccpp	2910	CCPP = gentoo-g++
2934	CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags	2911	CPPFLAGS = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
2935		2912
2936	NVCC = $arch_nvcc	2913	NVCC = $arch_nvcc
2937	NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)	2914	NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
Lines 2979-2985 $config_progname: y.tab.h \$(VMD_OBJS) Link Here
2979	if [ ! -r ./$arch_template_repository ]; then \\	2956	if [ ! -r ./$arch_template_repository ]; then \\
2980	ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\	2957	ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\
2981	fi; \\	2958	fi; \\
2982	\$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;	2959	\$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
2983	\$(COMPILERC) \$(RCFLAGS)	2960	\$(COMPILERC) \$(RCFLAGS)
2984		2961
2985	install:	2962	install:
Lines 3017-3024 install: Link Here
3017	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"	2994	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
3018	\$(CD) $vmd_bin_dir ; \\	2995	\$(CD) $vmd_bin_dir ; \\
3019	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\	2996	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
3020	if [ ! -x "/bin/csh" ]; then \\	2997	if [ -x "/bin/bash" ]; then \\
3021	\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
3022	\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\	2998	\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
3023	\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\	2999	\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
3024	\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\	3000	\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\