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Gentoo's Bugzilla – Attachment 265945 Details for
Bug 358981
sci-chemistry/vmd-1.9 version bump
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[patch]
vmd-1.9-gentoo.patch
vmd-1.9-gentoo.patch (text/plain), 45.35 KB, created by
Bjoern Olausson
on 2011-03-15 12:08:08 UTC
(
hide
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Description:
vmd-1.9-gentoo.patch
Filename:
MIME Type:
Creator:
Bjoern Olausson
Created:
2011-03-15 12:08:08 UTC
Size:
45.35 KB
patch
obsolete
>diff -Nrup old/plugins/Makefile new/plugins/Makefile >--- old/plugins/Makefile 2011-03-07 21:06:35.000000000 +0100 >+++ new/plugins/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -5,7 +5,6 @@ > ## > ## $Id: Makefile,v 1.125 2011/03/07 20:06:35 johns Exp $ > ## >-.SILENT: > > default: make-arch-help > >diff -Nrup old/plugins/Makefile.orig new/plugins/Makefile.orig >--- old/plugins/Makefile.orig 2009-02-25 00:28:11.000000000 +0100 >+++ new/plugins/Makefile.orig 2011-03-15 11:07:52.000000000 +0100 >@@ -4,7 +4,6 @@ > ## Theoretical and Computational Biophysics Group > ## > >-.SILENT: > > default: make-arch-help > >diff -Nrup old/plugins/aligntool/Makefile new/plugins/aligntool/Makefile >--- old/plugins/aligntool/Makefile 2005-02-16 03:58:58.000000000 +0100 >+++ new/plugins/aligntool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = aligntool.tcl cealign.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/apbsrun/Makefile new/plugins/apbsrun/Makefile >--- old/plugins/apbsrun/Makefile 2007-08-29 18:46:27.000000000 +0200 >+++ new/plugins/apbsrun/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = apbsrun.tcl pkgIndex.tcl radii.dat > VMVERSION = 1.3 >diff -Nrup old/plugins/atomedit/Makefile new/plugins/atomedit/Makefile >--- old/plugins/atomedit/Makefile 2005-07-20 00:26:59.000000000 +0200 >+++ new/plugins/atomedit/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = atomedit.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/autoimd/Makefile new/plugins/autoimd/Makefile >--- old/plugins/autoimd/Makefile 2009-12-07 18:14:58.000000000 +0100 >+++ new/plugins/autoimd/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > AUTOIMDFILES = autoimd.tcl autoimd-settings.tcl autoimd-api.tcl autoimd-gui.tcl pkgIndex.tcl autoimd-template.namd doc/ug.pdf namdrun.tcl > AUTOIMDVERSION = 1.7 >diff -Nrup old/plugins/autoionize/Makefile new/plugins/autoionize/Makefile >--- old/plugins/autoionize/Makefile 2011-01-28 20:54:10.000000000 +0100 >+++ new/plugins/autoionize/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = autoionize.tcl autoionizegui.tcl pkgIndex.tcl > VMVERSION = 1.3 >diff -Nrup old/plugins/bignum/Makefile new/plugins/bignum/Makefile >--- old/plugins/bignum/Makefile 2006-06-06 18:06:46.000000000 +0200 >+++ new/plugins/bignum/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = bignum.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/biocore/Makefile new/plugins/biocore/Makefile >--- old/plugins/biocore/Makefile 2006-06-20 17:47:23.000000000 +0200 >+++ new/plugins/biocore/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = biocore.tcl biocorechat.tcl biocorelogin.tcl biocorepubsync.tcl pkgIndex.tcl locked.gif unlocked.gif biocoreHelper.tcl biocoreutil.tcl > >diff -Nrup old/plugins/catdcd/Makefile new/plugins/catdcd/Makefile >--- old/plugins/catdcd/Makefile 2006-05-24 23:10:59.000000000 +0200 >+++ new/plugins/catdcd/Makefile 2011-03-15 11:10:29.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for catdcd > >-.SILENT: > > .SUFFIXES: > >@@ -45,8 +44,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${ > LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} > > # all other platforms >-${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a >- ${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm >+${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h >+ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm > > ${ARCHDIR}/hash.o: hash.h hash.c > ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o >diff -Nrup old/plugins/cgtools/Makefile new/plugins/cgtools/Makefile >--- old/plugins/cgtools/Makefile 2008-11-26 22:19:07.000000000 +0100 >+++ new/plugins/cgtools/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = cggui.tcl cgtools.tcl cgnetworking.tcl pkgIndex.tcl \ > protein.cgc water.cgc rbcg-2007.par rbcg-2007.top >diff -Nrup old/plugins/chirality/Makefile new/plugins/chirality/Makefile >--- old/plugins/chirality/Makefile 2010-12-01 02:59:38.000000000 +0100 >+++ new/plugins/chirality/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = chirality.tcl chirality_gui.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/cionize/Makefile new/plugins/cionize/Makefile >--- old/plugins/cionize/Makefile 2007-06-04 20:09:14.000000000 +0200 >+++ new/plugins/cionize/Makefile 2011-03-15 11:11:32.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for cionize > >-#.SILENT: > > .SUFFIXES: > >@@ -52,8 +51,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} $ > LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} > > # all other platforms >-${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a >- ${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm >+${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h >+ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm > > ${ARCHDIR}/hash.o: hash.h hash.c > ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o >diff -Nrup old/plugins/cionize/Makefile.mine new/plugins/cionize/Makefile.mine >--- old/plugins/cionize/Makefile.mine 2007-06-05 00:01:02.000000000 +0200 >+++ new/plugins/cionize/Makefile.mine 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for cionize > >-#.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/cionize/Makefile.mine.old new/plugins/cionize/Makefile.mine.old >--- old/plugins/cionize/Makefile.mine.old 2007-05-06 23:11:16.000000000 +0200 >+++ new/plugins/cionize/Makefile.mine.old 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for cionize > >-#.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/cionize/Makefile.specialbuilds new/plugins/cionize/Makefile.specialbuilds >--- old/plugins/cionize/Makefile.specialbuilds 2010-06-15 06:07:01.000000000 +0200 >+++ new/plugins/cionize/Makefile.specialbuilds 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for cionize > >-#.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/cionize/mcudahacks/Makefile.specialbuilds new/plugins/cionize/mcudahacks/Makefile.specialbuilds >--- old/plugins/cionize/mcudahacks/Makefile.specialbuilds 2008-06-13 05:16:07.000000000 +0200 >+++ new/plugins/cionize/mcudahacks/Makefile.specialbuilds 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for cionize > >-#.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/cispeptide/Makefile new/plugins/cispeptide/Makefile >--- old/plugins/cispeptide/Makefile 2010-12-01 02:59:38.000000000 +0100 >+++ new/plugins/cispeptide/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = cispeptide.tcl cispeptide_gui.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/cliptool/Makefile new/plugins/cliptool/Makefile >--- old/plugins/cliptool/Makefile 2005-02-16 03:59:21.000000000 +0100 >+++ new/plugins/cliptool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = cliptool.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/clonerep/Makefile new/plugins/clonerep/Makefile >--- old/plugins/clonerep/Makefile 2010-03-23 22:16:39.000000000 +0100 >+++ new/plugins/clonerep/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = clonerep.tcl pkgIndex.tcl > VMVERSION = 1.2 >diff -Nrup old/plugins/clustalw/Makefile new/plugins/clustalw/Makefile >--- old/plugins/clustalw/Makefile 2010-06-21 18:39:47.000000000 +0200 >+++ new/plugins/clustalw/Makefile 2011-03-15 11:13:09.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for clustalw > >-.SILENT: > > .SUFFIXES: > >@@ -66,7 +65,7 @@ OBJS = ${ARCHDIR}/alnscore.o \ > ${ARCHDIR}/clustalw.exe: ${OBJS} > LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe > ${ARCHDIR}/clustalw: ${OBJS} >- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm >+ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm > > > # Objects. >diff -Nrup old/plugins/cluster/Makefile new/plugins/cluster/Makefile >--- old/plugins/cluster/Makefile 2009-03-31 22:01:21.000000000 +0200 >+++ new/plugins/cluster/Makefile 2011-03-15 11:14:07.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for psfgen > >-.SILENT: > > .SUFFIXES: > >@@ -48,7 +47,7 @@ ${ARCHDIR}/cluster.exe : ${OBJS} > > # all other platforms > ${ARCHDIR}/cluster : ${OBJS} >- ${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm >+ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm > > ${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c > ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o >diff -Nrup old/plugins/colorscalebar/Makefile new/plugins/colorscalebar/Makefile >--- old/plugins/colorscalebar/Makefile 2009-09-17 21:43:02.000000000 +0200 >+++ new/plugins/colorscalebar/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = colorscalebar.tcl pkgIndex.tcl > VMVERSION = 1.3 >diff -Nrup old/plugins/contactmap/Makefile new/plugins/contactmap/Makefile >--- old/plugins/contactmap/Makefile 2005-02-16 03:59:25.000000000 +0100 >+++ new/plugins/contactmap/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = contactmap.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/dataimport/Makefile new/plugins/dataimport/Makefile >--- old/plugins/dataimport/Makefile 2005-12-20 00:01:13.000000000 +0100 >+++ new/plugins/dataimport/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = dataimport.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/demomaster/Makefile new/plugins/demomaster/Makefile >--- old/plugins/demomaster/Makefile 2005-05-20 22:33:20.000000000 +0200 >+++ new/plugins/demomaster/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = demomaster.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/dipwatch/Makefile new/plugins/dipwatch/Makefile >--- old/plugins/dipwatch/Makefile 2009-01-30 22:56:24.000000000 +0100 >+++ new/plugins/dipwatch/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = dipwatch.tcl pkgIndex.tcl > VMVERSION = 1.2 >diff -Nrup old/plugins/doc/Makefile new/plugins/doc/Makefile >--- old/plugins/doc/Makefile 2005-02-04 17:30:09.000000000 +0100 >+++ new/plugins/doc/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,7 +1,6 @@ > # > # Plugin documentation Makefile > # >-.SILENT: > > ECHO = echo > DELETEDIR = rm -rf >diff -Nrup old/plugins/dowser/Makefile new/plugins/dowser/Makefile >--- old/plugins/dowser/Makefile 2011-03-09 23:12:27.000000000 +0100 >+++ new/plugins/dowser/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = dowser.tcl dowser_gui.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/exectool/Makefile new/plugins/exectool/Makefile >--- old/plugins/exectool/Makefile 2006-08-19 21:59:28.000000000 +0200 >+++ new/plugins/exectool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = exectool.tcl jobmanager.tcl pkgIndex.tcl > VMVERSION = 1.2 >diff -Nrup old/plugins/extendedpdb/Makefile new/plugins/extendedpdb/Makefile >--- old/plugins/extendedpdb/Makefile 2005-09-16 16:05:13.000000000 +0200 >+++ new/plugins/extendedpdb/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-#.SILENT: > > VMFILES = extendedpdb.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/fmtool/Makefile new/plugins/fmtool/Makefile >--- old/plugins/fmtool/Makefile 2007-08-27 23:01:44.000000000 +0200 >+++ new/plugins/fmtool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for fmtool > >-.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/gofrgui/Makefile new/plugins/gofrgui/Makefile >--- old/plugins/gofrgui/Makefile 2011-02-21 18:51:21.000000000 +0100 >+++ new/plugins/gofrgui/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = gofrgui.tcl pkgIndex.tcl > VMVERSION = 1.2 >diff -Nrup old/plugins/hbonds/Makefile new/plugins/hbonds/Makefile >--- old/plugins/hbonds/Makefile 2011-03-09 22:41:03.000000000 +0100 >+++ new/plugins/hbonds/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = hbonds.tcl pkgIndex.tcl > VMVERSION = 1.2 >diff -Nrup old/plugins/idatm/Makefile new/plugins/idatm/Makefile >--- old/plugins/idatm/Makefile 2007-01-09 23:25:28.000000000 +0100 >+++ new/plugins/idatm/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = idatm.tcl pkgIndex.tcl > VMVERSION = 0.1 >diff -Nrup old/plugins/ilstools/Makefile new/plugins/ilstools/Makefile >--- old/plugins/ilstools/Makefile 2010-07-13 18:28:00.000000000 +0200 >+++ new/plugins/ilstools/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = ilstools.tcl pkgIndex.tcl oxygen.xyz nitricoxide.xyz \ > carbonmonoxide.xyz carbondioxide.xyz ethene.xyz methane.xyz \ >diff -Nrup old/plugins/imdmenu/Makefile new/plugins/imdmenu/Makefile >--- old/plugins/imdmenu/Makefile 2005-02-16 04:13:42.000000000 +0100 >+++ new/plugins/imdmenu/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > IMDMENUFILES = imdmenu.tcl pkgIndex.tcl > IMDMENUVERSION = 1.0 >diff -Nrup old/plugins/inorganicbuilder/Makefile new/plugins/inorganicbuilder/Makefile >--- old/plugins/inorganicbuilder/Makefile 2007-09-12 22:36:36.000000000 +0200 >+++ new/plugins/inorganicbuilder/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = inorganicbuilder.tcl pkgIndex.tcl > VMVERSION = 0.1 >diff -Nrup old/plugins/irspecgui/Makefile new/plugins/irspecgui/Makefile >--- old/plugins/irspecgui/Makefile 2009-01-30 23:17:06.000000000 +0100 >+++ new/plugins/irspecgui/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = irspecgui.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/jmvexport/Makefile new/plugins/jmvexport/Makefile >--- old/plugins/jmvexport/Makefile 2005-02-16 03:59:42.000000000 +0100 >+++ new/plugins/jmvexport/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = jmvexport.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/libbiokit/Makefile new/plugins/libbiokit/Makefile >--- old/plugins/libbiokit/Makefile 2009-03-31 22:01:23.000000000 +0200 >+++ new/plugins/libbiokit/Makefile 2011-03-15 11:16:46.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for libbiokit > >-.SILENT: > > .SUFFIXES: > >@@ -111,7 +110,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cp > ${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS} > LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe > ${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS} >- ${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm >+ ${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 > >@@ -119,7 +118,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/perci > ${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS} > LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe > ${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS} >- ${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm >+ ${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 > >@@ -127,7 +126,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair. > ${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS} > LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe > ${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS} >- ${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm >+ ${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 > >@@ -135,7 +134,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cp > ${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS} > LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe > ${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS} >- ${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm >+ ${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 > >@@ -143,7 +142,7 @@ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp > ${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS} > LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe > ${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS} >- ${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm >+ ${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 > >@@ -151,7 +150,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr. > ${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS} > LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe > ${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS} >- ${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm >+ ${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 > >diff -Nrup old/plugins/mdff/Makefile new/plugins/mdff/Makefile >--- old/plugins/mdff/Makefile 2009-08-06 22:07:33.000000000 +0200 >+++ new/plugins/mdff/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > 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 > >diff -Nrup old/plugins/membrane/Makefile new/plugins/membrane/Makefile >--- old/plugins/membrane/Makefile 2011-02-17 16:36:57.000000000 +0100 >+++ new/plugins/membrane/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = membrane.tcl pkgIndex.tcl \ > popc_box.pdb popc_box.psf \ >diff -Nrup old/plugins/mergestructs/Makefile new/plugins/mergestructs/Makefile >--- old/plugins/mergestructs/Makefile 2011-03-09 23:15:35.000000000 +0100 >+++ new/plugins/mergestructs/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = mergestructs.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/molefacture/Makefile new/plugins/molefacture/Makefile >--- old/plugins/molefacture/Makefile 2011-03-09 23:17:15.000000000 +0100 >+++ new/plugins/molefacture/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = molefacture.tcl molefacture_builder.tcl \ > molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \ >diff -Nrup old/plugins/molfile_plugin/Makefile new/plugins/molfile_plugin/Makefile >--- old/plugins/molfile_plugin/Makefile 2011-03-05 05:27:06.000000000 +0100 >+++ new/plugins/molfile_plugin/Makefile 2011-03-15 11:17:38.000000000 +0100 >@@ -1,7 +1,6 @@ > # Makefile for molecule file readers > # $Id: Makefile,v 1.112 2011/03/05 04:27:06 johns Exp $ > >-.SILENT: > > .SUFFIXES: > >@@ -14,8 +13,8 @@ INCDIR = -I../include -I${SRCDIR} > > VPATH = src ../include ${ARCHDIR} > >-SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" >-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" >+SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN" >+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN" > > # > # Rules >diff -Nrup old/plugins/molfile_plugin/src/cifplugin/Makefile new/plugins/molfile_plugin/src/cifplugin/Makefile >--- old/plugins/molfile_plugin/src/cifplugin/Makefile 2007-08-14 22:52:43.000000000 +0200 >+++ new/plugins/molfile_plugin/src/cifplugin/Makefile 2011-03-15 11:18:14.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for molecule file readers > >-.SILENT: > > .SUFFIXES: > >@@ -14,7 +13,7 @@ INCDIR = -I../include -I${SRCDIR} > VPATH = src ../include ${ARCHDIR} > > SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" >-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" >+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN" > > # > # Rules >diff -Nrup old/plugins/moltoptools/Makefile new/plugins/moltoptools/Makefile >--- old/plugins/moltoptools/Makefile 2007-01-09 23:25:30.000000000 +0100 >+++ new/plugins/moltoptools/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = moltoptools.tcl pkgIndex.tcl > VMVERSION = 0.1 >diff -Nrup old/plugins/multimolanim/Makefile new/plugins/multimolanim/Makefile >--- old/plugins/multimolanim/Makefile 2007-04-05 18:00:46.000000000 +0200 >+++ new/plugins/multimolanim/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = multimolanim.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/multiplot/Makefile new/plugins/multiplot/Makefile >--- old/plugins/multiplot/Makefile 2011-02-24 22:05:27.000000000 +0100 >+++ new/plugins/multiplot/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = multiplot.tcl pkgIndex.tcl > VMVERSION = 1.5 >diff -Nrup old/plugins/multitext/Makefile new/plugins/multitext/Makefile >--- old/plugins/multitext/Makefile 2009-01-30 23:07:00.000000000 +0100 >+++ new/plugins/multitext/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = multitext.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/namdenergy/Makefile new/plugins/namdenergy/Makefile >--- old/plugins/namdenergy/Makefile 2011-03-09 22:54:41.000000000 +0100 >+++ new/plugins/namdenergy/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = namdenergy.tcl pkgIndex.tcl > VMVERSION = 1.3 >diff -Nrup old/plugins/namdgui/Makefile new/plugins/namdgui/Makefile >--- old/plugins/namdgui/Makefile 2011-03-09 23:32:31.000000000 +0100 >+++ new/plugins/namdgui/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = namdgui.tcl namdgui_tclforces.tcl pkgIndex.tcl > VMVERSION = 1.3 >diff -Nrup old/plugins/namdplot/Makefile new/plugins/namdplot/Makefile >--- old/plugins/namdplot/Makefile 2006-01-12 17:24:35.000000000 +0100 >+++ new/plugins/namdplot/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = namdplot.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/namdserver/Makefile new/plugins/namdserver/Makefile >--- old/plugins/namdserver/Makefile 2006-08-19 22:52:45.000000000 +0200 >+++ new/plugins/namdserver/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = namdserver.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/nanotube/Makefile new/plugins/nanotube/Makefile >--- old/plugins/nanotube/Makefile 2011-03-04 04:34:00.000000000 +0100 >+++ new/plugins/nanotube/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = gui.tcl graphene.tcl nanotube.tcl pkgIndex.tcl > VMVERSION = 1.2 >diff -Nrup old/plugins/navfly/Makefile new/plugins/navfly/Makefile >--- old/plugins/navfly/Makefile 2006-05-03 22:37:00.000000000 +0200 >+++ new/plugins/navfly/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = navfly.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/navigate/Makefile new/plugins/navigate/Makefile >--- old/plugins/navigate/Makefile 2005-02-16 04:13:49.000000000 +0100 >+++ new/plugins/navigate/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > COPYFILES = navigate.tcl pkgIndex.tcl > DIR = $(PLUGINDIR)/noarch/tcl/navigate1.0 >diff -Nrup old/plugins/nlenergy/Makefile new/plugins/nlenergy/Makefile >--- old/plugins/nlenergy/Makefile 2009-01-14 22:22:55.000000000 +0100 >+++ new/plugins/nlenergy/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for nlenergy > >-.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/optimization/Makefile new/plugins/optimization/Makefile >--- old/plugins/optimization/Makefile 2006-04-28 18:59:52.000000000 +0200 >+++ new/plugins/optimization/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = optimization.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/palettetool/Makefile new/plugins/palettetool/Makefile >--- old/plugins/palettetool/Makefile 2006-08-16 07:19:45.000000000 +0200 >+++ new/plugins/palettetool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = palettetool.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/paratool/Makefile new/plugins/paratool/Makefile >--- old/plugins/paratool/Makefile 2009-05-18 06:45:21.000000000 +0200 >+++ new/plugins/paratool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = paratool.tcl paratool_atomedit.tcl paratool_aux.tcl \ > paratool_respcharges.tcl paratool_charmmcharges.tcl \ >diff -Nrup old/plugins/parsefep/Makefile new/plugins/parsefep/Makefile >--- old/plugins/parsefep/Makefile 2011-02-24 17:16:28.000000000 +0100 >+++ new/plugins/parsefep/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = parseFEP.tcl pkgIndex.tcl > VMVERSION = 1.4 >diff -Nrup old/plugins/pbctools/Makefile new/plugins/pbctools/Makefile >--- old/plugins/pbctools/Makefile 2009-11-05 17:46:56.000000000 +0100 >+++ new/plugins/pbctools/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = pbcbox.tcl pbcgui.tcl pbcjoin.tcl pbcset.tcl pbctools.tcl \ > pbcunwrap.tcl pbcwrap.tcl pkgIndex.tcl >diff -Nrup old/plugins/pdbtool/Makefile new/plugins/pdbtool/Makefile >--- old/plugins/pdbtool/Makefile 2005-02-16 04:00:00.000000000 +0100 >+++ new/plugins/pdbtool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = pdbtool.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/phylotree/Makefile new/plugins/phylotree/Makefile >--- old/plugins/phylotree/Makefile 2010-10-15 20:48:04.000000000 +0200 >+++ new/plugins/phylotree/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/plumed/Makefile new/plugins/plumed/Makefile >--- old/plugins/plumed/Makefile 2011-02-23 23:00:36.000000000 +0100 >+++ new/plugins/plumed/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = vmdplumed.tcl pkgIndex.tcl > VMVERSION = 0.9 >diff -Nrup old/plugins/pmepot/Makefile new/plugins/pmepot/Makefile >--- old/plugins/pmepot/Makefile 2006-02-21 02:34:15.000000000 +0100 >+++ new/plugins/pmepot/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for PME potential library > >-.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/psfgen/Makefile new/plugins/psfgen/Makefile >--- old/plugins/psfgen/Makefile 2009-02-04 20:12:01.000000000 +0100 >+++ new/plugins/psfgen/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for psfgen > >-.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/psfgen/Makefile.pluginio new/plugins/psfgen/Makefile.pluginio >--- old/plugins/psfgen/Makefile.pluginio 2008-10-19 00:18:07.000000000 +0200 >+++ new/plugins/psfgen/Makefile.pluginio 2011-03-15 11:07:52.000000000 +0100 >@@ -5,7 +5,6 @@ > # them itself, but at the moment this is a good short-term development > # path until we write something better. > >-.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/qmtool/Makefile new/plugins/qmtool/Makefile >--- old/plugins/qmtool/Makefile 2011-03-09 23:33:51.000000000 +0100 >+++ new/plugins/qmtool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = qmtool.tcl qmtool_analysis.tcl qmtool_atomedit.tcl \ > qmtool_aux.tcl qmtool_charges.tcl qmtool_intcoor.tcl \ >diff -Nrup old/plugins/ramaplot/Makefile new/plugins/ramaplot/Makefile >--- old/plugins/ramaplot/Makefile 2006-08-16 06:05:17.000000000 +0200 >+++ new/plugins/ramaplot/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > FILES = ramaplot.tcl pkgIndex.tcl > VERSION = 1.1 >diff -Nrup old/plugins/readcharmmpar/Makefile new/plugins/readcharmmpar/Makefile >--- old/plugins/readcharmmpar/Makefile 2011-03-11 17:37:58.000000000 +0100 >+++ new/plugins/readcharmmpar/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = readcharmmpar.tcl par_all27_prot_lipid_na.inp pkgIndex.tcl par_amber2charmm.inp par_all36_lipid.prm > VMVERSION = 1.2 >diff -Nrup old/plugins/readcharmmtop/Makefile new/plugins/readcharmmtop/Makefile >--- old/plugins/readcharmmtop/Makefile 2011-03-11 17:37:58.000000000 +0100 >+++ new/plugins/readcharmmtop/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = readcharmmtop.tcl pkgIndex.tcl top_all27_prot_lipid_na.inp top_all27_hybrid.inp top_amber2charmm.inp top_all36_lipid.rtf > VMVERSION = 1.1 >diff -Nrup old/plugins/resptool/Makefile new/plugins/resptool/Makefile >--- old/plugins/resptool/Makefile 2011-03-09 23:42:01.000000000 +0100 >+++ new/plugins/resptool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = resptool.tcl pkgIndex.tcl > VMVERSION = 1.2 >diff -Nrup old/plugins/rmsd/Makefile new/plugins/rmsd/Makefile >--- old/plugins/rmsd/Makefile 2005-02-16 04:00:38.000000000 +0100 >+++ new/plugins/rmsd/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = rmsd.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/rmsdtt/Makefile new/plugins/rmsdtt/Makefile >--- old/plugins/rmsdtt/Makefile 2006-04-04 23:55:10.000000000 +0200 >+++ new/plugins/rmsdtt/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = rmsdtt.tcl pkgIndex.tcl > VMVERSION = 2.0 >diff -Nrup old/plugins/rnaview/Makefile new/plugins/rnaview/Makefile >--- old/plugins/rnaview/Makefile 2009-12-07 18:19:00.000000000 +0100 >+++ new/plugins/rnaview/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for rnaview > >-.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/ruler/Makefile new/plugins/ruler/Makefile >--- old/plugins/ruler/Makefile 2007-06-13 20:58:52.000000000 +0200 >+++ new/plugins/ruler/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = ruler.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/runante/Makefile new/plugins/runante/Makefile >--- old/plugins/runante/Makefile 2008-02-20 19:05:11.000000000 +0100 >+++ new/plugins/runante/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = runante.tcl pkgIndex.tcl > VMVERSION = 0.1 >diff -Nrup old/plugins/runsqm/Makefile new/plugins/runsqm/Makefile >--- old/plugins/runsqm/Makefile 2010-08-25 02:18:08.000000000 +0200 >+++ new/plugins/runsqm/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = runsqm.tcl pkgIndex.tcl > VMVERSION = 0.1 >diff -Nrup old/plugins/saltbr/Makefile new/plugins/saltbr/Makefile >--- old/plugins/saltbr/Makefile 2011-03-09 22:59:48.000000000 +0100 >+++ new/plugins/saltbr/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = saltbr.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/solvate/Makefile new/plugins/solvate/Makefile >--- old/plugins/solvate/Makefile 2011-03-09 23:23:21.000000000 +0100 >+++ new/plugins/solvate/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > SOLVFILES = wat.top wat.pdb wat.psf solvate.tcl pkgIndex.tcl > SOLVVERSION = 1.4 >diff -Nrup old/plugins/ssrestraints/Makefile new/plugins/ssrestraints/Makefile >--- old/plugins/ssrestraints/Makefile 2011-03-09 23:24:31.000000000 +0100 >+++ new/plugins/ssrestraints/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = ssrestraints.tcl ssrestraints_stride.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/stamp/Makefile new/plugins/stamp/Makefile >--- old/plugins/stamp/Makefile 2009-03-31 22:01:29.000000000 +0200 >+++ new/plugins/stamp/Makefile 2011-03-15 11:19:11.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for stamp > >-.SILENT: > > .SUFFIXES: > >@@ -101,7 +100,7 @@ OBJS = ${ARCHDIR}/a3to1.o \ > ${ARCHDIR}/stamp.exe: ${OBJS} > LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe > ${ARCHDIR}/stamp: ${OBJS} >- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm >+ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm > > > # Objects. >diff -Nrup old/plugins/stingtool/Makefile new/plugins/stingtool/Makefile >--- old/plugins/stingtool/Makefile 2005-07-06 20:05:21.000000000 +0200 >+++ new/plugins/stingtool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = stingtool.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/symmetrytool/Makefile new/plugins/symmetrytool/Makefile >--- old/plugins/symmetrytool/Makefile 2009-09-22 21:31:04.000000000 +0200 >+++ new/plugins/symmetrytool/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = symmetry.tcl pkgIndex.tcl > VMVERSION = 1.3 >diff -Nrup old/plugins/textview/Makefile new/plugins/textview/Makefile >--- old/plugins/textview/Makefile 2006-08-20 05:56:50.000000000 +0200 >+++ new/plugins/textview/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = textview.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/plugins/timeline/Makefile new/plugins/timeline/Makefile >--- old/plugins/timeline/Makefile 2011-03-10 00:25:45.000000000 +0100 >+++ new/plugins/timeline/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = timeline.tcl pkgIndex.tcl > VMVERSION = 2.3 >diff -Nrup old/plugins/topotools/Makefile new/plugins/topotools/Makefile >--- old/plugins/topotools/Makefile 2009-11-30 18:02:33.000000000 +0100 >+++ new/plugins/topotools/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = pkgIndex.tcl README topotools.tcl topoatoms.tcl \ > topobonds.tcl topoangles.tcl topodihedrals.tcl topoimpropers.tcl \ >diff -Nrup old/plugins/trunctraj/Makefile new/plugins/trunctraj/Makefile >--- old/plugins/trunctraj/Makefile 2009-01-30 15:46:31.000000000 +0100 >+++ new/plugins/trunctraj/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = trunctraj.tcl pkgIndex.tcl > VMVERSION = 1.5 >diff -Nrup old/plugins/updater/Makefile new/plugins/updater/Makefile >--- old/plugins/updater/Makefile 2005-02-16 04:00:52.000000000 +0100 >+++ new/plugins/updater/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = updater.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/utilities/Makefile new/plugins/utilities/Makefile >--- old/plugins/utilities/Makefile 2007-09-07 08:55:52.000000000 +0200 >+++ new/plugins/utilities/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = utilities.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/vdna/Makefile new/plugins/vdna/Makefile >--- old/plugins/vdna/Makefile 2010-02-25 22:47:45.000000000 +0100 >+++ new/plugins/vdna/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = vdna.tcl pkgIndex.tcl > VMVERSION = 2.2 >diff -Nrup old/plugins/viewchangerender/Makefile new/plugins/viewchangerender/Makefile >--- old/plugins/viewchangerender/Makefile 2011-02-23 20:09:06.000000000 +0100 >+++ new/plugins/viewchangerender/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = vcr.tcl vcr_gui.tcl pkgIndex.tcl > VMVERSION = 1.5 >diff -Nrup old/plugins/viewmaster/Makefile new/plugins/viewmaster/Makefile >--- old/plugins/viewmaster/Makefile 2010-02-10 23:21:52.000000000 +0100 >+++ new/plugins/viewmaster/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = viewmaster.tcl pkgIndex.tcl > VMVERSION = 2.4 >diff -Nrup old/plugins/vmddebug/Makefile new/plugins/vmddebug/Makefile >--- old/plugins/vmddebug/Makefile 2011-02-26 19:09:33.000000000 +0100 >+++ new/plugins/vmddebug/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = vmddebug.tcl debugatomsel.tcl pkgIndex.tcl > VMVERSION = 1.0 >diff -Nrup old/plugins/vmdmovie/Makefile new/plugins/vmdmovie/Makefile >--- old/plugins/vmdmovie/Makefile 2010-03-09 06:31:17.000000000 +0100 >+++ new/plugins/vmdmovie/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = vmdmovie.tcl pkgIndex.tcl > VMVERSION = 1.8 >diff -Nrup old/plugins/vmdtkcon/Makefile new/plugins/vmdtkcon/Makefile >--- old/plugins/vmdtkcon/Makefile 2008-08-13 17:48:44.000000000 +0200 >+++ new/plugins/vmdtkcon/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > TKCONFILES = vmdtkcon.tcl tkcon-modified.tcl pkgIndex.tcl tkcon-2.3 README > DIR = $(PLUGINDIR)/noarch/tcl/vmdtkcon1.1 >diff -Nrup old/plugins/volmapgui/Makefile new/plugins/volmapgui/Makefile >--- old/plugins/volmapgui/Makefile 2009-05-29 19:47:24.000000000 +0200 >+++ new/plugins/volmapgui/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > COPYFILES = volmapgui.tcl pkgIndex.tcl > DIR = $(PLUGINDIR)/noarch/tcl/volmapgui1.1 >diff -Nrup old/plugins/volutil/Makefile new/plugins/volutil/Makefile >--- old/plugins/volutil/Makefile 2011-02-22 19:44:40.000000000 +0100 >+++ new/plugins/volutil/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,6 +1,5 @@ > # Makefile for volutil > >-.SILENT: > > .SUFFIXES: > >diff -Nrup old/plugins/zoomseq/Makefile new/plugins/zoomseq/Makefile >--- old/plugins/zoomseq/Makefile 2009-05-30 06:09:18.000000000 +0200 >+++ new/plugins/zoomseq/Makefile 2011-03-15 11:07:52.000000000 +0100 >@@ -1,4 +1,3 @@ >-.SILENT: > > VMFILES = zoomseq.tcl pkgIndex.tcl > VMVERSION = 1.1 >diff -Nrup old/vmd-1.9/configure new/vmd-1.9/configure >--- old/vmd-1.9/configure 2011-03-14 21:58:13.000000000 +0100 >+++ new/vmd-1.9/configure 2011-03-15 11:26:57.000000000 +0100 >@@ -13,10 +13,10 @@ > $install_name = "vmd"; > > # Directory where VMD startup script is installed, should be in users' paths. >-$install_bin_dir="/usr/local/bin"; >+$install_bin_dir="gentoo-bindir"; > > # Directory where VMD files and executables are installed >-$install_library_dir="/usr/local/lib/$install_name"; >+$install_library_dir="gentoo-libdir/$install_name"; > > > # optionally override hard-coded defaults above with environment variables >@@ -132,29 +132,6 @@ if ($ENV{VMDINSTALLLIBRARYDIR}) { > # 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'); >@@ -451,7 +428,7 @@ chop($arch_no_math_float); > > ################ Plugin options > # >-$plugin_dir = "../plugins"; >+$plugin_dir = "gentoo-plugindir"; > $plugin_include = "-I$plugin_dir/include"; > $plugin_library = ""; > $plugin_libs = ""; >@@ -464,7 +441,7 @@ $plugin_defines = ""; > @plugin_extra = (); > > if ($config_staticplugin) { >- $molfile_dir = "$plugin_dir/$config_arch/molfile"; >+ $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile"; > $plugin_include .= " -I$molfile_dir"; > $plugin_library .= " -L$molfile_dir"; > $plugin_libs .= " -lmolfile_plugin"; >@@ -564,8 +541,8 @@ $fltkopengl_defines = "-DVMDOPENGL - > ################ FLTK GUI > $fltk_defines = "-DVMDGUI -DVMDFLTK"; > $fltk_dir = "$vmd_library_dir/fltk"; >-$fltk_include = "-I$fltk_dir/include"; >-$fltk_library = "-L$fltk_dir/$config_arch"; >+$fltk_include = "-Igentoo-fltk-include"; >+$fltk_library = "-Lgentoo-fltk-libs"; > $fltk_libs = "-lfltk -lX11"; > #@fltk_cc = ('forms_ui.c'); > @fltk_cu = (); >@@ -626,8 +603,8 @@ $tcl_include = "-I$stock_tcl_includ > 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"; } >-$tcl_libs = "-ltcl8.5"; >-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; } >+$tcl_libs = "-ltcl"; >+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; } > > @tcl_cc = (); > @tcl_cu = (); >@@ -1004,8 +981,8 @@ $mpi_libs = "-L/usr/mpi/gcc/mvapi > ####################### > $netcdf_defines = ""; > $netcdf_dir = "$vmd_library_dir/netcdf"; >-$netcdf_include = "-I$netcdf_dir/include"; >-$netcdf_library = "-L$netcdf_dir/lib_$config_arch"; >+$netcdf_include = "-Igentoo-netcdf-include"; >+$netcdf_library = "-Lgentoo-netcdf-libs"; > $netcdf_libs = "-lnetcdf"; > @netcdf_cc = (); > @netcdf_cu = (); >@@ -1083,9 +1060,9 @@ $stock_numpy_include_dir=$ENV{"NUMPY_INC > $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include"; > > $python_defines = "-DVMDPYTHON"; >-$python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir"; >-$python_library = "-L$stock_python_library_dir"; >-$python_libs = "-lpython2.5 -lpthread"; >+$python_include = "-Igentoo-python-include -Igentoo-numpy-include"; >+$python_library = "-Lgentoo-python-lib"; >+$python_libs = "-lgentoo-python-link -lpthread"; > @python_h = ('PythonTextInterp.h', > 'VMDTkinterMenu.h', > 'py_commands.h', >@@ -1807,8 +1784,8 @@ if ($config_arch eq "LINUX") { > > # XFree 4.0 Direct Rendering Interface and GLX > $opengl_dir = "/usr/X11R6"; >- $opengl_include = "-I$opengl_dir/include"; >- $opengl_library = "-L$opengl_dir/lib"; >+ $opengl_include = "-Igentoo-opengl-include"; >+ $opengl_library = "-Lgentoo-opengl-libs"; > $opengl_libs = "-lGL -lGLU"; > # $opengl_libs = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11"; > >@@ -1836,15 +1813,15 @@ if ($config_arch eq "LINUX") { > $arch_lopts .= "-i-static "; > } else { > # compling with GCC >- $arch_cc = "gcc"; >- $arch_ccpp = "g++"; >+ $arch_cc = "gentoo-gcc"; >+ $arch_ccpp = "gentoo-g++"; > $arch_depend_flag = "-MM"; >- $arch_shld = "g++ -shared"; >+ $arch_shld = "gentoo-g++ -shared"; > $arch_shlibname = "so"; > $arch_shcppopts = "-fPIC"; >- $arch_shldopts = ""; >- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3"; >- $arch_copts = "-m32 -Wall -O3"; >+ $arch_shldopts = "gentoo-ldflags"; >+ $arch_opt_flag = "gentoo-cflags"; >+ $arch_copts = "gentoo-cflags"; > > if ($config_static) { > $arch_lopts = "-static"; >@@ -1955,7 +1932,7 @@ if ($config_arch eq "LINUXAMD64") { > $arch_template_repository = "foobar"; > $arch_shlibname = "so"; > $arch_shcppopts = "-fPIC"; >- $arch_shldopts = ""; >+ $arch_shldopts = "gentoo-ldflags"; > > if ($config_static) { > # link everything statically (this won't work due to libGL issues) >@@ -2927,11 +2904,11 @@ LIBDIRS = $LIBDIRS > DEFINES = $DEFINES > > # compiler and compiler directives >-CC = $arch_cc >-CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags >+CC = gentoo-gcc >+CFLAGS = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags > >-CCPP = $arch_ccpp >-CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$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) >@@ -2979,7 +2956,7 @@ $config_progname: y.tab.h \$(VMD_OBJS) > if [ ! -r ./$arch_template_repository ]; then \\ > ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\ > fi; \\ >- \$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; >+ \$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; > \$(COMPILERC) \$(RCFLAGS) > > install: >@@ -3017,8 +2994,7 @@ install: > -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir" > \$(CD) $vmd_bin_dir ; \\ > if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\ >- if [ ! -x "/bin/csh" ]; then \\ >- \$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\ >+ if [ -x "/bin/bash" ]; then \\ > \$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\ > \$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\ > \$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
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