From b541cc534a659965bd0cd0969dd5b410796a9b3d Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Mon, 13 Jun 2011 12:25:26 +0000 Subject: No binaryfiles in VCS please, #370915 (Portage version: 2.2.0_alpha40/cvs/Linux x86_64) --- sci-chemistry/vmd/ChangeLog | 8 +- sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch | 1240 -------------------- .../vmd/files/vmd-1.8.7-respect-flags.patch | 28 - sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch | 295 ----- .../vmd/files/vmd-1.9-gentoo-plugins.patch | 612 ---------- sci-chemistry/vmd/files/vmd.desktop | 14 - sci-chemistry/vmd/files/vmd.png | Bin 8365 -> 0 bytes sci-chemistry/vmd/vmd-1.8.7-r2.ebuild | 5 +- sci-chemistry/vmd/vmd-1.9.ebuild | 4 +- 9 files changed, 14 insertions(+), 2192 deletions(-) delete mode 100644 sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch delete mode 100644 sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch delete mode 100644 sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch delete mode 100644 sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch delete mode 100644 sci-chemistry/vmd/files/vmd.desktop delete mode 100644 sci-chemistry/vmd/files/vmd.png (limited to 'sci-chemistry/vmd') diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog index 7348e4ca0042..bf28d47d0bb7 100644 --- a/sci-chemistry/vmd/ChangeLog +++ b/sci-chemistry/vmd/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/vmd # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.38 2011/03/27 11:02:31 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.39 2011/06/13 12:25:25 jlec Exp $ + + 13 Jun 2011; Justin Lecher vmd-1.8.7-r2.ebuild, + -files/vmd-1.8.7-gentoo.patch, -files/vmd-1.8.7-respect-flags.patch, + vmd-1.9.ebuild, -files/vmd-1.9-gentoo-base.patch, + -files/vmd-1.9-gentoo-plugins.patch, -files/vmd.desktop, -files/vmd.png: + No binaryfiles in VCS please, #370915 27 Mar 2011; Justin Lecher vmd-1.9.ebuild: Correct version of cuda dep, #360401 diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch deleted file mode 100644 index e8c82c2bf872..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch +++ /dev/null @@ -1,1240 +0,0 @@ -diff --git a/plugins/Makefile b/plugins/Makefile -index e2e5e5e..f2eabaf 100755 ---- a/plugins/Makefile -+++ b/plugins/Makefile -@@ -4,7 +4,6 @@ - ## Theoretical and Computational Biophysics Group - ## - --.SILENT: - - default: make-arch-help - -diff --git a/plugins/Makefile.newmultiseq b/plugins/Makefile.newmultiseq -index c271b44..d00522c 100644 ---- a/plugins/Makefile.newmultiseq -+++ b/plugins/Makefile.newmultiseq -@@ -4,7 +4,6 @@ - ## Theoretical and Computational Biophysics Group - ## - --.SILENT: - - default: make-arch-help - -diff --git a/plugins/Makefile.orig b/plugins/Makefile.orig -index e6406fd..6208576 100644 ---- a/plugins/Makefile.orig -+++ b/plugins/Makefile.orig -@@ -4,7 +4,6 @@ - ## Theoretical and Computational Biophysics Group - ## - --.SILENT: - - default: make-arch-help - -diff --git a/plugins/Makefile.rej b/plugins/Makefile.rej -index 1b6ea67..d13aca1 100644 ---- a/plugins/Makefile.rej -+++ b/plugins/Makefile.rej -@@ -3,7 +3,6 @@ - # Makefile for molecule file readers - # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $ - --- .SILENT: - - .SUFFIXES: - -@@ -17,7 +16,6 @@ - # Makefile for molecule file readers - # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $ - --+ .SILENT: - - .SUFFIXES: - -diff --git a/plugins/aligntool/Makefile b/plugins/aligntool/Makefile -index 8155a6d..e4df74c 100644 ---- a/plugins/aligntool/Makefile -+++ b/plugins/aligntool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = aligntool.tcl cealign.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/apbsrun/Makefile b/plugins/apbsrun/Makefile -index aca0b4e..b86ee59 100644 ---- a/plugins/apbsrun/Makefile -+++ b/plugins/apbsrun/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = apbsrun.tcl pkgIndex.tcl radii.dat - VMVERSION = 1.3 -diff --git a/plugins/atomedit/Makefile b/plugins/atomedit/Makefile -index 558606c..05d7f90 100644 ---- a/plugins/atomedit/Makefile -+++ b/plugins/atomedit/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = atomedit.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/autoimd/Makefile b/plugins/autoimd/Makefile -index 9d432e4..7f0a802 100644 ---- a/plugins/autoimd/Makefile -+++ b/plugins/autoimd/Makefile -@@ -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 = 1.6 -diff --git a/plugins/autoionize/Makefile b/plugins/autoionize/Makefile -index c74ad01..b392d3f 100644 ---- a/plugins/autoionize/Makefile -+++ b/plugins/autoionize/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = autoionize.tcl autoionizegui.tcl pkgIndex.tcl ions.top - VMVERSION = 1.2 -diff --git a/plugins/bignum/Makefile b/plugins/bignum/Makefile -index 9c90f17..c35322d 100644 ---- a/plugins/bignum/Makefile -+++ b/plugins/bignum/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = bignum.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/biocore/Makefile b/plugins/biocore/Makefile -index 887b592..d2919dd 100644 ---- a/plugins/biocore/Makefile -+++ b/plugins/biocore/Makefile -@@ -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 --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile -index 7a8f0f8..bbc4c01 100644 ---- a/plugins/catdcd/Makefile -+++ b/plugins/catdcd/Makefile -@@ -1,6 +1,5 @@ - # Makefile for catdcd - --.SILENT: - - .SUFFIXES: - -@@ -45,8 +44,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi - 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 --git a/plugins/cgtools/Makefile b/plugins/cgtools/Makefile -index adca18b..84bf723 100644 ---- a/plugins/cgtools/Makefile -+++ b/plugins/cgtools/Makefile -@@ -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 --git a/plugins/cionize/.#Makefile.specialbuilds.1.1 b/plugins/cionize/.#Makefile.specialbuilds.1.1 -index 4672932..181ba85 100644 ---- a/plugins/cionize/.#Makefile.specialbuilds.1.1 -+++ b/plugins/cionize/.#Makefile.specialbuilds.1.1 -@@ -1,6 +1,5 @@ - # Makefile for cionize - --#.SILENT: - - .SUFFIXES: - -diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile -index c5fe136..b72116f 100644 ---- a/plugins/cionize/Makefile -+++ b/plugins/cionize/Makefile -@@ -1,6 +1,5 @@ - # Makefile for cionize - --#.SILENT: - - .SUFFIXES: - -@@ -52,8 +51,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI - 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 --git a/plugins/cionize/Makefile.mine b/plugins/cionize/Makefile.mine -index 5ee841a..1588837 100644 ---- a/plugins/cionize/Makefile.mine -+++ b/plugins/cionize/Makefile.mine -@@ -1,6 +1,5 @@ - # Makefile for cionize - --#.SILENT: - - .SUFFIXES: - -diff --git a/plugins/cionize/Makefile.mine.old b/plugins/cionize/Makefile.mine.old -index 48714b6..0dc4085 100644 ---- a/plugins/cionize/Makefile.mine.old -+++ b/plugins/cionize/Makefile.mine.old -@@ -1,6 +1,5 @@ - # Makefile for cionize - --#.SILENT: - - .SUFFIXES: - -diff --git a/plugins/cionize/Makefile.specialbuilds b/plugins/cionize/Makefile.specialbuilds -index a529758..f85bcfe 100644 ---- a/plugins/cionize/Makefile.specialbuilds -+++ b/plugins/cionize/Makefile.specialbuilds -@@ -1,6 +1,5 @@ - # Makefile for cionize - --#.SILENT: - - .SUFFIXES: - -diff --git a/plugins/cionize/mcudahacks/Makefile.specialbuilds b/plugins/cionize/mcudahacks/Makefile.specialbuilds -index e93cad2..dc7b632 100644 ---- a/plugins/cionize/mcudahacks/Makefile.specialbuilds -+++ b/plugins/cionize/mcudahacks/Makefile.specialbuilds -@@ -1,6 +1,5 @@ - # Makefile for cionize - --#.SILENT: - - .SUFFIXES: - -diff --git a/plugins/cliptool/Makefile b/plugins/cliptool/Makefile -index 9c41370..679abbe 100644 ---- a/plugins/cliptool/Makefile -+++ b/plugins/cliptool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = cliptool.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/clonerep/Makefile b/plugins/clonerep/Makefile -index e8a4949..e101e56 100755 ---- a/plugins/clonerep/Makefile -+++ b/plugins/clonerep/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = clonerep.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile -index 6329f64..c343b1c 100644 ---- a/plugins/clustalw/Makefile -+++ b/plugins/clustalw/Makefile -@@ -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 --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile -index 99d347e..dc542f1 100644 ---- a/plugins/cluster/Makefile -+++ b/plugins/cluster/Makefile -@@ -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 --git a/plugins/colorscalebar/Makefile b/plugins/colorscalebar/Makefile -index 1413898..f58074a 100644 ---- a/plugins/colorscalebar/Makefile -+++ b/plugins/colorscalebar/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = colorscalebar.tcl pkgIndex.tcl - VMVERSION = 1.2 -diff --git a/plugins/contactmap/Makefile b/plugins/contactmap/Makefile -index 36f6b18..3336e41 100644 ---- a/plugins/contactmap/Makefile -+++ b/plugins/contactmap/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = contactmap.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/plugins/dataimport/Makefile b/plugins/dataimport/Makefile -index e63ebca..71b59fb 100644 ---- a/plugins/dataimport/Makefile -+++ b/plugins/dataimport/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = dataimport.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/demomaster/Makefile b/plugins/demomaster/Makefile -index 6264d76..27a3d20 100644 ---- a/plugins/demomaster/Makefile -+++ b/plugins/demomaster/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = demomaster.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/dipwatch/Makefile b/plugins/dipwatch/Makefile -index 7d36042..4af35c7 100755 ---- a/plugins/dipwatch/Makefile -+++ b/plugins/dipwatch/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = dipwatch.tcl pkgIndex.tcl - VMVERSION = 1.2 -diff --git a/plugins/doc/Makefile b/plugins/doc/Makefile -index ed1ce9d..07ff534 100644 ---- a/plugins/doc/Makefile -+++ b/plugins/doc/Makefile -@@ -1,7 +1,6 @@ - # - # Plugin documentation Makefile - # --.SILENT: - - ECHO = echo - DELETEDIR = rm -rf -diff --git a/plugins/dowser/Makefile b/plugins/dowser/Makefile -index 1795db3..d00cacc 100644 ---- a/plugins/dowser/Makefile -+++ b/plugins/dowser/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = dowser.tcl dowser_gui.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/exectool/Makefile b/plugins/exectool/Makefile -index afa024d..6ba1889 100644 ---- a/plugins/exectool/Makefile -+++ b/plugins/exectool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = exectool.tcl jobmanager.tcl pkgIndex.tcl - VMVERSION = 1.2 -diff --git a/plugins/extendedpdb/Makefile b/plugins/extendedpdb/Makefile -index 9061aa1..5a5fb8f 100644 ---- a/plugins/extendedpdb/Makefile -+++ b/plugins/extendedpdb/Makefile -@@ -1,4 +1,3 @@ --#.SILENT: - - VMFILES = extendedpdb.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/fmtool/Makefile b/plugins/fmtool/Makefile -index 76a9e69..a3f320d 100644 ---- a/plugins/fmtool/Makefile -+++ b/plugins/fmtool/Makefile -@@ -1,6 +1,5 @@ - # Makefile for fmtool - --.SILENT: - - .SUFFIXES: - -diff --git a/plugins/gofrgui/Makefile b/plugins/gofrgui/Makefile -index e192f02..7251884 100644 ---- a/plugins/gofrgui/Makefile -+++ b/plugins/gofrgui/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = gofrgui.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/plugins/hbonds/Makefile b/plugins/hbonds/Makefile -index 6bee92d..45f1fe3 100644 ---- a/plugins/hbonds/Makefile -+++ b/plugins/hbonds/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = hbonds.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/plugins/idatm/Makefile b/plugins/idatm/Makefile -index e23ca1c..4280b6a 100644 ---- a/plugins/idatm/Makefile -+++ b/plugins/idatm/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = idatm.tcl pkgIndex.tcl - VMVERSION = 0.1 -diff --git a/plugins/ilstools/Makefile b/plugins/ilstools/Makefile -index e145c30..7cc9d1b 100644 ---- a/plugins/ilstools/Makefile -+++ b/plugins/ilstools/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - COPYFILES = ilstools.tcl pkgIndex.tcl oxygen.xyz nitricoxide.xyz \ - carbonmonoxide.xyz carbondioxide.xyz ethene.xyz methane.xyz \ -diff --git a/plugins/imdmenu/Makefile b/plugins/imdmenu/Makefile -index dca0e25..277f386 100644 ---- a/plugins/imdmenu/Makefile -+++ b/plugins/imdmenu/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - IMDMENUFILES = imdmenu.tcl pkgIndex.tcl - IMDMENUVERSION = 1.0 -diff --git a/plugins/inorganicbuilder/Makefile b/plugins/inorganicbuilder/Makefile -index 8e0439a..4af2b0f 100755 ---- a/plugins/inorganicbuilder/Makefile -+++ b/plugins/inorganicbuilder/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = inorganicbuilder.tcl pkgIndex.tcl - VMVERSION = 0.1 -diff --git a/plugins/irspecgui/Makefile b/plugins/irspecgui/Makefile -index 754ebc8..e86b09a 100755 ---- a/plugins/irspecgui/Makefile -+++ b/plugins/irspecgui/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = irspecgui.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/plugins/jmvexport/Makefile b/plugins/jmvexport/Makefile -index 7f45260..9eb996b 100644 ---- a/plugins/jmvexport/Makefile -+++ b/plugins/jmvexport/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = jmvexport.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile -index 7a66d08..12e1fd3 100644 ---- a/plugins/libbiokit/Makefile -+++ b/plugins/libbiokit/Makefile -@@ -1,6 +1,5 @@ - # Makefile for libbiokit - --.SILENT: - - .SUFFIXES: - -@@ -111,7 +110,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i - ${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}/percid.cpp - ${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.cpp - ${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.cpp - ${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.cpp - ${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 --git a/plugins/membrane/Makefile b/plugins/membrane/Makefile -index f92c426..38a9c06 100644 ---- a/plugins/membrane/Makefile -+++ b/plugins/membrane/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = membrane.tcl pkgIndex.tcl \ - popc_box.pdb popc_box.psf \ -diff --git a/plugins/mergestructs/Makefile b/plugins/mergestructs/Makefile -index d6a4225..66ba9b2 100644 ---- a/plugins/mergestructs/Makefile -+++ b/plugins/mergestructs/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = mergestructs.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/molefacture/Makefile b/plugins/molefacture/Makefile -index 96e70dc..8d10ef4 100644 ---- a/plugins/molefacture/Makefile -+++ b/plugins/molefacture/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = molefacture.tcl molefacture_builder.tcl \ - molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \ -diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile -index 18fb6dc..e32b130 100644 ---- a/plugins/molfile_plugin/Makefile -+++ b/plugins/molfile_plugin/Makefile -@@ -1,7 +1,6 @@ - # Makefile for molecule file readers - # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec 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) $(DEF)"STATIC_PLUGIN" - - # - # Rules -diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile -index 1dfa768..e3f380b 100644 ---- a/plugins/molfile_plugin/src/cifplugin/Makefile -+++ b/plugins/molfile_plugin/src/cifplugin/Makefile -@@ -1,6 +1,5 @@ - # Makefile for molecule file readers - --.SILENT: - - .SUFFIXES: - -@@ -14,7 +13,7 @@ INCDIR = -I../include -I${SRCDIR} - VPATH = src ../include ${ARCHDIR} - - SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" --SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" -+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN" - - # - # Rules -diff --git a/plugins/moltoptools/Makefile b/plugins/moltoptools/Makefile -index 3599cb7..8d80ec2 100644 ---- a/plugins/moltoptools/Makefile -+++ b/plugins/moltoptools/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = moltoptools.tcl pkgIndex.tcl - VMVERSION = 0.1 -diff --git a/plugins/multimolanim/Makefile b/plugins/multimolanim/Makefile -index 09b4cb1..39b3139 100755 ---- a/plugins/multimolanim/Makefile -+++ b/plugins/multimolanim/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = multimolanim.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/multiplot/Makefile b/plugins/multiplot/Makefile -index 520bf3e..a5b7bc5 100644 ---- a/plugins/multiplot/Makefile -+++ b/plugins/multiplot/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = multiplot.tcl pkgIndex.tcl - VMVERSION = 1.4 -diff --git a/plugins/multitext/Makefile b/plugins/multitext/Makefile -index cc98bde..453c0da 100644 ---- a/plugins/multitext/Makefile -+++ b/plugins/multitext/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = multitext.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/namdenergy/Makefile b/plugins/namdenergy/Makefile -index 9d4c11c..229f6cc 100644 ---- a/plugins/namdenergy/Makefile -+++ b/plugins/namdenergy/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = namdenergy.tcl pkgIndex.tcl - VMVERSION = 1.2 -diff --git a/plugins/namdgui/Makefile b/plugins/namdgui/Makefile -index 2e25b19..c03d87b 100644 ---- a/plugins/namdgui/Makefile -+++ b/plugins/namdgui/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = namdgui.tcl namdgui_tclforces.tcl pkgIndex.tcl - VMVERSION = 1.2 -diff --git a/plugins/namdplot/Makefile b/plugins/namdplot/Makefile -index e155387..88969e6 100644 ---- a/plugins/namdplot/Makefile -+++ b/plugins/namdplot/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = namdplot.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/namdserver/Makefile b/plugins/namdserver/Makefile -index 378d203..84dcb24 100644 ---- a/plugins/namdserver/Makefile -+++ b/plugins/namdserver/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = namdserver.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/plugins/nanotube/Makefile b/plugins/nanotube/Makefile -index 6662cd5..deaf55c 100644 ---- a/plugins/nanotube/Makefile -+++ b/plugins/nanotube/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = nanotube.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/navfly/Makefile b/plugins/navfly/Makefile -index 82d913b..0194be8 100644 ---- a/plugins/navfly/Makefile -+++ b/plugins/navfly/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = navfly.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/navigate/Makefile b/plugins/navigate/Makefile -index 6d48c3e..cf18738 100644 ---- a/plugins/navigate/Makefile -+++ b/plugins/navigate/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - COPYFILES = navigate.tcl pkgIndex.tcl - DIR = $(PLUGINDIR)/noarch/tcl/navigate1.0 -diff --git a/plugins/nlenergy/Makefile b/plugins/nlenergy/Makefile -index 8c028ca..3c295fd 100644 ---- a/plugins/nlenergy/Makefile -+++ b/plugins/nlenergy/Makefile -@@ -1,6 +1,5 @@ - # Makefile for nlenergy - --.SILENT: - - .SUFFIXES: - -diff --git a/plugins/optimization/Makefile b/plugins/optimization/Makefile -index e38a9dc..4188e7f 100644 ---- a/plugins/optimization/Makefile -+++ b/plugins/optimization/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = optimization.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/palettetool/Makefile b/plugins/palettetool/Makefile -index 6317657..166d423 100644 ---- a/plugins/palettetool/Makefile -+++ b/plugins/palettetool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = palettetool.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/paratool/Makefile b/plugins/paratool/Makefile -index 8f24cc1..cbf1618 100644 ---- a/plugins/paratool/Makefile -+++ b/plugins/paratool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = paratool.tcl paratool_atomedit.tcl paratool_aux.tcl \ - paratool_respcharges.tcl paratool_charmmcharges.tcl \ -diff --git a/plugins/pbctools/Makefile b/plugins/pbctools/Makefile -index 164c456..bcf6851 100755 ---- a/plugins/pbctools/Makefile -+++ b/plugins/pbctools/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = pbcbox.tcl pbcgui.tcl pbcjoin.tcl pbcset.tcl pbctools.tcl \ - pbcunwrap.tcl pbcwrap.tcl pkgIndex.tcl -diff --git a/plugins/pdbtool/Makefile b/plugins/pdbtool/Makefile -index c05579d..3f120c5 100644 ---- a/plugins/pdbtool/Makefile -+++ b/plugins/pdbtool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = pdbtool.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/pmepot/Makefile b/plugins/pmepot/Makefile -index 1858d13..fa6ac36 100644 ---- a/plugins/pmepot/Makefile -+++ b/plugins/pmepot/Makefile -@@ -1,6 +1,5 @@ - # Makefile for PME potential library - --.SILENT: - - .SUFFIXES: - -diff --git a/plugins/psfgen/Makefile b/plugins/psfgen/Makefile -index d9c7c85..0d9b80e 100644 ---- a/plugins/psfgen/Makefile -+++ b/plugins/psfgen/Makefile -@@ -1,6 +1,5 @@ - # Makefile for psfgen - --.SILENT: - - .SUFFIXES: - -diff --git a/plugins/psfgen/Makefile.pluginio b/plugins/psfgen/Makefile.pluginio -index 29444f2..28a6213 100644 ---- a/plugins/psfgen/Makefile.pluginio -+++ b/plugins/psfgen/Makefile.pluginio -@@ -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 --git a/plugins/qmtool/Makefile b/plugins/qmtool/Makefile -index a8aafff..2a45307 100644 ---- a/plugins/qmtool/Makefile -+++ b/plugins/qmtool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = qmtool.tcl qmtool_analysis.tcl qmtool_atomedit.tcl \ - qmtool_aux.tcl qmtool_charges.tcl qmtool_intcoor.tcl \ -diff --git a/plugins/ramaplot/Makefile b/plugins/ramaplot/Makefile -index 29a1f23..be6e86a 100644 ---- a/plugins/ramaplot/Makefile -+++ b/plugins/ramaplot/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - FILES = ramaplot.tcl pkgIndex.tcl - VERSION = 1.1 -diff --git a/plugins/readcharmmpar/Makefile b/plugins/readcharmmpar/Makefile -index fffb98e..d257edd 100644 ---- a/plugins/readcharmmpar/Makefile -+++ b/plugins/readcharmmpar/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = readcharmmpar.tcl par_all27_prot_lipid_na.inp pkgIndex.tcl par_amber2charmm.inp - VMVERSION = 1.1 -diff --git a/plugins/readcharmmtop/Makefile b/plugins/readcharmmtop/Makefile -index 88c7ab5..c8cb771 100644 ---- a/plugins/readcharmmtop/Makefile -+++ b/plugins/readcharmmtop/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = readcharmmtop.tcl pkgIndex.tcl top_all27_prot_lipid_na.inp top_all27_hybrid.inp top_amber2charmm.inp - VMVERSION = 1.0 -diff --git a/plugins/resptool/Makefile b/plugins/resptool/Makefile -index 1f20b70..80e01eb 100644 ---- a/plugins/resptool/Makefile -+++ b/plugins/resptool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = resptool.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/plugins/rmsd/Makefile b/plugins/rmsd/Makefile -index 23df59b..c328322 100644 ---- a/plugins/rmsd/Makefile -+++ b/plugins/rmsd/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = rmsd.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/rmsdtt/Makefile b/plugins/rmsdtt/Makefile -index c914531..62b14fd 100644 ---- a/plugins/rmsdtt/Makefile -+++ b/plugins/rmsdtt/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = rmsdtt.tcl pkgIndex.tcl - VMVERSION = 2.0 -diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile -index f020ca0..9ab6914 100644 ---- a/plugins/rnaview/Makefile -+++ b/plugins/rnaview/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = rnaview.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/ruler/Makefile b/plugins/ruler/Makefile -index 146cc4c..a7864d1 100644 ---- a/plugins/ruler/Makefile -+++ b/plugins/ruler/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = ruler.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/runante/Makefile b/plugins/runante/Makefile -index 0410d50..a8fbe81 100644 ---- a/plugins/runante/Makefile -+++ b/plugins/runante/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = runante.tcl pkgIndex.tcl - VMVERSION = 0.1 -diff --git a/plugins/saltbr/Makefile b/plugins/saltbr/Makefile -index 7e4234a..f5358e2 100644 ---- a/plugins/saltbr/Makefile -+++ b/plugins/saltbr/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = saltbr.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/solvate/Makefile b/plugins/solvate/Makefile -index b1c5d92..7dfcd9b 100644 ---- a/plugins/solvate/Makefile -+++ b/plugins/solvate/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - SOLVFILES = wat.top wat.pdb wat.psf solvate.tcl pkgIndex.tcl - SOLVVERSION = 1.3 -diff --git a/plugins/ssrestraints/Makefile b/plugins/ssrestraints/Makefile -index 81b79d8..dca38e7 100644 ---- a/plugins/ssrestraints/Makefile -+++ b/plugins/ssrestraints/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = ssrestraints.tcl ssrestraints_stride.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile -index f0fb515..c077d53 100644 ---- a/plugins/stamp/Makefile -+++ b/plugins/stamp/Makefile -@@ -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 --git a/plugins/stingtool/Makefile b/plugins/stingtool/Makefile -index d7b84fe..477a97c 100644 ---- a/plugins/stingtool/Makefile -+++ b/plugins/stingtool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = stingtool.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/symmetrytool/Makefile b/plugins/symmetrytool/Makefile -index 43adc25..6898a43 100644 ---- a/plugins/symmetrytool/Makefile -+++ b/plugins/symmetrytool/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = symmetry.tcl pkgIndex.tcl - VMVERSION = 1.2 -diff --git a/plugins/textview/Makefile b/plugins/textview/Makefile -index 5e35a4a..ba98391 100644 ---- a/plugins/textview/Makefile -+++ b/plugins/textview/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = textview.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/plugins/timeline/Makefile b/plugins/timeline/Makefile -index 3b9e7ac..a09c572 100644 ---- a/plugins/timeline/Makefile -+++ b/plugins/timeline/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = timeline.tcl pkgIndex.tcl - VMVERSION = 2.0 -diff --git a/plugins/topotools/Makefile b/plugins/topotools/Makefile -index a8af827..beb4b54 100644 ---- a/plugins/topotools/Makefile -+++ b/plugins/topotools/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = pkgIndex.tcl README topotools.tcl topoatoms.tcl \ - topobonds.tcl topoangles.tcl topodihedrals.tcl topoimpropers.tcl \ -diff --git a/plugins/trunctraj/Makefile b/plugins/trunctraj/Makefile -index 624b3e6..991b4e1 100644 ---- a/plugins/trunctraj/Makefile -+++ b/plugins/trunctraj/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = trunctraj.tcl pkgIndex.tcl - VMVERSION = 1.5 -diff --git a/plugins/updater/Makefile b/plugins/updater/Makefile -index 4e29538..3122421 100644 ---- a/plugins/updater/Makefile -+++ b/plugins/updater/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = updater.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/utilities/Makefile b/plugins/utilities/Makefile -index df1ccf4..c18c048 100644 ---- a/plugins/utilities/Makefile -+++ b/plugins/utilities/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = utilities.tcl pkgIndex.tcl - VMVERSION = 1.0 -diff --git a/plugins/vdna/Makefile b/plugins/vdna/Makefile -index f994198..dd2d57b 100644 ---- a/plugins/vdna/Makefile -+++ b/plugins/vdna/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = vdna.tcl pkgIndex.tcl - VMVERSION = 2.0 -diff --git a/plugins/viewmaster/Makefile b/plugins/viewmaster/Makefile -index c5d1625..8d25c7e 100644 ---- a/plugins/viewmaster/Makefile -+++ b/plugins/viewmaster/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = viewmaster.tcl pkgIndex.tcl - VMVERSION = 2.2 -diff --git a/plugins/vmdmovie/Makefile b/plugins/vmdmovie/Makefile -index 10af8e2..cacc294 100644 ---- a/plugins/vmdmovie/Makefile -+++ b/plugins/vmdmovie/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = vmdmovie.tcl pkgIndex.tcl - VMVERSION = 1.7 -diff --git a/plugins/vmdtkcon/Makefile b/plugins/vmdtkcon/Makefile -index 5f6a05d..04de94f 100644 ---- a/plugins/vmdtkcon/Makefile -+++ b/plugins/vmdtkcon/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - TKCONFILES = vmdtkcon.tcl tkcon-modified.tcl pkgIndex.tcl tkcon-2.3 README - DIR = $(PLUGINDIR)/noarch/tcl/vmdtkcon1.1 -diff --git a/plugins/volmapgui/Makefile b/plugins/volmapgui/Makefile -index 9ece112..57ec111 100644 ---- a/plugins/volmapgui/Makefile -+++ b/plugins/volmapgui/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - COPYFILES = volmapgui.tcl pkgIndex.tcl - DIR = $(PLUGINDIR)/noarch/tcl/volmapgui1.1 -diff --git a/plugins/zoomseq/Makefile b/plugins/zoomseq/Makefile -index aa95b41..66ee516 100644 ---- a/plugins/zoomseq/Makefile -+++ b/plugins/zoomseq/Makefile -@@ -1,4 +1,3 @@ --.SILENT: - - VMFILES = zoomseq.tcl pkgIndex.tcl - VMVERSION = 1.1 -diff --git a/vmd-1.8.7/configure b/vmd-1.8.7/configure -index f01944a..b04bade 100755 ---- a/vmd-1.8.7/configure -+++ b/vmd-1.8.7/configure -@@ -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/$install_name"; - - - # optionally override hard-coded defaults above with environment variables -@@ -128,29 +128,6 @@ if ($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', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64'); -@@ -435,7 +412,7 @@ chop($arch_no_math_float); - - ################ Plugin options - # --$plugin_dir = "../plugins"; -+$plugin_dir = "gentoo-plugindir"; - $plugin_include = "-I$plugin_dir/include"; - $plugin_library = ""; - $plugin_libs = ""; -@@ -448,7 +425,7 @@ $plugin_defines = ""; - @plugin_extra = (); - - if ($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"; -@@ -550,8 +527,8 @@ $fltkopengl_defines = "-DVMDOPENGL -DVMDFLTKOPENGL -DVMDGRAPHICS"; - ################ 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 = (); -@@ -612,8 +589,8 @@ $tcl_include = "-I$stock_tcl_include_dir"; - 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 = (); -@@ -938,8 +915,8 @@ $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart"; - ####################### - $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 = (); -@@ -1007,9 +984,9 @@ $pthreads_libs = "-lpthread"; - $python_defines = "-DVMDPYTHON"; - $python_dir = "$vmd_library_dir/python"; - $numpy_dir = "$vmd_library_dir/numpy"; --$python_include = "-I$python_dir/lib_$config_arch/include/python2.5 -I$numpy_dir/lib_$config_arch/include -I$python_dir/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include"; --$python_library = "-L$python_dir/lib_$config_arch/lib/python2.5/config"; --$python_libs = "-lpython2.5 -lpthread"; -+$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', -@@ -1621,8 +1598,8 @@ 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"; - # $opengl_libs = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11"; - -@@ -1650,15 +1627,15 @@ if ($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) { - $arch_lopts = "-static"; -@@ -1768,7 +1745,7 @@ if ($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) -@@ -2714,11 +2691,11 @@ 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) -@@ -2766,7 +2743,7 @@ $config_progname: y.tab.h \$(VMD_OBJS) - if [ ! -r ./$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$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; - \$(COMPILERC) \$(RCFLAGS) - - install: -@@ -2804,8 +2781,7 @@ install: - -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$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 ; \\ -diff --git a/vmd-1.8.7/src/Makefile b/vmd-1.8.7/src/Makefile -index 971a8c1..fe4c635 100755 ---- a/vmd-1.8.7/src/Makefile -+++ b/vmd-1.8.7/src/Makefile -@@ -432,7 +432,7 @@ vmd_WIN32: y.tab.h $(VMD_OBJS) - if [ ! -r ./ ]; then \ - ln -s ../src/ ./ ; \ - fi; \ -- $(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; -+ $(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; - $(COMPILERC) $(RCFLAGS) - - install: diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch b/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch deleted file mode 100644 index cd1281e3b682..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch +++ /dev/null @@ -1,28 +0,0 @@ -diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile -index 18fb6dc..8659573 100644 ---- a/plugins/molfile_plugin/Makefile -+++ b/plugins/molfile_plugin/Makefile -@@ -14,8 +14,8 @@ INCDIR = -I../include -I${SRCDIR} - - VPATH = src ../include ${ARCHDIR} - --SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" --SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" -+SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN" -+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN" - - # - # Rules -diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile -index 1dfa768..9de3f6b 100644 ---- a/plugins/molfile_plugin/src/cifplugin/Makefile -+++ b/plugins/molfile_plugin/src/cifplugin/Makefile -@@ -14,7 +14,7 @@ INCDIR = -I../include -I${SRCDIR} - VPATH = src ../include ${ARCHDIR} - - SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" --SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" -+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN" - - # - # Rules diff --git a/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch b/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch deleted file mode 100644 index 4fb7da420de9..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch +++ /dev/null @@ -1,295 +0,0 @@ - vmd-1.9/bin/vmd.sh | 3 ++ - vmd-1.9/configure | 88 +++++++++++++++++++------------------------------- - vmd-1.9/src/Makefile | 6 +--- - 3 files changed, 37 insertions(+), 60 deletions(-) - -diff --git a/vmd-1.9/bin/vmd.sh b/vmd-1.9/bin/vmd.sh -index 2da6656..6e5308f 100755 ---- a/vmd-1.9/bin/vmd.sh -+++ b/vmd-1.9/bin/vmd.sh -@@ -400,6 +400,7 @@ esac - - # set the path to a few external programs - # Stride -- used to generate cartoon representations etc. -+export STRIDE_BIN="gentoo-stride" - if [ -z "$STRIDE_BIN" ] - then - if [ -x "$MASTERVMDDIR/stride_$ARCH" ] -@@ -410,6 +411,7 @@ then - fi - - # Surf -- used to generate molecular surfaces -+export SURF_BIN="gentoo-surf" - if [ -z "$SURF_BIN" ] - then - if [ -x "$MASTERVMDDIR/surf_$ARCH" ] -@@ -420,6 +422,7 @@ then - fi - - # Tachyon -- used to generate ray traced graphics -+export TACHYON_BIN="gentoo-tachyon" - if [ -z "$TACHYON_BIN" ] - then - if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ] -diff --git a/vmd-1.9/configure b/vmd-1.9/configure -index 926bab0..d8c1459 100755 ---- a/vmd-1.9/configure -+++ b/vmd-1.9/configure -@@ -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/$install_name"; - - - # optionally override hard-coded defaults above with environment variables -@@ -132,28 +132,6 @@ if ($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 -@@ -413,7 +391,7 @@ $arch_rcflags = "No resource compiler required on this platform."; - - $arch_cc = "cc"; - $arch_ccpp = "CC"; --$arch_nvcc = "/usr/local/encap/cuda-3.0/bin/nvcc"; -+$arch_nvcc = "gentoo-nvcc"; - $arch_nvccflags = "--ptxas-options=-v " . - "-gencode arch=compute_10,code=sm_10 " . - "-gencode arch=compute_13,code=sm_13 " . -@@ -451,7 +429,7 @@ chop($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 +442,7 @@ $plugin_defines = ""; - @plugin_extra = (); - - if ($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 +542,8 @@ $fltkopengl_defines = "-DVMDOPENGL -DVMDFLTKOPENGL"; - ################ 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 +604,8 @@ $tcl_include = "-I$stock_tcl_include_dir"; - 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 +982,8 @@ $mpi_libs = "-L/usr/mpi/gcc/mvapich-1.0.0/lib -lmpich -libverbs -libumad - ####################### - $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 = (); -@@ -1076,6 +1054,7 @@ $pthreads_libs = "-lpthread"; - #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib"; - $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5"; - $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config"; -+$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config"; - - #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include"; - #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib"; -@@ -1085,7 +1064,7 @@ $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/l - $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_libs = "$stock_python_library -lpthread"; - @python_h = ('PythonTextInterp.h', - 'VMDTkinterMenu.h', - 'py_commands.h', -@@ -1807,8 +1786,8 @@ if ($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"; - # $opengl_libs = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11"; - -@@ -1836,15 +1815,15 @@ if ($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) { - $arch_lopts = "-static"; -@@ -1864,8 +1843,8 @@ if ($config_arch eq "LINUX") { - $arch_cppopts = ""; - - if ($config_cuda) { -- $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include"; -- $cuda_library = "-L/usr/local/encap/cuda-3.0/lib"; -+ $arch_nvccflags .= "gentoo-nvflags $cuda_include"; -+ $cuda_library = "-Lgentoo-cuda-lib"; - } - # a hack - to be removed, just keeps make happy - $arch_template_repository = "foobar"; -@@ -1955,7 +1934,7 @@ if ($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) -@@ -1986,7 +1965,7 @@ if ($config_arch eq "LINUXAMD64") { - - if ($config_cuda) { - $arch_nvccflags .= " --machine 64 -O3 $cuda_include"; -- $cuda_library = "-L/usr/local/encap/cuda-3.0/lib64"; -+ $cuda_library = "-Lgentoo-cuda-lib"; - } - - $arch_lex = "flex"; # has problems with vendor lex -@@ -2354,7 +2333,7 @@ if ($config_arch eq "MACOSXX86" || $config_arch eq "MACOSXX86_64") { - # $arch_nvccflags .= " -O3 $cuda_include"; - # make it continue to work with the older rev of CUDA for now - $arch_nvccflags = " --ptxas-options=-v -O3 $cuda_include"; -- $cuda_library = "-L/usr/local/cuda/lib"; -+ $cuda_library = "-Lgentoo-cuda-lib"; - } - if ($config_opencl) { - $opencl_libs = "-framework OpenCL"; -@@ -2545,7 +2524,7 @@ if ($config_arch eq "SOLARISX86" || $config_arch eq "SOLARISX86_64") { - $arch_nvcc = "/usr/local/cuda/bin/nvcc"; - $arch_nvccflags .= " -m64 -O3 -I/usr/local/cuda/include"; - $cuda_libs = "-lcudart"; -- $cuda_library = "-L/usr/local/cuda/lib"; -+ $cuda_library = "-Lgentoo-cuda-lib"; - } - } else { - print "Configured for a 32-bit build.\n"; -@@ -2927,11 +2906,11 @@ 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 +2958,7 @@ $config_progname: y.tab.h \$(VMD_OBJS) - if [ ! -r ./$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$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; - \$(COMPILERC) \$(RCFLAGS) - - install: -@@ -3017,8 +2996,7 @@ install: - -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$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 ; \\ -diff --git a/vmd-1.9/src/Makefile b/vmd-1.9/src/Makefile -index 18eff40..c301f91 100644 ---- a/vmd-1.9/src/Makefile -+++ b/vmd-1.9/src/Makefile -@@ -446,7 +446,7 @@ vmd_WIN32: y.tab.h $(VMD_OBJS) - if [ ! -r ./ ]; then \ - ln -s ../src/ ./ ; \ - fi; \ -- $(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; -+ $(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; - $(COMPILERC) $(RCFLAGS) - - install: -@@ -459,10 +459,6 @@ install: - if [ ! -d "/usr/local/lib/vmd"/doc ]; then \ - $(MAKEDIR) "/usr/local/lib/vmd"/doc; \ - fi -- -$(COPY) ../Announcement "/usr/local/lib/vmd" -- -$(COPY) ../README "/usr/local/lib/vmd" -- -$(COPY) ../LICENSE "/usr/local/lib/vmd" -- -$(COPY) ../doc/ug.pdf "/usr/local/lib/vmd"/doc - if [ -f /usr/local/lib/vmd/vmd_WIN32 ]; then \ - $(MOVE) "/usr/local/lib/vmd/vmd_WIN32" "/usr/local/lib/vmd/OLD_vmd_WIN32" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_WIN32" ; fi - -$(COPY) ../WIN32/vmd_WIN32 "/usr/local/lib/vmd" diff --git a/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch b/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch deleted file mode 100644 index d6b1afb0cafd..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch +++ /dev/null @@ -1,612 +0,0 @@ - plugins/Make-arch | 3 +- - plugins/Makefile | 20 ++++--- - plugins/autopsf/Makefile | 4 +- - plugins/catdcd/Makefile | 4 +- - plugins/cionize/Makefile | 4 +- - plugins/clustalw/Makefile | 2 +- - plugins/cluster/Makefile | 2 +- - plugins/hesstrans/Makefile | 2 +- - plugins/libbiokit/Makefile | 14 +++--- - plugins/molfile_plugin/Makefile | 62 ++++++++++++------------ - plugins/molfile_plugin/src/cifplugin/Makefile | 66 ++++++++++++------------ - plugins/phylotree/Makefile | 2 +- - plugins/rnaview/Makefile | 2 +- - plugins/stamp/Makefile | 2 +- - 14 files changed, 96 insertions(+), 93 deletions(-) - -diff --git a/plugins/Make-arch b/plugins/Make-arch -index 5d59ef3..ab57459 100755 ---- a/plugins/Make-arch -+++ b/plugins/Make-arch -@@ -336,7 +336,8 @@ LINUX: - "AR = ar" \ - "NM = nm -p" \ - "RANLIB = touch" \ -- "SHLD = gcc -shared" -+ "SHLD = gcc -shared" \ -+ "SHXXLD = g++ -shared" - - LINUXALPHA: - $(MAKE) dynlibs staticlibs bins \ -diff --git a/plugins/Makefile b/plugins/Makefile -index 19f0e8b..57cbe32 100644 ---- a/plugins/Makefile -+++ b/plugins/Makefile -@@ -132,25 +132,27 @@ distrib: - - include Make-arch - --molfilelibs: -- cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1 -- cd molfile_plugin; $(MAKE) staticlibs && cd .. || exit 1 -+molfilelibs_static: -+ $(MAKE) -C molfile_plugin staticlibs -+ -+molfilelibs_dyn: -+ $(MAKE) -C molfile_plugin dynlibs - - win32molfilelibs: - cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1 - cd molfile_plugin; $(MAKE) win32staticlibs && cd .. || exit 1 - --dynlibs: molfilelibs -- for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) dynlibs && cd .. || exit 1 ; done -+dynlibs: molfilelibs_dyn -+ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir dynlibs; done - --staticlibs: molfilelibs -- for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) staticlibs && cd .. || exit 1 ; done -+staticlibs: molfilelibs_static -+ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir staticlibs; done - - win32staticlibs: win32molfilelibs - for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) win32staticlibs && cd .. || exit 1 ; done - --bins: -- for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) bins && cd .. || exit 1 ; done -+bins: molfilelibs_dyn -+ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir bins; done - - win32bins: - for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) win32bins && cd .. || exit 1 ; done -diff --git a/plugins/autopsf/Makefile b/plugins/autopsf/Makefile -index e63d3c4..d217ed8 100644 ---- a/plugins/autopsf/Makefile -+++ b/plugins/autopsf/Makefile -@@ -49,8 +49,8 @@ AUTOPSFOBJS=${ARCHDIR}/psfatom.o \ - - ${ARCHDIR}/psfcheck.so : ${AUTOPSFOBJS} - if [ -n "${TCLSHLD}" ]; \ -- then ${TCLSHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ -- else ${SHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ -+ then ${TCLSHLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \ -+ else ${SHXXLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \ - fi - - ${ARCHDIR}/psfatom.o : psfatom.h psfatom.C -diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile -index 7a8f0f8..dc0d7a5 100644 ---- a/plugins/catdcd/Makefile -+++ b/plugins/catdcd/Makefile -@@ -45,8 +45,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi - 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 --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile -index c5fe136..5e9a379 100644 ---- a/plugins/cionize/Makefile -+++ b/plugins/cionize/Makefile -@@ -52,8 +52,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI - 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 --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile -index b8fbba5..988ad06 100644 ---- a/plugins/clustalw/Makefile -+++ b/plugins/clustalw/Makefile -@@ -66,7 +66,7 @@ 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 --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile -index 99d347e..c2d30ae 100644 ---- a/plugins/cluster/Makefile -+++ b/plugins/cluster/Makefile -@@ -48,7 +48,7 @@ ${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 --git a/plugins/hesstrans/Makefile b/plugins/hesstrans/Makefile -index 903e88b..50fa625 100644 ---- a/plugins/hesstrans/Makefile -+++ b/plugins/hesstrans/Makefile -@@ -67,7 +67,7 @@ HESSTRANSOBJS=${ARCHDIR}/newmat1.o \ - ${ARCHDIR}/hesstrans.so : ${HESSTRANSOBJS} - if [ -n "${TCLSHLD}" ]; \ - then ${TCLSHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ -- else ${SHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ -+ else ${SHXXLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ - fi - - # -diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile -index 7a66d08..da764dd 100644 ---- a/plugins/libbiokit/Makefile -+++ b/plugins/libbiokit/Makefile -@@ -98,7 +98,7 @@ OBJS = ${DYNLIBOBJS} \ - ${ARCHDIR}/tcl_libbiokit.so : ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} - if [ -n "${TCLSHLD}" ]; \ - then ${TCLSHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ -- else ${SHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ -+ else ${SHXXLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ - fi - ${ARCHDIR}/tcl_libbiokit_wrap.o : ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp - ${CXX} ${CXXFLAGS} ${TCLINC} ${INCDIR} -c ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp $(COPTO)${ARCHDIR}/tcl_libbiokit_wrap.o -@@ -111,7 +111,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i - ${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 +119,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp - ${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 +127,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp - ${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 +135,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp - ${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 +143,7 @@ ${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 +151,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp - ${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 --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile -index 172a217..345f64c 100644 ---- a/plugins/molfile_plugin/Makefile -+++ b/plugins/molfile_plugin/Makefile -@@ -15,7 +15,7 @@ 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 -@@ -142,7 +142,7 @@ abinitplugin.so: ${ARCHDIR}/abinitplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -@@ -163,13 +163,13 @@ babelplugin.so: ${ARCHDIR}/babelplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - hoomdplugin.so: ${ARCHDIR}/hoomdplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS) - - parmplugin.so: ${ARCHDIR}/parmplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS) -@@ -187,40 +187,40 @@ webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS) - - graspplugin.so: ${ARCHDIR}/graspplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - msmsplugin.so: ${ARCHDIR}/msmsplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - stlplugin.so: ${ARCHDIR}/stlplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - cubeplugin.so: ${ARCHDIR}/cubeplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - edmplugin.so: ${ARCHDIR}/edmplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - brixplugin.so: ${ARCHDIR}/brixplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - pltplugin.so: ${ARCHDIR}/pltplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - rst7plugin.so: ${ARCHDIR}/rst7plugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - parm7plugin.so: ${ARCHDIR}/parm7plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - vtfplugin.so: ${ARCHDIR}/vtfplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -@@ -235,7 +235,7 @@ tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -@@ -265,52 +265,52 @@ moldenplugin.so: ${ARCHDIR}/moldenplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - phiplugin.so: ${ARCHDIR}/phiplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - grdplugin.so: ${ARCHDIR}/grdplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - dxplugin.so: ${ARCHDIR}/dxplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - situsplugin.so: ${ARCHDIR}/situsplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - spiderplugin.so: ${ARCHDIR}/spiderplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - mapplugin.so: ${ARCHDIR}/mapplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - avsplugin.so: ${ARCHDIR}/avsplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - fs4plugin.so: ${ARCHDIR}/fs4plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - pqrplugin.so: ${ARCHDIR}/pqrplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - mol2plugin.so: ${ARCHDIR}/mol2plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - bgfplugin.so: ${ARCHDIR}/bgfplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - gridplugin.so: ${ARCHDIR}/gridplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - carplugin.so: ${ARCHDIR}/carplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - mdfplugin.so: ${ARCHDIR}/mdfplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - cpmdlogplugin.so: ${ARCHDIR}/cpmdlogplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -@@ -325,7 +325,7 @@ basissetplugin.so: ${ARCHDIR}/basissetplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - xsfplugin.so: ${ARCHDIR}/xsfplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - jsplugin.so: ${ARCHDIR}/jsplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile -index 1dfa768..bd6eceb 100644 ---- a/plugins/molfile_plugin/src/cifplugin/Makefile -+++ b/plugins/molfile_plugin/src/cifplugin/Makefile -@@ -13,8 +13,8 @@ INCDIR = -I../include -I${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 -@@ -84,10 +84,10 @@ mesg: - # - - biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - cifplugin.so: ${ARCHDIR}/cifplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -@@ -105,10 +105,10 @@ babelplugin.so: ${ARCHDIR}/babelplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - parmplugin.so: ${ARCHDIR}/parmplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS) -@@ -126,40 +126,40 @@ webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS) - - graspplugin.so: ${ARCHDIR}/graspplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - msmsplugin.so: ${ARCHDIR}/msmsplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - stlplugin.so: ${ARCHDIR}/stlplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - cubeplugin.so: ${ARCHDIR}/cubeplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - edmplugin.so: ${ARCHDIR}/edmplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - brixplugin.so: ${ARCHDIR}/brixplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - pltplugin.so: ${ARCHDIR}/pltplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - rst7plugin.so: ${ARCHDIR}/rst7plugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - parm7plugin.so: ${ARCHDIR}/parm7plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - vtfplugin.so: ${ARCHDIR}/vtfplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -@@ -174,7 +174,7 @@ tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -@@ -201,58 +201,58 @@ moldenplugin.so: ${ARCHDIR}/moldenplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - phiplugin.so: ${ARCHDIR}/phiplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - grdplugin.so: ${ARCHDIR}/grdplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - dxplugin.so: ${ARCHDIR}/dxplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - situsplugin.so: ${ARCHDIR}/situsplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - spiderplugin.so: ${ARCHDIR}/spiderplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - mapplugin.so: ${ARCHDIR}/mapplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - avsplugin.so: ${ARCHDIR}/avsplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - fs4plugin.so: ${ARCHDIR}/fs4plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - pqrplugin.so: ${ARCHDIR}/pqrplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - mol2plugin.so: ${ARCHDIR}/mol2plugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - bgfplugin.so: ${ARCHDIR}/bgfplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - gridplugin.so: ${ARCHDIR}/gridplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - carplugin.so: ${ARCHDIR}/carplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - mdfplugin.so: ${ARCHDIR}/mdfplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - gamessplugin.so: ${ARCHDIR}/gamessplugin.o - $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - xsfplugin.so: ${ARCHDIR}/xsfplugin.o -- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) -+ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) - - # - # object files -diff --git a/plugins/phylotree/Makefile b/plugins/phylotree/Makefile -index 6442747..0aceb4d 100644 ---- a/plugins/phylotree/Makefile -+++ b/plugins/phylotree/Makefile -@@ -54,7 +54,7 @@ ${ARCHDIR}/upgmaclu.exe : ${OBJS} - - # all other platforms - ${ARCHDIR}/upgmaclu : ${OBJS} -- ${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm -+ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm - - ${ARCHDIR}/upgmaclu.o: ${SRCDIR}/upgmaclu.c - ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/upgmaclu.c $(COPTO)${ARCHDIR}/upgmaclu.o -diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile -index 503695e..e7019a6 100644 ---- a/plugins/rnaview/Makefile -+++ b/plugins/rnaview/Makefile -@@ -67,7 +67,7 @@ OBJS = ${ARCHDIR}/analyze.o \ - ${ARCHDIR}/rnaview.exe: ${OBJS} - LINK ${OBJS} /OUT:${ARCHDIR}/rnaview.exe - ${ARCHDIR}/rnaview: ${OBJS} -- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm -+ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm - - ${ARCHDIR}/analyze.o: ${SRCDIR}/analyze.c - ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/analyze.c $(COPTO)${ARCHDIR}/analyze.o -diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile -index f0fb515..aa8f6b6 100644 ---- a/plugins/stamp/Makefile -+++ b/plugins/stamp/Makefile -@@ -101,7 +101,7 @@ 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 ${ARCHDIR}/stamp -lm - - - # Objects. diff --git a/sci-chemistry/vmd/files/vmd.desktop b/sci-chemistry/vmd/files/vmd.desktop deleted file mode 100644 index fe09518a8eef..000000000000 --- a/sci-chemistry/vmd/files/vmd.desktop +++ /dev/null @@ -1,14 +0,0 @@ -[Desktop Entry] -Comment=Visual Molecular Dynamics -Exec=/usr/bin/vmd -GenericName=Visual Molecular Dynamics -Icon=/usr/share/pixmaps/vmd.png -Name=VMD -NoDisplay=false -Path=$HOME -StartupNotify=true -Terminal=1 -TerminalOptions= -Type=Application -Categories=Science;Application; -X-KDE-SubstituteUID=false diff --git a/sci-chemistry/vmd/files/vmd.png b/sci-chemistry/vmd/files/vmd.png deleted file mode 100644 index 33126483ca80..000000000000 Binary files a/sci-chemistry/vmd/files/vmd.png and /dev/null differ diff --git a/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild b/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild index 96a0c3c74252..ffbab7cecf10 100644 --- a/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild +++ b/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild,v 1.7 2011/03/22 13:53:26 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild,v 1.8 2011/06/13 12:25:25 jlec Exp $ EAPI="3" @@ -50,8 +50,11 @@ QA_DT_HASH_x86="usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" pkg_nofetch() { elog "Please download ${A} from" elog "${VMD_DOWNLOAD}" + elog "and" + elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" elog "after agreeing to the license and then move it to " elog "${DISTDIR}" + } src_prepare() { diff --git a/sci-chemistry/vmd/vmd-1.9.ebuild b/sci-chemistry/vmd/vmd-1.9.ebuild index 137dc78023d6..41b5b15758fe 100644 --- a/sci-chemistry/vmd/vmd-1.9.ebuild +++ b/sci-chemistry/vmd/vmd-1.9.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.ebuild,v 1.3 2011/03/27 11:02:31 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.ebuild,v 1.4 2011/06/13 12:25:25 jlec Exp $ EAPI="3" @@ -55,6 +55,8 @@ QA_DT_HASH_x86="usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" pkg_nofetch() { elog "Please download ${A} from" elog "${VMD_DOWNLOAD}" + elog "and" + elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" elog "after agreeing to the license and then move it to " elog "${DISTDIR}" } -- cgit v1.2.3-65-gdbad