sci-chemistry/vmd: Apply fixes to plugins

Adapt patch to 1.9.4

Closes: https://bugs.gentoo.org/741978
Thanks-to: Hypoon
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Pacho Ramos <pacho@gentoo.org>

2 files changed, 610 insertions, 0 deletions

diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch
new file mode 100644
index 000000000000..c6ea769932f3
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch
@@ -0,0 +1,604 @@
+From c33a68684cd06424ec78c6983f93336109d91cb5 Mon Sep 17 00:00:00 2001
+From: Stefan Kuczera <stefan.ku@yahoo.com>
+Date: Sat, 21 Jan 2017 13:20:45 +0100
+Subject: [PATCH] Squashed patches
+
+---
+ plugins/Make-arch               |   3 +-
+ plugins/Makefile                |  20 +++---
+ plugins/autopsf/Makefile        |   4 +-
+ plugins/catdcd/Makefile         |   4 +-
+ plugins/cionize/Makefile        |   6 +-
+ plugins/clustalw/Makefile       |   2 +-
+ plugins/cluster/Makefile        |   2 +-
+ plugins/hesstrans/Makefile      |   2 +-
+ plugins/libbiokit/Makefile      |  14 ++--
+ plugins/molfile_plugin/Makefile | 144 ++++++++++++++++++++--------------------
+ plugins/phylotree/Makefile      |   2 +-
+ plugins/rnaview/Makefile        |   2 +-
+ plugins/stamp/Makefile          |   2 +-
+ 13 files changed, 105 insertions(+), 102 deletions(-)
+
+diff --git a/plugins/Make-arch b/plugins/Make-arch
+index 19d2b6c..937ad9e 100755
+--- a/plugins/Make-arch
++++ b/plugins/Make-arch
+@@ -313,7 +313,8 @@ 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 0fee349..6b07606 100755
+--- a/plugins/Makefile
++++ b/plugins/Makefile
+@@ -150,25 +150,27 @@ 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 && $(MAKE) win32bins && cd .. || exit 1 ; done
+diff --git a/plugins/autopsf/Makefile b/plugins/autopsf/Makefile
+index 3b35d10..8e1527e 100644
+--- a/plugins/autopsf/Makefile
++++ b/plugins/autopsf/Makefile
+@@ -49,8 +49,8 @@ AUTOPSFOBJS=${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 d6c58c5..1637a3c 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} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS}
+ 
+ # all other platforms
+-${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} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
++${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} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -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 bcb2510..e02241b 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} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS}
+ 
+ # all other platforms
+-${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} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
++${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} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
+ 
+ ${ARCHDIR}/hash.o: hash.h hash.c
+ 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
+@@ -66,7 +66,7 @@ ${ARCHDIR}/util.o: util.h util.c
+ 
+ ${ARCHDIR}/getplugins.o: getplugins.h getplugins.c
+ 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/getplugins.c $(COPTO)${ARCHDIR}/getplugins.o
+-	
++
+ ${ARCHDIR}/energythr.o: energythr.h energythr.c ${ARCHDIR}/util.o ${ARCHDIR}/threads.o
+ 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/energythr.c $(COPTO)${ARCHDIR}/energythr.o
+ 
+diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile
+index 6329f64..3443720 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 76ee306..db46b82 100644
+--- a/plugins/hesstrans/Makefile
++++ b/plugins/hesstrans/Makefile
+@@ -85,7 +85,7 @@ 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 4c47615..1c77ddf 100644
+--- a/plugins/molfile_plugin/Makefile
++++ b/plugins/molfile_plugin/Makefile
+@@ -15,7 +15,7 @@
+ VPATH = src ../include ${ARCHDIR}
+ 
+ SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
+ 
+ #
+ # Rules
+@@ -206,209 +206,209 @@
+ #
+ 
+ abinitplugin.so: ${ARCHDIR}/abinitplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ amiraplugin.so: ${ARCHDIR}/amiraplugin.o 
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ avsplugin.so: ${ARCHDIR}/avsplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ babelplugin.so: ${ARCHDIR}/babelplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ basissetplugin.so: ${ARCHDIR}/basissetplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ bgfplugin.so: ${ARCHDIR}/bgfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ binposplugin.so: ${ARCHDIR}/binposplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ brixplugin.so: ${ARCHDIR}/brixplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ carplugin.so: ${ARCHDIR}/carplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ corplugin.so: ${ARCHDIR}/corplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ crdplugin.so: ${ARCHDIR}/crdplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ cubeplugin.so: ${ARCHDIR}/cubeplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ dcdplugin.so: ${ARCHDIR}/dcdplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ dlpolyplugin.so: ${ARCHDIR}/dlpolyplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ dxplugin.so: ${ARCHDIR}/dxplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ edmplugin.so: ${ARCHDIR}/edmplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ fs4plugin.so: ${ARCHDIR}/fs4plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gamessplugin.so: ${ARCHDIR}/gamessplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ graspplugin.so: ${ARCHDIR}/graspplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ grdplugin.so: ${ARCHDIR}/grdplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gridplugin.so: ${ARCHDIR}/gridplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ jsplugin.so: ${ARCHDIR}/jsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ lammpsplugin.so: ${ARCHDIR}/lammpsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mapplugin.so: ${ARCHDIR}/mapplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mdfplugin.so: ${ARCHDIR}/mdfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ mol2plugin.so: ${ARCHDIR}/mol2plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ moldenplugin.so: ${ARCHDIR}/moldenplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ molemeshplugin.so: ${ARCHDIR}/molemeshplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ msmsplugin.so: ${ARCHDIR}/msmsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ namdbinplugin.so: ${ARCHDIR}/namdbinplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ offplugin.so: ${ARCHDIR}/offplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ orcaplugin.so: ${ARCHDIR}/orcaplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ parm7plugin.so: ${ARCHDIR}/parm7plugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ parmplugin.so: ${ARCHDIR}/parmplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pdbplugin.so: ${ARCHDIR}/pdbplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pdbxplugin.so: ${ARCHDIR}/pdbxplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ phiplugin.so: ${ARCHDIR}/phiplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pltplugin.so: ${ARCHDIR}/pltplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ plyplugin.so: ${ARCHDIR}/plyplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ pqrplugin.so: ${ARCHDIR}/pqrplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ psfplugin.so: ${ARCHDIR}/psfplugin.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)
++	$(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)
+ 
+ stlplugin.so: ${ARCHDIR}/stlplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vaspoutcarplugin.so: ${ARCHDIR}/vaspoutcarplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vaspparchgplugin.so: ${ARCHDIR}/vaspparchgplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vaspposcarplugin.so: ${ARCHDIR}/vaspposcarplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vasp5xdatcarplugin.so: ${ARCHDIR}/vasp5xdatcarplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vaspxdatcarplugin.so: ${ARCHDIR}/vaspxdatcarplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vaspxmlplugin.so: ${ARCHDIR}/vaspxmlplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ vtkplugin.so: ${ARCHDIR}/vtkplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ xsfplugin.so: ${ARCHDIR}/xsfplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ xyzplugin.so: ${ARCHDIR}/xyzplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ 
+ ##
+ ## In-development plugins that aren't part of the build quite yet...
+ ##
+ cpmdlogplugin.so: ${ARCHDIR}/cpmdlogplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ gaussianplugin.so: ${ARCHDIR}/gaussianplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ 
+ ##
+@@ -416,31 +416,31 @@
+ ## dependencies of some kind
+ ##
+ dmsplugin.so: ${ARCHDIR}/dmsplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(SQLITELIB) $(SQLITELDFLAGS) $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(SQLITELIB) $(SQLITELDFLAGS) $(LDFLAGS)
+ 
+ dtrplugin.so: ${ARCHDIR}/dtrplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ hoomdplugin.so: ${ARCHDIR}/hoomdplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS)
+ 
+ lmplugin.so: ${ARCHDIR}/lmplugin.o
+ 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(HDFLIB) $(HDFLDFLAGS) $(LDFLAGS)
+ 
+ maeffplugin.so: ${ARCHDIR}/maeffplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+ 
+ netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
+ 
+ tngplugin.so: ${ARCHDIR}/tngplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TNGLIB) $(TNGLDFLAGS) $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TNGLIB) $(TNGLDFLAGS) $(LDFLAGS)
+ 
+ vtfplugin.so: ${ARCHDIR}/vtfplugin.o
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
+ 
+ webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o 
+-	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
++	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
+ 
+ 
+ #
+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 16f070a..da71248 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 ${ARCHDIR}/stamp -lm
+     
+     
+ # Objects.
+-- 
+2.5.5
+
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
index 8ffb5a090074..db9e4f49e522 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -83,6 +83,10 @@ src_prepare() {
 	cd "${WORKDIR}"
 	xdg_src_prepare
 
+	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
+	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
+	eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-plugins.patch
+
 	use cuda && cuda_sanitize
 
 	# Prepare plugins
@@ -117,6 +121,8 @@ src_prepare() {
 	cd "${S}" || die
 
 	eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch
+
+	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
 	eapply "${FILESDIR}"/${PN}-1.9.4-tmpdir.patch
 
 	# PREFIX