sci-chemistry/vmd: fix SizeViolation issue

Closes: https://bugs.gentoo.org/748210
Signed-off-by: Joonas Niilola <juippis@gentoo.org>

3 files changed, 3 insertions, 605 deletions

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index f2c96b248550..e2e670e4391c 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,2 +1,3 @@
 DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
 DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
+DIST vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63
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
deleted file mode 100644
index c6ea769932f3..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch
+++ /dev/null
@@ -1,604 +0,0 @@
-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 ${ARCHDIR}/stamp -lm
-     
-     
- # Objects.
--- 
-2.5.5
-
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
index db9e4f49e522..d449af190b42 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -14,6 +14,7 @@ MY_P="${PN}-${MY_PV}"
 SRC_URI="
 	${MY_P}.src.tar
 	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz
+	https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch
 "
 
 SLOT="0"
@@ -85,7 +86,7 @@ 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
+	eapply "${DISTDIR}"/${PN}-1.9.4-gentoo-plugins.patch
 
 	use cuda && cuda_sanitize