[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/, sci-chemistry/vmd/files/

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* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/, sci-chemistry/vmd/files/
@ 2020-11-15 15:31 Joonas Niilola
  0 siblings, 0 replies; 4+ messages in thread
From: Joonas Niilola @ 2020-11-15 15:31 UTC (permalink / raw
  To: gentoo-commits

commit:     4cff8d78afd97a9c1763c773b95e8a18b225d85e
Author:     Joonas Niilola <juippis <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 15 14:05:28 2020 +0000
Commit:     Joonas Niilola <juippis <AT> gentoo <DOT> org>
CommitDate: Sun Nov 15 15:31:19 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4cff8d78

sci-chemistry/vmd: fix SizeViolation issue

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

 sci-chemistry/vmd/Manifest                         |   1 +
 .../vmd/files/vmd-1.9.4-gentoo-plugins.patch       | 604 ---------------------
 sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild         |   3 +-
 3 files changed, 3 insertions(+), 605 deletions(-)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index f2c96b24855..e2e670e4391 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 c6ea769932f..00000000000
--- 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 db9e4f49e52..d449af190b4 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
 


^ permalink raw reply related	[flat|nested] 4+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/, sci-chemistry/vmd/files/
@ 2020-09-24 14:46 Pacho Ramos
  0 siblings, 0 replies; 4+ messages in thread
From: Pacho Ramos @ 2020-09-24 14:46 UTC (permalink / raw
  To: gentoo-commits

commit:     2176533fcbc07aabe6a5c9a45e6bb1e499773592
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 24 14:46:15 2020 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu Sep 24 14:46:25 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2176533f

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 <AT> gentoo.org>

 .../vmd/files/vmd-1.9.4-gentoo-plugins.patch       | 604 +++++++++++++++++++++
 sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild         |   6 +
 2 files changed, 610 insertions(+)

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 00000000000..c6ea769932f
--- /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 8ffb5a09007..db9e4f49e52 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


^ permalink raw reply related	[flat|nested] 4+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/, sci-chemistry/vmd/files/
@ 2020-07-21  9:54 Pacho Ramos
  0 siblings, 0 replies; 4+ messages in thread
From: Pacho Ramos @ 2020-07-21  9:54 UTC (permalink / raw
  To: gentoo-commits

commit:     ca543cde3fd9c01494d9f33fe40c55b16d98a91f
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Tue Jul 21 09:54:29 2020 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Tue Jul 21 09:54:38 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ca543cde

sci-chemistry/vmd: Drop old

Package-Manager: Portage-3.0.0, Repoman-2.3.23
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/Manifest                         |   2 -
 .../vmd/files/vmd-1.9.1-cuda-device_ptr.patch      |  28 ---
 .../vmd/files/vmd-1.9.2-format-security.patch      |  16 --
 sci-chemistry/vmd/vmd-1.9.2.ebuild                 | 256 -------------------
 sci-chemistry/vmd/vmd-1.9.3-r1.ebuild              | 267 --------------------
 sci-chemistry/vmd/vmd-1.9.3-r4.ebuild              | 271 ---------------------
 sci-chemistry/vmd/vmd-1.9.3.ebuild                 | 255 -------------------
 7 files changed, 1095 deletions(-)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 49868a8280d..977dcfa66a2 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,4 +1,2 @@
-DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51
-DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef
 DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
 DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba

diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
deleted file mode 100644
index 67eb11bbd36..00000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
+++ /dev/null
@@ -1,28 +0,0 @@
- vmd-1.9.1/src/CUDAMarchingCubes.cu | 1 +
- vmd-1.9.1/src/CUDAQuickSurf.cu     | 1 +
- 2 files changed, 2 insertions(+)
-
-diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu
-index 5bfe7bf..36faaf0 100755
---- a/src/CUDAMarchingCubes.cu
-+++ b/src/CUDAMarchingCubes.cu
-@@ -45,6 +45,7 @@
- #include "CUDAMarchingCubes.h"
- #include <thrust/scan.h>
- #include <thrust/functional.h>
-+#include <thrust/device_ptr.h>
- 
- // The number of threads to use for triangle generation 
- // (limited by shared memory size)
-diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu
-index a21ebde..56a42c8 100755
---- a/src/CUDAQuickSurf.cu
-+++ b/src/CUDAQuickSurf.cu
-@@ -22,6 +22,7 @@
- #include <stdlib.h>
- #include <string.h>
- #include <cuda.h>
-+#include <thrust/device_ptr.h>
- 
- #if CUDART_VERSION < 4000
- #error The VMD QuickSurf feature requires CUDA 4.0 or later

diff --git a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch
deleted file mode 100644
index 3f9ea5c8c2e..00000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- plugins/molfile_plugin/src/maeffplugin.cxx | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/plugins/molfile_plugin/src/maeffplugin.cxx b/plugins/molfile_plugin/src/maeffplugin.cxx
-index cfe1223..41d92bb 100644
---- a/plugins/molfile_plugin/src/maeffplugin.cxx
-+++ b/plugins/molfile_plugin/src/maeffplugin.cxx
-@@ -1979,7 +1979,7 @@ namespace {
-       }
-     }
-     catch (std::exception &e) {
--      fprintf(stderr, e.what());
-+      fprintf(stderr, "%s", e.what());
-       return MOLFILE_ERROR;
-     }
-     return MOLFILE_SUCCESS;

diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild
deleted file mode 100644
index 92daf030477..00000000000
--- a/sci-chemistry/vmd/vmd-1.9.2.ebuild
+++ /dev/null
@@ -1,256 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
-	${P}.src.tar.gz"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
-	>=dev-lang/tk-8.6.1
-	dev-lang/perl
-	dev-libs/expat
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	${PYTHON_DEPS}
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	dev-lang/swig"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-	"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${P}.src.tar.gz from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
-}
-
-src_prepare() {
-	use cuda && cuda_sanitize
-
-	epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
-
-	cd "${WORKDIR}"/plugins || die
-
-	epatch \
-		"${WORKDIR}"/${P}-gentoo-plugins.patch \
-		"${FILESDIR}"/${P}-format-security.patch
-
-	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
-
-	sed \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
-		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e '/^AR /s:=:?=:g' \
-		-e '/^RANLIB /s:=:?=:g' \
-		-i ../plugins/*/Makefile || die
-
-	tc-export AR RANLIB
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# prepare vmd itself
-	cd "${S}" || die
-
-	epatch "${WORKDIR}"/${P}-gentoo-base.patch
-
-	# PREFIX
-	sed \
-		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-		-i configure || die
-
-	sed \
-		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-gcc:$(tc-getCC):g" \
-		-e "s:gentoo-g++:$(tc-getCXX):g" \
-		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-		-e "s:gentoo-cflags:${CFLAGS}:g" \
-		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-		-e "s:gentoo-nvflags::g" \
-		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-i configure || die
-
-	if use cuda; then
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-			-i configure src/Makefile || die
-		sed \
-			-e '/compute_/d' \
-			-i configure || die
-		sed \
-			-e 's:-gencode .*code=sm_..::' \
-			-i src/Makefile || die
-	fi
-
-	sed \
-		-e "s:LINUXPPC:LINUX:g" \
-		-e "s:LINUXALPHA:LINUX:g" \
-		-e "s:LINUXAMD64:LINUX:g" \
-		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
-
-	EMAKEOPTS=(
-		TCLINC="-I${EPREFIX}/usr/include"
-		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
-		TCLLDFLAGS="-shared"
-		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
-		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include"
-		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
-		NETCDFDYNAMIC=1
-		EXPATINC="-I${EPREFIX}/usr/include"
-		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
-		EXPATLDFLAGS="-shared"
-		EXPATDYNAMIC=1
-	)
-	if use gromacs; then
-		EMAKEOPTS+=(
-			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
-			TNGINC="-I${EPREFIX}/usr/include"
-			TNGLDFLAGS="-shared"
-			TNGDYNAMIC=1
-		)
-	fi
-	if use sqlite; then
-		EMAKEOPTS+=(
-			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
-			SQLITEINC="-I${EPREFIX}/usr/include"
-			SQLITELDFLAGS="-shared"
-			SQLITEDYNAMIC=1
-		)
-	fi
-}
-
-src_configure() {
-	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
-	rm -f configure.options && echo $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
deleted file mode 100644
index f42cb4d104f..00000000000
--- a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
+++ /dev/null
@@ -1,267 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
-	${P}.src.tar
-"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
-	>=dev-lang/tk-8.6.1:0=
-	dev-lang/perl
-	dev-libs/expat
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	${PYTHON_DEPS}
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )
-"
-DEPEND="${CDEPEND}"
-BDEPEND="
-	virtual/pkgconfig
-	dev-lang/swig
-"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${P}.src.tar from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
-	elog
-	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
-	elog "file may get downloaded as a compressed tarball or not. In that case"
-	elog "you will need to ensure you uncompress the file and rename it"
-	elog "as ${P}.src.tar"
-}
-
-src_prepare() {
-	default
-
-	use cuda && cuda_sanitize
-
-	eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
-
-	cd "${WORKDIR}"/plugins || die
-
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch
-
-	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
-
-	sed \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
-		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e '/^AR /s:=:?=:g' \
-		-e '/^RANLIB /s:=:?=:g' \
-		-i ../plugins/*/Makefile || die
-
-	tc-export AR RANLIB
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# prepare vmd itself
-	cd "${S}" || die
-
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch
-	eapply "${FILESDIR}"/${P}-configure-libtachyon.patch
-
-	# PREFIX
-	sed \
-		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-		-i configure || die
-
-	sed \
-		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-gcc:$(tc-getCC):g" \
-		-e "s:gentoo-g++:$(tc-getCXX):g" \
-		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-		-e "s:gentoo-cflags:${CFLAGS}:g" \
-		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-		-e "s:gentoo-nvflags::g" \
-		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
-		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-i configure || die
-
-	if use cuda; then
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-			-i configure src/Makefile || die
-		sed \
-			-e '/compute_/d' \
-			-i configure || die
-		sed \
-			-e 's:-gencode .*code=sm_..::' \
-			-i src/Makefile || die
-	fi
-
-	sed \
-		-e "s:LINUXPPC:LINUX:g" \
-		-e "s:LINUXALPHA:LINUX:g" \
-		-e "s:LINUXAMD64:LINUX:g" \
-		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
-
-	EMAKEOPTS=(
-		TCLINC="-I${EPREFIX}/usr/include"
-		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
-		TCLLDFLAGS="-shared"
-		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
-		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
-		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
-		NETCDFDYNAMIC=1
-		EXPATINC="-I${EPREFIX}/usr/include"
-		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
-		EXPATLDFLAGS="-shared"
-		EXPATDYNAMIC=1
-	)
-	if use gromacs; then
-		EMAKEOPTS+=(
-			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
-			TNGINC="-I${EPREFIX}/usr/include"
-			TNGLDFLAGS="-shared"
-			TNGDYNAMIC=1
-		)
-	fi
-	if use sqlite; then
-		EMAKEOPTS+=(
-			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
-			SQLITEINC="-I${EPREFIX}/usr/include"
-			SQLITELDFLAGS="-shared"
-			SQLITEDYNAMIC=1
-		)
-	fi
-}
-
-src_configure() {
-	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
-	rm -f configure.options && echo $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
deleted file mode 100644
index 39e7a9751ce..00000000000
--- a/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
+++ /dev/null
@@ -1,271 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
-	${P}.src.tar
-"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
-	>=dev-lang/tk-8.6.1:0=
-	dev-lang/perl
-	dev-libs/expat
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	${PYTHON_DEPS}
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )
-"
-DEPEND="${CDEPEND}"
-BDEPEND="
-	virtual/pkgconfig
-	dev-lang/swig
-"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/chemical-mime-data
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${P}.src.tar from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
-	elog
-	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
-	elog "file may get downloaded as a compressed tarball or not. In that case"
-	elog "you will need to ensure you uncompress the file and rename it"
-	elog "as ${P}.src.tar"
-}
-
-src_prepare() {
-	xdg_src_prepare
-
-	use cuda && cuda_sanitize
-
-	eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
-
-	cd "${WORKDIR}"/plugins || die
-
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch
-
-	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
-
-	sed \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
-		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e '/^AR /s:=:?=:g' \
-		-e '/^RANLIB /s:=:?=:g' \
-		-i ../plugins/*/Makefile || die
-
-	tc-export AR RANLIB
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# prepare vmd itself
-	cd "${S}" || die
-
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch
-	eapply "${FILESDIR}"/${P}-configure-libtachyon.patch
-	eapply "${FILESDIR}"/${P}-tmpdir.patch
-
-	# PREFIX
-	sed \
-		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-		-i configure || die
-
-	sed \
-		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-gcc:$(tc-getCC):g" \
-		-e "s:gentoo-g++:$(tc-getCXX):g" \
-		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-		-e "s:gentoo-cflags:${CFLAGS}:g" \
-		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-		-e "s:gentoo-nvflags::g" \
-		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
-		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-i configure || die
-
-	if use cuda; then
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-			-i configure src/Makefile || die
-		sed \
-			-e '/compute_/d' \
-			-i configure || die
-		sed \
-			-e 's:-gencode .*code=sm_..::' \
-			-i src/Makefile || die
-	fi
-
-	sed \
-		-e "s:LINUXPPC:LINUX:g" \
-		-e "s:LINUXALPHA:LINUX:g" \
-		-e "s:LINUXAMD64:LINUX:g" \
-		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
-
-	EMAKEOPTS=(
-		TCLINC="-I${EPREFIX}/usr/include"
-		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
-		TCLLDFLAGS="-shared"
-		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
-		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
-		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
-		NETCDFDYNAMIC=1
-		EXPATINC="-I${EPREFIX}/usr/include"
-		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
-		EXPATLDFLAGS="-shared"
-		EXPATDYNAMIC=1
-	)
-	if use gromacs; then
-		EMAKEOPTS+=(
-			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
-			TNGINC="-I${EPREFIX}/usr/include"
-			TNGLDFLAGS="-shared"
-			TNGDYNAMIC=1
-		)
-	fi
-	if use sqlite; then
-		EMAKEOPTS+=(
-			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
-			SQLITEINC="-I${EPREFIX}/usr/include"
-			SQLITELDFLAGS="-shared"
-			SQLITEDYNAMIC=1
-		)
-	fi
-}
-
-src_configure() {
-	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
-	rm -f configure.options && echo $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	# Open PDB files with VMD
-	echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}

diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild
deleted file mode 100644
index 88394af1970..00000000000
--- a/sci-chemistry/vmd/vmd-1.9.3.ebuild
+++ /dev/null
@@ -1,255 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
-	${P}.src.tar"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
-	>=dev-lang/tk-8.6.1
-	dev-lang/perl
-	dev-libs/expat
-	$(python_gen_cond_dep '
-		|| (
-			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
-			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
-		)
-	')
-	sci-libs/netcdf:0=
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	${PYTHON_DEPS}
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	dev-lang/swig"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/surf
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-	"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${P}.src.tar.gz from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
-}
-
-src_prepare() {
-	use cuda && cuda_sanitize
-
-	epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
-
-	cd "${WORKDIR}"/plugins || die
-
-	epatch \
-		"${WORKDIR}"/${P}-gentoo-plugins.patch
-
-	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
-
-	sed \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
-		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e '/^AR /s:=:?=:g' \
-		-e '/^RANLIB /s:=:?=:g' \
-		-i ../plugins/*/Makefile || die
-
-	tc-export AR RANLIB
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# prepare vmd itself
-	cd "${S}" || die
-
-	epatch "${WORKDIR}"/${P}-gentoo-base.patch
-
-	# PREFIX
-	sed \
-		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-		-i configure || die
-
-	sed \
-		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-gcc:$(tc-getCC):g" \
-		-e "s:gentoo-g++:$(tc-getCXX):g" \
-		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-		-e "s:gentoo-cflags:${CFLAGS}:g" \
-		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-		-e "s:gentoo-nvflags::g" \
-		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-i configure || die
-
-	if use cuda; then
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-			-i configure src/Makefile || die
-		sed \
-			-e '/compute_/d' \
-			-i configure || die
-		sed \
-			-e 's:-gencode .*code=sm_..::' \
-			-i src/Makefile || die
-	fi
-
-	sed \
-		-e "s:LINUXPPC:LINUX:g" \
-		-e "s:LINUXALPHA:LINUX:g" \
-		-e "s:LINUXAMD64:LINUX:g" \
-		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
-
-	EMAKEOPTS=(
-		TCLINC="-I${EPREFIX}/usr/include"
-		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
-		TCLLDFLAGS="-shared"
-		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
-		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include"
-		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
-		NETCDFDYNAMIC=1
-		EXPATINC="-I${EPREFIX}/usr/include"
-		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
-		EXPATLDFLAGS="-shared"
-		EXPATDYNAMIC=1
-	)
-	if use gromacs; then
-		EMAKEOPTS+=(
-			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
-			TNGINC="-I${EPREFIX}/usr/include"
-			TNGLDFLAGS="-shared"
-			TNGDYNAMIC=1
-		)
-	fi
-	if use sqlite; then
-		EMAKEOPTS+=(
-			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
-			SQLITEINC="-I${EPREFIX}/usr/include"
-			SQLITELDFLAGS="-shared"
-			SQLITEDYNAMIC=1
-		)
-	fi
-}
-
-src_configure() {
-	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
-	rm -f configure.options && echo $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd.png
-	eprefixify "${WORKDIR}"/vmd.desktop
-	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
-	domenu "${WORKDIR}"/vmd.desktop
-}


^ permalink raw reply related	[flat|nested] 4+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/, sci-chemistry/vmd/files/
@ 2019-05-30 11:15 Pacho Ramos
  0 siblings, 0 replies; 4+ messages in thread
From: Pacho Ramos @ 2019-05-30 11:15 UTC (permalink / raw
  To: gentoo-commits

commit:     3e2a2a3baebbc26bdcd1ee23a765bf04ebed7ee3
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu May 30 11:14:56 2019 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu May 30 11:14:56 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e2a2a3b

sci-chemistry/vmd: Multiple fixes and update ebuild

- Longer explanation to download sources files (#640440)
- Fix tachyon support (#644122)
- Install netcdf plugin (#661636)

Bug: https://bugs.gentoo.org/640440
Closes: https://bugs.gentoo.org/644122
Closes: https://bugs.gentoo.org/661636
Package-Manager: Portage-2.3.66, Repoman-2.3.12
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 .../vmd/files/vmd-1.9.1-cuda-device_ptr.patch      |   8 +-
 .../vmd/files/vmd-1.9.3-configure-libtachyon.patch |  13 +
 sci-chemistry/vmd/vmd-1.9.3-r1.ebuild              | 262 +++++++++++++++++++++
 3 files changed, 279 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
index ce842448dec..67eb11bbd36 100644
--- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
+++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch
@@ -4,8 +4,8 @@
 
 diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu
 index 5bfe7bf..36faaf0 100755
---- a/vmd-1.9.1/src/CUDAMarchingCubes.cu
-+++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu
+--- a/src/CUDAMarchingCubes.cu
++++ b/src/CUDAMarchingCubes.cu
 @@ -45,6 +45,7 @@
  #include "CUDAMarchingCubes.h"
  #include <thrust/scan.h>
@@ -16,8 +16,8 @@ index 5bfe7bf..36faaf0 100755
  // (limited by shared memory size)
 diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu
 index a21ebde..56a42c8 100755
---- a/vmd-1.9.1/src/CUDAQuickSurf.cu
-+++ b/vmd-1.9.1/src/CUDAQuickSurf.cu
+--- a/src/CUDAQuickSurf.cu
++++ b/src/CUDAQuickSurf.cu
 @@ -22,6 +22,7 @@
  #include <stdlib.h>
  #include <string.h>

diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch
new file mode 100644
index 00000000000..b71cd97210a
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch
@@ -0,0 +1,13 @@
+--- a/configure.old	2019-05-16 17:26:05.347560700 +0200
++++ b/configure	2019-05-16 17:30:25.478455770 +0200
+@@ -1105,8 +1105,8 @@
+ # This may be commented out if not required.
+ $libtachyon_defines     = "-DVMDLIBTACHYON";
+ $libtachyon_dir         = "$vmd_library_dir/tachyon";
+-$libtachyon_include     = "-I$libtachyon_dir/include";
+-$libtachyon_library     = "-L$libtachyon_dir/lib_$config_arch";
++$libtachyon_include     = "-Igentoo-libtachyon-include";
++$libtachyon_library     = "-Lgentoo-libtachyon-libs";
+ $libtachyon_libs        = "-ltachyon";
+ @libtachyon_cc          = ();
+ @libtachyon_cu          = ();

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
new file mode 100644
index 00000000000..392e380ece1
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
@@ -0,0 +1,262 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python2_7 )
+
+inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
+	${P}.src.tar
+"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+	>=dev-lang/tk-8.6.1:0=
+	dev-lang/perl
+	dev-libs/expat
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/netcdf:0=
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	${PYTHON_DEPS}
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
+	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
+	sqlite? ( dev-db/sqlite:3= )
+	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
+	xinerama? ( x11-libs/libXinerama )
+"
+DEPEND="${CDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+	dev-lang/swig
+"
+RDEPEND="${CDEPEND}
+	sci-biology/stride
+	sci-chemistry/surf
+	x11-terms/xterm
+	msms? ( sci-chemistry/msms-bin )
+	povray? ( media-gfx/povray )
+"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+
+pkg_nofetch() {
+	elog "Please download ${P}.src.tar from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and get"
+	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
+	elog "Place both into your DISTDIR directory"
+	elog
+	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
+	elog "file may get downloaded as a compressed tarball or not. In that case"
+	elog "you will need to ensure you uncompress the file and rename it"
+	elog "as ${P}.src.tar"
+}
+
+src_prepare() {
+	default
+
+	use cuda && cuda_sanitize
+
+	eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
+
+	cd "${WORKDIR}"/plugins || die
+
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch	
+
+	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
+
+	sed \
+		-e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
+		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
+		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
+		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
+		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
+		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
+		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	sed \
+		-e '/^AR /s:=:?=:g' \
+		-e '/^RANLIB /s:=:?=:g' \
+		-i ../plugins/*/Makefile || die
+
+	tc-export AR RANLIB
+
+	sed \
+		-e "s:\$(CXXFLAGS)::g" \
+		-i hesstrans/Makefile || die
+
+	# prepare vmd itself
+	cd "${S}" || die
+
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch
+	eapply "${FILESDIR}"/${P}-configure-libtachyon.patch
+
+	# PREFIX
+	sed \
+		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
+		-i configure || die
+
+	sed \
+		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
+		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-gcc:$(tc-getCC):g" \
+		-e "s:gentoo-g++:$(tc-getCXX):g" \
+		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
+		-e "s:gentoo-cflags:${CFLAGS}:g" \
+		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
+		-e "s:gentoo-nvflags::g" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
+		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
+		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
+		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
+		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-i configure || die
+
+	if use cuda; then
+		sed \
+			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
+			-i configure src/Makefile || die
+		sed \
+			-e '/compute_/d' \
+			-i configure || die
+		sed \
+			-e 's:-gencode .*code=sm_..::' \
+			-i src/Makefile || die
+	fi
+
+	sed \
+		-e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
+		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
+		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
+		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+
+	EMAKEOPTS=(
+		TCLINC="-I${EPREFIX}/usr/include"
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
+		TCLLDFLAGS="-shared"
+		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
+		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
+		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
+		NETCDFDYNAMIC=1
+		EXPATINC="-I${EPREFIX}/usr/include"
+		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
+		EXPATLDFLAGS="-shared"
+		EXPATDYNAMIC=1
+	)
+	if use gromacs; then
+		EMAKEOPTS+=(
+			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
+			TNGINC="-I${EPREFIX}/usr/include"
+			TNGLDFLAGS="-shared"
+			TNGDYNAMIC=1
+		)
+	fi
+	if use sqlite; then
+		EMAKEOPTS+=(
+			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
+			SQLITEINC="-I${EPREFIX}/usr/include"
+			SQLITELDFLAGS="-shared"
+			SQLITEDYNAMIC=1
+		)
+	fi
+}
+
+src_configure() {
+	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+	rm -f configure.options && echo $myconf >> configure.options
+
+	use cuda && myconf+=" CUDA"
+#	use mpi && myconf+=" MPI"
+	use tachyon && myconf+=" LIBTACHYON"
+	use xinerama && myconf+=" XINERAMA"
+
+	export \
+		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
+		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
+		PYTHON_LIBRARY="$(python_get_LIBS)" \
+		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
+		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
+
+	perl ./configure LINUX \
+		${myconf} || die
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins || die
+
+	emake \
+		${EMAKEOPTS[@]} \
+		LINUX
+
+	# build vmd
+	cd "${S}"/src || die
+	emake
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins || die
+	emake \
+			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
+			distrib
+
+	# install vmd
+	cd "${S}"/src || die
+	emake install
+
+	# install docs
+	cd "${S}" || die
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in
+	# /usr/lib
+	cd "${ED}"/usr/$(get_libdir)/vmd || die
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed \
+		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
+		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
+		|| die "failed to set up vmd wrapper script"
+
+	# install icon and generate desktop entry
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}"/vmd.png
+	eprefixify "${WORKDIR}"/vmd.desktop
+	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
+	domenu "${WORKDIR}"/vmd.desktop
+}


^ permalink raw reply related	[flat|nested] 4+ messages in thread

end of thread, other threads:[~2020-11-15 15:31 UTC | newest]

Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2020-11-15 15:31 [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/, sci-chemistry/vmd/files/ Joonas Niilola
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2020-09-24 14:46 Pacho Ramos
2020-07-21  9:54 Pacho Ramos
2019-05-30 11:15 Pacho Ramos

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