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authorV3n3RiX <venerix@redcorelinux.org>2020-09-30 17:27:54 +0100
committerV3n3RiX <venerix@redcorelinux.org>2020-09-30 17:27:54 +0100
commitf70a1bfc721336d4fc7dfb711c2f518a6b18cf16 (patch)
treee907cb121b30e3c1df1710719c0ddf4029597a47 /sci-chemistry
parentdb063b515939ab15261136b24e4bc44386335c0c (diff)
gentoo resync : 30.09.2020
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/Manifest.gzbin11370 -> 11367 bytes
-rw-r--r--sci-chemistry/theseus/Manifest4
-rw-r--r--sci-chemistry/theseus/theseus-2.0.6.ebuild64
-rw-r--r--sci-chemistry/theseus/theseus-3.0.0.ebuild69
-rw-r--r--sci-chemistry/vmd/Manifest3
-rw-r--r--sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch604
-rw-r--r--sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild6
7 files changed, 612 insertions, 138 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index fe2ae16e7a21..1fecf4e508f9 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
Binary files differ
diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest
index bc633387ad18..742af600c3fc 100644
--- a/sci-chemistry/theseus/Manifest
+++ b/sci-chemistry/theseus/Manifest
@@ -1,7 +1,3 @@
-DIST theseus_2.0.6.tar.gz 1257560 BLAKE2B 80115f5ace6fe306b10254f9a7b889e5bc61afbd3cff4941953b9a82750ce1b36ac5724a94fd7e7892622684d7e5bf6ae9ed7c96d76364329d756114efbe1dd0 SHA512 70604c468eb841b92e77a3e91cd57120b96c171512fb1cc31a407b7c4816150dfa31ec123fb9568a842e623f3252c60df0dc53d40fa2a4aece6e3c77039f4696
-DIST theseus_3.0.0.tar.gz 1213574 BLAKE2B 17021c7d36b3ac3d8e7f84bbe2614523d461a3877bca4b20b6891b67de02b0d02376e695f0db813e8f598f7dee32076548444defc30b016588b70be14cf3f308 SHA512 251e6273624126406609691e1205d9693c18dcbc8c81e10c77101ac4a1b6bdffcb56a47fd5fdc7ed6ed4fa107c2ed26b03a1780f951f9cc69a25c0722996e7b2
DIST theseus_3.3.0.tar.gz 22548124 BLAKE2B 0ad49f768e1584bf40e90ff6fd0d884b6b27ee59ad31ce75050293b817a3747969ab0c4b4ff982aadbdc5301c1c56522540b78aab045e841c099a80dd546c8e9 SHA512 1fba3e8019a40214defdae13d4721d170ee698337d8efd4e872af22f8ab3cb1fdd52fa9f19a858ee51bc98150692af0c6016033feb0d76f29acaf7fffbb430e2
-EBUILD theseus-2.0.6.ebuild 1449 BLAKE2B 8d6282e40e0cb06a26171e11fa220dbf00e28ec682e1ebb97bdb13658b1e661cff2f31d88a3251dbd8664ad44e9d19b0624d80b5372c02827d10a28021dc2683 SHA512 35fce318510a70da251151061013e52dc0c16b0bdb8aed4ecd1dca2deb53a662290d4700a5df3bfa755c785e8b481cdd7f83a2263a3823823261044079e69a26
-EBUILD theseus-3.0.0.ebuild 1499 BLAKE2B 23e60b603438314d0a5068651cfbbe6a9eeec9569a276ca9695eb4a24a5969ee798265085023c734038aabea515f5c9f6b49876569428da10ad08a62ac5a6327 SHA512 edbe86d80416fa9256b26ee95ae77e3973b2cd171e3a6ab02976127b8dfaa7541a1f35f1500afcc7200140a54bc22309bcbeaaa341b5032e6549fb5e85bfdfda
EBUILD theseus-3.3.0.ebuild 1499 BLAKE2B 23e60b603438314d0a5068651cfbbe6a9eeec9569a276ca9695eb4a24a5969ee798265085023c734038aabea515f5c9f6b49876569428da10ad08a62ac5a6327 SHA512 edbe86d80416fa9256b26ee95ae77e3973b2cd171e3a6ab02976127b8dfaa7541a1f35f1500afcc7200140a54bc22309bcbeaaa341b5032e6549fb5e85bfdfda
MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/theseus/theseus-2.0.6.ebuild b/sci-chemistry/theseus/theseus-2.0.6.ebuild
deleted file mode 100644
index 7c3f3783602c..000000000000
--- a/sci-chemistry/theseus/theseus-2.0.6.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit multilib toolchain-funcs
-
-DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
-HOMEPAGE="http://www.theseus3d.org/"
-SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-RDEPEND="
- sci-libs/gsl
- || (
- sci-biology/muscle
- sci-biology/probcons
- sci-biology/mafft
- sci-biology/t-coffee
- sci-biology/kalign
- sci-biology/clustalw:2
- )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}"/${PN}_src/
-
-src_prepare() {
- cat >> make.inc <<- EOF
- ARCH = $(tc-getAR)
- ARCHFLAGS = -rvs
- RANLIB = $(tc-getRANLIB)
- LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
- SYSLIBS = $(pkg-config --libs gsl) -lpthread
- LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
- LIBDIR = -L./lib
- INSTALLDIR = "${ED}"/usr/bin
- OPT =
- WARN =
- CFLAGS = ${CFLAGS} \$(WARN)
- CC = $(tc-getCC)
- EOF
-
- sed \
- -e 's|theseus:|theseus: libs|g' \
- -e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
- -i Makefile || die
-
- sed \
- -e 's:/usr/bin/sed:sed:g' \
- -e "s:/usr/local/bin/:/usr/bin/:g" \
- -e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \
- -i theseus_align || die
-}
-
-src_install() {
- dobin theseus theseus_align
- dodoc theseus_man.pdf README AUTHORS
- use examples && insinto /usr/share/${PN} && doins -r examples
-}
diff --git a/sci-chemistry/theseus/theseus-3.0.0.ebuild b/sci-chemistry/theseus/theseus-3.0.0.ebuild
deleted file mode 100644
index 583bdf1e28c5..000000000000
--- a/sci-chemistry/theseus/theseus-3.0.0.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit multilib toolchain-funcs
-
-DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
-HOMEPAGE="http://www.theseus3d.org/"
-SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-RDEPEND="
- sci-libs/gsl
- || (
- sci-biology/muscle
- sci-biology/probcons
- sci-biology/mafft
- sci-biology/t-coffee
- sci-biology/kalign
- sci-biology/clustalw:2
- )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}"/${PN}_src/
-
-src_prepare() {
- cat >> make.inc <<- EOF
- ARCH = $(tc-getAR)
- ARCHFLAGS = -rvs
- RANLIB = $(tc-getRANLIB)
- LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
- SYSLIBS = $(pkg-config --libs gsl) -lpthread
- LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
- LIBDIR = -L./lib
- INSTALLDIR = "${ED}"/usr/bin
- OPT =
- WARN =
- CFLAGS = ${CFLAGS} -std=c11 \$(WARN)
- CC = $(tc-getCC)
- EOF
-
- sed \
- -e 's|theseus:|theseus: libs|g' \
- -e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
- -i Makefile || die
-
- sed \
- -e 's:/usr/bin/sed:sed:g' \
- -e "s:/usr/local/bin/:/usr/bin/:g" \
- -e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \
- -i theseus_align || die
-}
-
-src_compile() {
- emake ltheseus
- default
-}
-
-src_install() {
- dobin theseus theseus_align
- dodoc theseus_man.pdf README AUTHORS
- use examples && insinto /usr/share/${PN} && doins -r examples
-}
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index d9163127f214..5584e3b1e4cc 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,6 +1,7 @@
AUX vmd-1.9.4-gentoo-paths.patch 11523 BLAKE2B 3e02c73b49a3686ce00deb44f4bca0809c527a53d7fb13315c5799c5e9fe1d8ada9664452e41f49ad084abed96d2e5a6d01b000e49393e97eeb5fb2378af888f SHA512 da8e723d12ca7728d67dffcd0bf2e9c856764917d3f3ef07756febbc981bae20b061e0ead3fa617de18b94918d855c09f68c24a979c6f9f0cdea12b343a22756
+AUX vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63
AUX vmd-1.9.4-tmpdir.patch 398 BLAKE2B cf61240688f111d4763f458f0e10319a8154c5427172ba99d4bcfc7a9d8fd559fe7777c1ff703f81b68b2f10ec2a8c4af5cf61fd91d147aec2f4fafcf6753c82 SHA512 c5f96b3ef880ccdcf86d3927308c85aeaf3260ed0e54d60cbf186a0d63f6a88da16e49b14d6815d97bfd1ff4500bf9ce99d183d26ee78b67fed388e2217a7f10
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
-EBUILD vmd-1.9.4_alpha43.ebuild 7643 BLAKE2B 298be7052331709d194263c557558bbf0ca66936f460dcb1ac7aeb59add81519a856bdc61d61ab1ad216f5da199435eefb515a14cab59378a052bf8ae4bf6bce SHA512 4b504629e6d784d1da6ccf7db9f5a14da4b00869705851f3842c7d6f07cd0ac4ee45125c779b91862cceea54836eb06e84773098d3113a0d0b856fbb775ff07e
+EBUILD vmd-1.9.4_alpha43.ebuild 7910 BLAKE2B 79a150dca7841f97bbc47c75f30f99a9c88dca284655ecf54ad328516ae6207b4bc800d6de3584c4e14b30b7789562c14a9c46c49d99b15567e14612ccbfbe3f SHA512 63393f786285588f970f2e817145b77f93c0d62c3e87e2b83e7edd52a168f2556fcec14c8ce06c67e521e8b92d04470bbdfd143f505acc8a6b64f457ca24107a
MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch
new file mode 100644
index 000000000000..c6ea769932f3
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch
@@ -0,0 +1,604 @@
+From c33a68684cd06424ec78c6983f93336109d91cb5 Mon Sep 17 00:00:00 2001
+From: Stefan Kuczera <stefan.ku@yahoo.com>
+Date: Sat, 21 Jan 2017 13:20:45 +0100
+Subject: [PATCH] Squashed patches
+
+---
+ plugins/Make-arch | 3 +-
+ plugins/Makefile | 20 +++---
+ plugins/autopsf/Makefile | 4 +-
+ plugins/catdcd/Makefile | 4 +-
+ plugins/cionize/Makefile | 6 +-
+ plugins/clustalw/Makefile | 2 +-
+ plugins/cluster/Makefile | 2 +-
+ plugins/hesstrans/Makefile | 2 +-
+ plugins/libbiokit/Makefile | 14 ++--
+ plugins/molfile_plugin/Makefile | 144 ++++++++++++++++++++--------------------
+ plugins/phylotree/Makefile | 2 +-
+ plugins/rnaview/Makefile | 2 +-
+ plugins/stamp/Makefile | 2 +-
+ 13 files changed, 105 insertions(+), 102 deletions(-)
+
+diff --git a/plugins/Make-arch b/plugins/Make-arch
+index 19d2b6c..937ad9e 100755
+--- a/plugins/Make-arch
++++ b/plugins/Make-arch
+@@ -313,7 +313,8 @@ LINUX:
+ "AR = ar" \
+ "NM = nm -p" \
+ "RANLIB = touch" \
+- "SHLD = gcc -shared"
++ "SHLD = gcc -shared" \
++ "SHXXLD = g++ -shared"
+
+ LINUXALPHA:
+ $(MAKE) dynlibs staticlibs bins \
+diff --git a/plugins/Makefile b/plugins/Makefile
+index 0fee349..6b07606 100755
+--- a/plugins/Makefile
++++ b/plugins/Makefile
+@@ -150,25 +150,27 @@ distrib:
+
+ include Make-arch
+
+-molfilelibs:
+- cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1
+- cd molfile_plugin; $(MAKE) staticlibs && cd .. || exit 1
++molfilelibs_static:
++ $(MAKE) -C molfile_plugin staticlibs
++
++molfilelibs_dyn:
++ $(MAKE) -C molfile_plugin dynlibs
+
+ win32molfilelibs:
+ cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1
+ cd molfile_plugin; $(MAKE) win32staticlibs && cd .. || exit 1
+
+-dynlibs: molfilelibs
+- for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) dynlibs && cd .. || exit 1 ; done
++dynlibs: molfilelibs_dyn
++ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir dynlibs; done
+
+-staticlibs: molfilelibs
+- for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) staticlibs && cd .. || exit 1 ; done
++staticlibs: molfilelibs_static
++ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir staticlibs; done
+
+ win32staticlibs: win32molfilelibs
+ for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) win32staticlibs && cd .. || exit 1 ; done
+
+-bins:
+- for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) bins && cd .. || exit 1 ; done
++bins: molfilelibs_dyn
++ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir bins; done
+
+ win32bins:
+ for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) win32bins && cd .. || exit 1 ; done
+diff --git a/plugins/autopsf/Makefile b/plugins/autopsf/Makefile
+index 3b35d10..8e1527e 100644
+--- a/plugins/autopsf/Makefile
++++ b/plugins/autopsf/Makefile
+@@ -49,8 +49,8 @@ AUTOPSFOBJS=${ARCHDIR}/psfatom.o \
+
+ ${ARCHDIR}/psfcheck.so : ${AUTOPSFOBJS}
+ if [ -n "${TCLSHLD}" ]; \
+- then ${TCLSHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+- else ${SHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
++ then ${TCLSHLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \
++ else ${SHXXLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \
+ fi
+
+ ${ARCHDIR}/psfatom.o : psfatom.h psfatom.C
+diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile
+index d6c58c5..1637a3c 100644
+--- a/plugins/catdcd/Makefile
++++ b/plugins/catdcd/Makefile
+@@ -45,8 +45,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi
+ LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS}
+
+ # all other platforms
+-${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
+- ${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
++${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
+
+ ${ARCHDIR}/hash.o: hash.h hash.c
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
+diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile
+index bcb2510..e02241b 100644
+--- a/plugins/cionize/Makefile
++++ b/plugins/cionize/Makefile
+@@ -52,8 +52,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI
+ LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS}
+
+ # all other platforms
+-${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
+- ${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
++${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm
+
+ ${ARCHDIR}/hash.o: hash.h hash.c
+ ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
+@@ -66,7 +66,7 @@ ${ARCHDIR}/util.o: util.h util.c
+
+ ${ARCHDIR}/getplugins.o: getplugins.h getplugins.c
+ ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/getplugins.c $(COPTO)${ARCHDIR}/getplugins.o
+-
++
+ ${ARCHDIR}/energythr.o: energythr.h energythr.c ${ARCHDIR}/util.o ${ARCHDIR}/threads.o
+ ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/energythr.c $(COPTO)${ARCHDIR}/energythr.o
+
+diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile
+index 6329f64..3443720 100644
+--- a/plugins/clustalw/Makefile
++++ b/plugins/clustalw/Makefile
+@@ -66,7 +66,7 @@ OBJS = ${ARCHDIR}/alnscore.o \
+ ${ARCHDIR}/clustalw.exe: ${OBJS}
+ LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe
+ ${ARCHDIR}/clustalw: ${OBJS}
+- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
++ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
+
+
+ # Objects.
+diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile
+index 99d347e..c2d30ae 100644
+--- a/plugins/cluster/Makefile
++++ b/plugins/cluster/Makefile
+@@ -48,7 +48,7 @@ ${ARCHDIR}/cluster.exe : ${OBJS}
+
+ # all other platforms
+ ${ARCHDIR}/cluster : ${OBJS}
+- ${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
+
+ ${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o
+diff --git a/plugins/hesstrans/Makefile b/plugins/hesstrans/Makefile
+index 76ee306..db46b82 100644
+--- a/plugins/hesstrans/Makefile
++++ b/plugins/hesstrans/Makefile
+@@ -85,7 +85,7 @@ HESSTRANSOBJS=${ARCHDIR}/newmat1.o \
+ ${ARCHDIR}/hesstrans.so : ${HESSTRANSOBJS}
+ if [ -n "${TCLSHLD}" ]; \
+ then ${TCLSHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+- else ${SHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
++ else ${SHXXLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+ fi
+
+
+diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile
+index 7a66d08..da764dd 100644
+--- a/plugins/libbiokit/Makefile
++++ b/plugins/libbiokit/Makefile
+@@ -98,7 +98,7 @@ OBJS = ${DYNLIBOBJS} \
+ ${ARCHDIR}/tcl_libbiokit.so : ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS}
+ if [ -n "${TCLSHLD}" ]; \
+ then ${TCLSHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+- else ${SHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
++ else ${SHXXLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
+ fi
+ ${ARCHDIR}/tcl_libbiokit_wrap.o : ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp
+ ${CXX} ${CXXFLAGS} ${TCLINC} ${INCDIR} -c ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp $(COPTO)${ARCHDIR}/tcl_libbiokit_wrap.o
+@@ -111,7 +111,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i
+ ${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}
+ LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe
+ ${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}
+- ${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
+ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o
+
+@@ -119,7 +119,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
+ ${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}
+ LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe
+ ${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}
+- ${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
+ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o
+
+@@ -127,7 +127,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
+ ${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}
+ LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe
+ ${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}
+- ${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
+ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o
+
+@@ -135,7 +135,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
+ ${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}
+ LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe
+ ${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}
+- ${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
+ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o
+
+@@ -143,7 +143,7 @@ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
+ ${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}
+ LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe
+ ${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}
+- ${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
+ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o
+
+@@ -151,7 +151,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
+ ${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}
+ LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe
+ ${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}
+- ${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
+ ${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o
+
+diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
+index 4c47615..1c77ddf 100644
+--- a/plugins/molfile_plugin/Makefile
++++ b/plugins/molfile_plugin/Makefile
+@@ -15,7 +15,7 @@
+ VPATH = src ../include ${ARCHDIR}
+
+ SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
+
+ #
+ # Rules
+@@ -206,209 +206,209 @@
+ #
+
+ abinitplugin.so: ${ARCHDIR}/abinitplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ amiraplugin.so: ${ARCHDIR}/amiraplugin.o
+ $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ avsplugin.so: ${ARCHDIR}/avsplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ babelplugin.so: ${ARCHDIR}/babelplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ basissetplugin.so: ${ARCHDIR}/basissetplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ bgfplugin.so: ${ARCHDIR}/bgfplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ binposplugin.so: ${ARCHDIR}/binposplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ brixplugin.so: ${ARCHDIR}/brixplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ carplugin.so: ${ARCHDIR}/carplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o
+ $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ corplugin.so: ${ARCHDIR}/corplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ crdplugin.so: ${ARCHDIR}/crdplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ cubeplugin.so: ${ARCHDIR}/cubeplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ dcdplugin.so: ${ARCHDIR}/dcdplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ dlpolyplugin.so: ${ARCHDIR}/dlpolyplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o
+ $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ dxplugin.so: ${ARCHDIR}/dxplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ edmplugin.so: ${ARCHDIR}/edmplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ fs4plugin.so: ${ARCHDIR}/fs4plugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ gamessplugin.so: ${ARCHDIR}/gamessplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ graspplugin.so: ${ARCHDIR}/graspplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ grdplugin.so: ${ARCHDIR}/grdplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ gridplugin.so: ${ARCHDIR}/gridplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ jsplugin.so: ${ARCHDIR}/jsplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ lammpsplugin.so: ${ARCHDIR}/lammpsplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ mapplugin.so: ${ARCHDIR}/mapplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ mdfplugin.so: ${ARCHDIR}/mdfplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ mol2plugin.so: ${ARCHDIR}/mol2plugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ moldenplugin.so: ${ARCHDIR}/moldenplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ molemeshplugin.so: ${ARCHDIR}/molemeshplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ msmsplugin.so: ${ARCHDIR}/msmsplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ namdbinplugin.so: ${ARCHDIR}/namdbinplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ offplugin.so: ${ARCHDIR}/offplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ orcaplugin.so: ${ARCHDIR}/orcaplugin.o
+ $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ parm7plugin.so: ${ARCHDIR}/parm7plugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ parmplugin.so: ${ARCHDIR}/parmplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ pdbplugin.so: ${ARCHDIR}/pdbplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ pdbxplugin.so: ${ARCHDIR}/pdbxplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ phiplugin.so: ${ARCHDIR}/phiplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ pltplugin.so: ${ARCHDIR}/pltplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ plyplugin.so: ${ARCHDIR}/plyplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ pqrplugin.so: ${ARCHDIR}/pqrplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ psfplugin.so: ${ARCHDIR}/psfplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ rst7plugin.so: ${ARCHDIR}/rst7plugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ situsplugin.so: ${ARCHDIR}/situsplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ spiderplugin.so: ${ARCHDIR}/spiderplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ stlplugin.so: ${ARCHDIR}/stlplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ vaspoutcarplugin.so: ${ARCHDIR}/vaspoutcarplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ vaspparchgplugin.so: ${ARCHDIR}/vaspparchgplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ vaspposcarplugin.so: ${ARCHDIR}/vaspposcarplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ vasp5xdatcarplugin.so: ${ARCHDIR}/vasp5xdatcarplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ vaspxdatcarplugin.so: ${ARCHDIR}/vaspxdatcarplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ vaspxmlplugin.so: ${ARCHDIR}/vaspxmlplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ vtkplugin.so: ${ARCHDIR}/vtkplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ xsfplugin.so: ${ARCHDIR}/xsfplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ xyzplugin.so: ${ARCHDIR}/xyzplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+
+ ##
+ ## In-development plugins that aren't part of the build quite yet...
+ ##
+ cpmdlogplugin.so: ${ARCHDIR}/cpmdlogplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ gaussianplugin.so: ${ARCHDIR}/gaussianplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+
+ ##
+@@ -416,31 +416,31 @@
+ ## dependencies of some kind
+ ##
+ dmsplugin.so: ${ARCHDIR}/dmsplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(SQLITELIB) $(SQLITELDFLAGS) $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(SQLITELIB) $(SQLITELDFLAGS) $(LDFLAGS)
+
+ dtrplugin.so: ${ARCHDIR}/dtrplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ hoomdplugin.so: ${ARCHDIR}/hoomdplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS)
+
+ lmplugin.so: ${ARCHDIR}/lmplugin.o
+ $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(HDFLIB) $(HDFLDFLAGS) $(LDFLAGS)
+
+ maeffplugin.so: ${ARCHDIR}/maeffplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
+
+ netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
+
+ tngplugin.so: ${ARCHDIR}/tngplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TNGLIB) $(TNGLDFLAGS) $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TNGLIB) $(TNGLDFLAGS) $(LDFLAGS)
+
+ vtfplugin.so: ${ARCHDIR}/vtfplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
+
+ webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o
+- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
+
+
+ #
+diff --git a/plugins/phylotree/Makefile b/plugins/phylotree/Makefile
+index 6442747..0aceb4d 100644
+--- a/plugins/phylotree/Makefile
++++ b/plugins/phylotree/Makefile
+@@ -54,7 +54,7 @@ ${ARCHDIR}/upgmaclu.exe : ${OBJS}
+
+ # all other platforms
+ ${ARCHDIR}/upgmaclu : ${OBJS}
+- ${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm
++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm
+
+ ${ARCHDIR}/upgmaclu.o: ${SRCDIR}/upgmaclu.c
+ ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/upgmaclu.c $(COPTO)${ARCHDIR}/upgmaclu.o
+diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile
+index 16f070a..da71248 100644
+--- a/plugins/rnaview/Makefile
++++ b/plugins/rnaview/Makefile
+@@ -67,7 +67,7 @@ OBJS = ${ARCHDIR}/analyze.o \
+ ${ARCHDIR}/rnaview.exe: ${OBJS}
+ LINK ${OBJS} /OUT:${ARCHDIR}/rnaview.exe
+ ${ARCHDIR}/rnaview: ${OBJS}
+- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm
++ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm
+
+ ${ARCHDIR}/analyze.o: ${SRCDIR}/analyze.c
+ ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/analyze.c $(COPTO)${ARCHDIR}/analyze.o
+diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile
+index f0fb515..aa8f6b6 100644
+--- a/plugins/stamp/Makefile
++++ b/plugins/stamp/Makefile
+@@ -101,7 +101,7 @@ OBJS = ${ARCHDIR}/a3to1.o \
+ ${ARCHDIR}/stamp.exe: ${OBJS}
+ LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe
+ ${ARCHDIR}/stamp: ${OBJS}
+- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
++ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
+
+
+ # Objects.
+--
+2.5.5
+
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
index 8ffb5a090074..db9e4f49e522 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -83,6 +83,10 @@ src_prepare() {
cd "${WORKDIR}"
xdg_src_prepare
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
+ eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-plugins.patch
+
use cuda && cuda_sanitize
# Prepare plugins
@@ -117,6 +121,8 @@ src_prepare() {
cd "${S}" || die
eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch
+
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
eapply "${FILESDIR}"/${PN}-1.9.4-tmpdir.patch
# PREFIX