No binaryfiles in VCS please, #370915

Package-Manager: portage-2.2.0_alpha40/cvs/Linux x86_64
author: Justin Lecher <jlec@gentoo.org> 2011-06-13 12:25:26 +0000
committer: Justin Lecher <jlec@gentoo.org> 2011-06-13 12:25:26 +0000
commit: 64070377e5a19bb7e35463bd17bbe2b6a2538367 (patch)
tree: d36f8e106d17a384278ae0fc440a565a2bd976a9 /sci-chemistry/vmd
parent: Removed FEATURES=loadpolicy for profiles/selinux (diff)
download: historical-64070377e5a19bb7e35463bd17bbe2b6a2538367.tar.gz
historical-64070377e5a19bb7e35463bd17bbe2b6a2538367.tar.bz2
historical-64070377e5a19bb7e35463bd17bbe2b6a2538367.zip
10 files changed, 17 insertions, 2211 deletions
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 7348e4ca0042..bf28d47d0bb7 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/vmd
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.38 2011/03/27 11:02:31 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.39 2011/06/13 12:25:25 jlec Exp $
+
+  13 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+  -files/vmd-1.8.7-gentoo.patch, -files/vmd-1.8.7-respect-flags.patch,
+  vmd-1.9.ebuild, -files/vmd-1.9-gentoo-base.patch,
+  -files/vmd-1.9-gentoo-plugins.patch, -files/vmd.desktop, -files/vmd.png:
+  No binaryfiles in VCS please, #370915
 
   27 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild:
   Correct version of cuda dep, #360401
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 4542d48800fc..4f93a8c6db90 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,22 +1,6 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-AUX vmd-1.8.7-gentoo.patch 40425 RMD160 ff4969a813a8bdb93c69a445d30ffdab8f46f64e SHA1 f001456e38e927c0cbc6502444676544d8187524 SHA256 a0af0c88c7bbbd3387b1c69b527f4b28f667a063d1be293c3c4a1c3f0db203ac
-AUX vmd-1.8.7-respect-flags.patch 954 RMD160 1b4162173e8856801a9d37faf527d870ccc0a5a1 SHA1 7684b9c95cd87f4033aff6713a25841e31216eb9 SHA256 fbd8d610550673e58d336fcc9b780248241f78a9a418230f877972a480aac9b4
-AUX vmd-1.9-gentoo-base.patch 12442 RMD160 f3d5789c18e204cbda677aa6c58664bb55e1f7b0 SHA1 5a7dd45feae0909f66a8a31b775cf2d3793006f9 SHA256 98a0168597e5901fb21d801f4678aa9cb67738e6b966e748f00df363e11389d2
-AUX vmd-1.9-gentoo-plugins.patch 24984 RMD160 5b17808cfa392b4f61ef95b1e640de18d978810c SHA1 e0c8853b80ddaca8ee4720edc4eb2b4a65c6305e SHA256 1c79f11f0c5ad90f503942c7d555cbdf013395e2ea12589ce9c033f80618a0d9
-AUX vmd.desktop 296 RMD160 83dbf38b9b90b42b1b913a8a4a572d5570e55f2e SHA1 077d414e2a1ba3fcbdac02559b9efdfeb26fa9dd SHA256 5008ea2c950955f416061a14c35a2b2146df29df290b7f5b1e2f3c48d7ce7d8d
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 DIST vmd-1.8.7.src.tar.gz 23853864 RMD160 1c4751552d7b3f376f91a4b28ee9d4a028ded01a SHA1 409b6f8959d551f581991073f98885b47c21c25c SHA256 72fe2fb7eff4c805a886ea929c7e143a3a1be57cc817b5d1719d29e591d80316
 DIST vmd-1.9.src.tar.gz 28639907 RMD160 96a6cf99d34bdd264550aec334f2cd8c5cfdaceb SHA1 b555a01815a2cf16be910ef6977793f1670a62f1 SHA256 4209b06faba3af324575570bd0533258471f6c782262c0727b52cdce9de89579
-EBUILD vmd-1.8.7-r2.ebuild 5647 RMD160 c98d1b7ec49841c0c3a5a92069319a186f33a358 SHA1 ba9d1ab00bc9a590c9e4a8352b390407186cb5a4 SHA256 fbc4f8bade464026472ad7b01bfe73210b4b55f8df9dacab999e840050fbd657
-EBUILD vmd-1.9.ebuild 6290 RMD160 6e508e50e35678a9417dc2b3024a3fef7e26bdd0 SHA1 3110ede23db3191870e458d787a4a65fc96de92c SHA256 57963c515f854ba774f7e94d8c4f9638d9aaed49ccac1046f5f9afc2f5dbe38c
-MISC ChangeLog 7278 RMD160 a78c82fde92326dab54edbc8388f3e73a07dda97 SHA1 4bd2843ef39879117f20e15b1a8efa1080851fd5 SHA256 9d1a87988c07114c3c74c3b321a52c8fede47ceab911ebccca06dfe0670c9e80
+EBUILD vmd-1.8.7-r2.ebuild 5733 RMD160 fa8a1050a2228f8ad11ef84bdaa3392f8b829528 SHA1 e0182c2d97846fff74e749eb00342f206b1f1207 SHA256 094a3a993ad5dae5231fda5413a74108e8ef6f594179a7e5c7114b26e7ce1930
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 MISC metadata.xml 692 RMD160 9130eefac530062c2b1445fb7bc8baa977d449b9 SHA1 df9fed5cfa000d121f3b5359e50eb64fab1c09fb SHA256 f659ba576cce359509e370998b9e234e413f85be3ffa7b1aed4dfd2770443e08
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diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch
deleted file mode 100644
index e8c82c2bf872..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch
+++ /dev/null
@@ -1,1240 +0,0 @@
-diff --git a/plugins/Makefile b/plugins/Makefile
-index e2e5e5e..f2eabaf 100755
---- a/plugins/Makefile
-+++ b/plugins/Makefile
-@@ -4,7 +4,6 @@
- ## Theoretical and Computational Biophysics Group
- ##
- 
--.SILENT:
- 
- default: make-arch-help
- 
-diff --git a/plugins/Makefile.newmultiseq b/plugins/Makefile.newmultiseq
-index c271b44..d00522c 100644
---- a/plugins/Makefile.newmultiseq
-+++ b/plugins/Makefile.newmultiseq
-@@ -4,7 +4,6 @@
- ## Theoretical and Computational Biophysics Group
- ##
- 
--.SILENT:
- 
- default: make-arch-help
- 
-diff --git a/plugins/Makefile.orig b/plugins/Makefile.orig
-index e6406fd..6208576 100644
---- a/plugins/Makefile.orig
-+++ b/plugins/Makefile.orig
-@@ -4,7 +4,6 @@
- ## Theoretical and Computational Biophysics Group
- ##
- 
--.SILENT:
- 
- default: make-arch-help
- 
-diff --git a/plugins/Makefile.rej b/plugins/Makefile.rej
-index 1b6ea67..d13aca1 100644
---- a/plugins/Makefile.rej
-+++ b/plugins/Makefile.rej
-@@ -3,7 +3,6 @@
-   # Makefile for molecule file readers
-   # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
-   
--- .SILENT:
-   
-   .SUFFIXES:
-   
-@@ -17,7 +16,6 @@
-   # Makefile for molecule file readers
-   # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
-   
--+ .SILENT:
-   
-   .SUFFIXES:
-   
-diff --git a/plugins/aligntool/Makefile b/plugins/aligntool/Makefile
-index 8155a6d..e4df74c 100644
---- a/plugins/aligntool/Makefile
-+++ b/plugins/aligntool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = aligntool.tcl cealign.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/apbsrun/Makefile b/plugins/apbsrun/Makefile
-index aca0b4e..b86ee59 100644
---- a/plugins/apbsrun/Makefile
-+++ b/plugins/apbsrun/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = apbsrun.tcl pkgIndex.tcl radii.dat
- VMVERSION = 1.3
-diff --git a/plugins/atomedit/Makefile b/plugins/atomedit/Makefile
-index 558606c..05d7f90 100644
---- a/plugins/atomedit/Makefile
-+++ b/plugins/atomedit/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = atomedit.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/autoimd/Makefile b/plugins/autoimd/Makefile
-index 9d432e4..7f0a802 100644
---- a/plugins/autoimd/Makefile
-+++ b/plugins/autoimd/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- AUTOIMDFILES = autoimd.tcl autoimd-settings.tcl autoimd-api.tcl autoimd-gui.tcl pkgIndex.tcl autoimd-template.namd doc/ug.pdf namdrun.tcl
- AUTOIMDVERSION = 1.6
-diff --git a/plugins/autoionize/Makefile b/plugins/autoionize/Makefile
-index c74ad01..b392d3f 100644
---- a/plugins/autoionize/Makefile
-+++ b/plugins/autoionize/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = autoionize.tcl autoionizegui.tcl pkgIndex.tcl ions.top
- VMVERSION = 1.2
-diff --git a/plugins/bignum/Makefile b/plugins/bignum/Makefile
-index 9c90f17..c35322d 100644
---- a/plugins/bignum/Makefile
-+++ b/plugins/bignum/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = bignum.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/biocore/Makefile b/plugins/biocore/Makefile
-index 887b592..d2919dd 100644
---- a/plugins/biocore/Makefile
-+++ b/plugins/biocore/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = biocore.tcl biocorechat.tcl biocorelogin.tcl biocorepubsync.tcl pkgIndex.tcl locked.gif unlocked.gif biocoreHelper.tcl biocoreutil.tcl
- 
-diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile
-index 7a8f0f8..bbc4c01 100644
---- a/plugins/catdcd/Makefile
-+++ b/plugins/catdcd/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for catdcd
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-@@ -45,8 +44,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi
- 	LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
- 
- # all other platforms
--${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
--	${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
-+${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
- 
- ${ARCHDIR}/hash.o: hash.h hash.c
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
-diff --git a/plugins/cgtools/Makefile b/plugins/cgtools/Makefile
-index adca18b..84bf723 100644
---- a/plugins/cgtools/Makefile
-+++ b/plugins/cgtools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = cggui.tcl cgtools.tcl cgnetworking.tcl pkgIndex.tcl \
-           protein.cgc water.cgc rbcg-2007.par rbcg-2007.top
-diff --git a/plugins/cionize/.#Makefile.specialbuilds.1.1 b/plugins/cionize/.#Makefile.specialbuilds.1.1
-index 4672932..181ba85 100644
---- a/plugins/cionize/.#Makefile.specialbuilds.1.1
-+++ b/plugins/cionize/.#Makefile.specialbuilds.1.1
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile
-index c5fe136..b72116f 100644
---- a/plugins/cionize/Makefile
-+++ b/plugins/cionize/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-@@ -52,8 +51,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI
- 	LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
- 
- # all other platforms
--${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
-+${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
- 
- ${ARCHDIR}/hash.o: hash.h hash.c
- 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
-diff --git a/plugins/cionize/Makefile.mine b/plugins/cionize/Makefile.mine
-index 5ee841a..1588837 100644
---- a/plugins/cionize/Makefile.mine
-+++ b/plugins/cionize/Makefile.mine
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/Makefile.mine.old b/plugins/cionize/Makefile.mine.old
-index 48714b6..0dc4085 100644
---- a/plugins/cionize/Makefile.mine.old
-+++ b/plugins/cionize/Makefile.mine.old
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/Makefile.specialbuilds b/plugins/cionize/Makefile.specialbuilds
-index a529758..f85bcfe 100644
---- a/plugins/cionize/Makefile.specialbuilds
-+++ b/plugins/cionize/Makefile.specialbuilds
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/mcudahacks/Makefile.specialbuilds b/plugins/cionize/mcudahacks/Makefile.specialbuilds
-index e93cad2..dc7b632 100644
---- a/plugins/cionize/mcudahacks/Makefile.specialbuilds
-+++ b/plugins/cionize/mcudahacks/Makefile.specialbuilds
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cliptool/Makefile b/plugins/cliptool/Makefile
-index 9c41370..679abbe 100644
---- a/plugins/cliptool/Makefile
-+++ b/plugins/cliptool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = cliptool.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/clonerep/Makefile b/plugins/clonerep/Makefile
-index e8a4949..e101e56 100755
---- a/plugins/clonerep/Makefile
-+++ b/plugins/clonerep/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = clonerep.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile
-index 6329f64..c343b1c 100644
---- a/plugins/clustalw/Makefile
-+++ b/plugins/clustalw/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for clustalw
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-@@ -66,7 +65,7 @@ OBJS = ${ARCHDIR}/alnscore.o \
- ${ARCHDIR}/clustalw.exe: ${OBJS}
- 	LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe
- ${ARCHDIR}/clustalw: ${OBJS}
--	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
-+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
-     
-     
- # Objects.
-diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile
-index 99d347e..dc542f1 100644
---- a/plugins/cluster/Makefile
-+++ b/plugins/cluster/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for psfgen
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-@@ -48,7 +47,7 @@ ${ARCHDIR}/cluster.exe : ${OBJS}
- 
- # all other platforms
- ${ARCHDIR}/cluster : ${OBJS}
--	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
- 
- ${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o
-diff --git a/plugins/colorscalebar/Makefile b/plugins/colorscalebar/Makefile
-index 1413898..f58074a 100644
---- a/plugins/colorscalebar/Makefile
-+++ b/plugins/colorscalebar/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = colorscalebar.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/contactmap/Makefile b/plugins/contactmap/Makefile
-index 36f6b18..3336e41 100644
---- a/plugins/contactmap/Makefile
-+++ b/plugins/contactmap/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = contactmap.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/dataimport/Makefile b/plugins/dataimport/Makefile
-index e63ebca..71b59fb 100644
---- a/plugins/dataimport/Makefile
-+++ b/plugins/dataimport/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = dataimport.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/demomaster/Makefile b/plugins/demomaster/Makefile
-index 6264d76..27a3d20 100644
---- a/plugins/demomaster/Makefile
-+++ b/plugins/demomaster/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = demomaster.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/dipwatch/Makefile b/plugins/dipwatch/Makefile
-index 7d36042..4af35c7 100755
---- a/plugins/dipwatch/Makefile
-+++ b/plugins/dipwatch/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = dipwatch.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/doc/Makefile b/plugins/doc/Makefile
-index ed1ce9d..07ff534 100644
---- a/plugins/doc/Makefile
-+++ b/plugins/doc/Makefile
-@@ -1,7 +1,6 @@
- #
- # Plugin documentation Makefile
- #
--.SILENT:
- 
- ECHO            = echo
- DELETEDIR       = rm -rf
-diff --git a/plugins/dowser/Makefile b/plugins/dowser/Makefile
-index 1795db3..d00cacc 100644
---- a/plugins/dowser/Makefile
-+++ b/plugins/dowser/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = dowser.tcl dowser_gui.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/exectool/Makefile b/plugins/exectool/Makefile
-index afa024d..6ba1889 100644
---- a/plugins/exectool/Makefile
-+++ b/plugins/exectool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = exectool.tcl jobmanager.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/extendedpdb/Makefile b/plugins/extendedpdb/Makefile
-index 9061aa1..5a5fb8f 100644
---- a/plugins/extendedpdb/Makefile
-+++ b/plugins/extendedpdb/Makefile
-@@ -1,4 +1,3 @@
--#.SILENT:
- 
- VMFILES = extendedpdb.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/fmtool/Makefile b/plugins/fmtool/Makefile
-index 76a9e69..a3f320d 100644
---- a/plugins/fmtool/Makefile
-+++ b/plugins/fmtool/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for fmtool
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/gofrgui/Makefile b/plugins/gofrgui/Makefile
-index e192f02..7251884 100644
---- a/plugins/gofrgui/Makefile
-+++ b/plugins/gofrgui/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = gofrgui.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/hbonds/Makefile b/plugins/hbonds/Makefile
-index 6bee92d..45f1fe3 100644
---- a/plugins/hbonds/Makefile
-+++ b/plugins/hbonds/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = hbonds.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/idatm/Makefile b/plugins/idatm/Makefile
-index e23ca1c..4280b6a 100644
---- a/plugins/idatm/Makefile
-+++ b/plugins/idatm/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = idatm.tcl pkgIndex.tcl
- VMVERSION = 0.1
-diff --git a/plugins/ilstools/Makefile b/plugins/ilstools/Makefile
-index e145c30..7cc9d1b 100644
---- a/plugins/ilstools/Makefile
-+++ b/plugins/ilstools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- COPYFILES = ilstools.tcl pkgIndex.tcl oxygen.xyz nitricoxide.xyz \
-             carbonmonoxide.xyz carbondioxide.xyz ethene.xyz methane.xyz \
-diff --git a/plugins/imdmenu/Makefile b/plugins/imdmenu/Makefile
-index dca0e25..277f386 100644
---- a/plugins/imdmenu/Makefile
-+++ b/plugins/imdmenu/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- IMDMENUFILES = imdmenu.tcl pkgIndex.tcl
- IMDMENUVERSION = 1.0
-diff --git a/plugins/inorganicbuilder/Makefile b/plugins/inorganicbuilder/Makefile
-index 8e0439a..4af2b0f 100755
---- a/plugins/inorganicbuilder/Makefile
-+++ b/plugins/inorganicbuilder/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = inorganicbuilder.tcl pkgIndex.tcl
- VMVERSION = 0.1
-diff --git a/plugins/irspecgui/Makefile b/plugins/irspecgui/Makefile
-index 754ebc8..e86b09a 100755
---- a/plugins/irspecgui/Makefile
-+++ b/plugins/irspecgui/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = irspecgui.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/jmvexport/Makefile b/plugins/jmvexport/Makefile
-index 7f45260..9eb996b 100644
---- a/plugins/jmvexport/Makefile
-+++ b/plugins/jmvexport/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = jmvexport.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile
-index 7a66d08..12e1fd3 100644
---- a/plugins/libbiokit/Makefile
-+++ b/plugins/libbiokit/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for libbiokit
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-@@ -111,7 +110,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i
- ${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}
- 	LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe
- ${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
- ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o
- 
-@@ -119,7 +118,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
- ${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}
- 	LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe
- ${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
- ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o
- 
-@@ -127,7 +126,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
- ${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}
- 	LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe
- ${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
- ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o
- 
-@@ -135,7 +134,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
- ${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}
- 	LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe
- ${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
- ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o
- 
-@@ -143,7 +142,7 @@ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
- ${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}
- 	LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe
- ${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
- ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o
- 
-@@ -151,7 +150,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
- ${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}
- 	LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe
- ${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
- ${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o
-     
-diff --git a/plugins/membrane/Makefile b/plugins/membrane/Makefile
-index f92c426..38a9c06 100644
---- a/plugins/membrane/Makefile
-+++ b/plugins/membrane/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = membrane.tcl pkgIndex.tcl \
- 	popc_box.pdb popc_box.psf \
-diff --git a/plugins/mergestructs/Makefile b/plugins/mergestructs/Makefile
-index d6a4225..66ba9b2 100644
---- a/plugins/mergestructs/Makefile
-+++ b/plugins/mergestructs/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = mergestructs.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/molefacture/Makefile b/plugins/molefacture/Makefile
-index 96e70dc..8d10ef4 100644
---- a/plugins/molefacture/Makefile
-+++ b/plugins/molefacture/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = molefacture.tcl molefacture_builder.tcl \
- 	molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \
-diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
-index 18fb6dc..e32b130 100644
---- a/plugins/molfile_plugin/Makefile
-+++ b/plugins/molfile_plugin/Makefile
-@@ -1,7 +1,6 @@
- # Makefile for molecule file readers
- # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
- 
--.SILENT:
- 
- .SUFFIXES:
- 
-@@ -14,8 +13,8 @@ INCDIR = -I../include -I${SRCDIR}
- 
- VPATH = src ../include ${ARCHDIR}
- 
--SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
--SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
- 
- #
- # Rules
-diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
-index 1dfa768..e3f380b 100644
---- a/plugins/molfile_plugin/src/cifplugin/Makefile
-+++ b/plugins/molfile_plugin/src/cifplugin/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for molecule file readers
- 
--.SILENT:
- 
- .SUFFIXES:
- 
-@@ -14,7 +13,7 @@ INCDIR = -I../include -I${SRCDIR}
- VPATH = src ../include ${ARCHDIR}
- 
- SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
--SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
- 
- #
- # Rules
-diff --git a/plugins/moltoptools/Makefile b/plugins/moltoptools/Makefile
-index 3599cb7..8d80ec2 100644
---- a/plugins/moltoptools/Makefile
-+++ b/plugins/moltoptools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = moltoptools.tcl pkgIndex.tcl
- VMVERSION = 0.1
-diff --git a/plugins/multimolanim/Makefile b/plugins/multimolanim/Makefile
-index 09b4cb1..39b3139 100755
---- a/plugins/multimolanim/Makefile
-+++ b/plugins/multimolanim/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = multimolanim.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/multiplot/Makefile b/plugins/multiplot/Makefile
-index 520bf3e..a5b7bc5 100644
---- a/plugins/multiplot/Makefile
-+++ b/plugins/multiplot/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = multiplot.tcl pkgIndex.tcl
- VMVERSION = 1.4
-diff --git a/plugins/multitext/Makefile b/plugins/multitext/Makefile
-index cc98bde..453c0da 100644
---- a/plugins/multitext/Makefile
-+++ b/plugins/multitext/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = multitext.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/namdenergy/Makefile b/plugins/namdenergy/Makefile
-index 9d4c11c..229f6cc 100644
---- a/plugins/namdenergy/Makefile
-+++ b/plugins/namdenergy/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = namdenergy.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/namdgui/Makefile b/plugins/namdgui/Makefile
-index 2e25b19..c03d87b 100644
---- a/plugins/namdgui/Makefile
-+++ b/plugins/namdgui/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = namdgui.tcl namdgui_tclforces.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/namdplot/Makefile b/plugins/namdplot/Makefile
-index e155387..88969e6 100644
---- a/plugins/namdplot/Makefile
-+++ b/plugins/namdplot/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = namdplot.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/namdserver/Makefile b/plugins/namdserver/Makefile
-index 378d203..84dcb24 100644
---- a/plugins/namdserver/Makefile
-+++ b/plugins/namdserver/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = namdserver.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/nanotube/Makefile b/plugins/nanotube/Makefile
-index 6662cd5..deaf55c 100644
---- a/plugins/nanotube/Makefile
-+++ b/plugins/nanotube/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = nanotube.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/navfly/Makefile b/plugins/navfly/Makefile
-index 82d913b..0194be8 100644
---- a/plugins/navfly/Makefile
-+++ b/plugins/navfly/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = navfly.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/navigate/Makefile b/plugins/navigate/Makefile
-index 6d48c3e..cf18738 100644
---- a/plugins/navigate/Makefile
-+++ b/plugins/navigate/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- COPYFILES = navigate.tcl pkgIndex.tcl
- DIR = $(PLUGINDIR)/noarch/tcl/navigate1.0
-diff --git a/plugins/nlenergy/Makefile b/plugins/nlenergy/Makefile
-index 8c028ca..3c295fd 100644
---- a/plugins/nlenergy/Makefile
-+++ b/plugins/nlenergy/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for nlenergy
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/optimization/Makefile b/plugins/optimization/Makefile
-index e38a9dc..4188e7f 100644
---- a/plugins/optimization/Makefile
-+++ b/plugins/optimization/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = optimization.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/palettetool/Makefile b/plugins/palettetool/Makefile
-index 6317657..166d423 100644
---- a/plugins/palettetool/Makefile
-+++ b/plugins/palettetool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = palettetool.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/paratool/Makefile b/plugins/paratool/Makefile
-index 8f24cc1..cbf1618 100644
---- a/plugins/paratool/Makefile
-+++ b/plugins/paratool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = paratool.tcl paratool_atomedit.tcl paratool_aux.tcl \
-           paratool_respcharges.tcl paratool_charmmcharges.tcl \
-diff --git a/plugins/pbctools/Makefile b/plugins/pbctools/Makefile
-index 164c456..bcf6851 100755
---- a/plugins/pbctools/Makefile
-+++ b/plugins/pbctools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = pbcbox.tcl pbcgui.tcl pbcjoin.tcl pbcset.tcl pbctools.tcl \
- 	pbcunwrap.tcl pbcwrap.tcl pkgIndex.tcl
-diff --git a/plugins/pdbtool/Makefile b/plugins/pdbtool/Makefile
-index c05579d..3f120c5 100644
---- a/plugins/pdbtool/Makefile
-+++ b/plugins/pdbtool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = pdbtool.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/pmepot/Makefile b/plugins/pmepot/Makefile
-index 1858d13..fa6ac36 100644
---- a/plugins/pmepot/Makefile
-+++ b/plugins/pmepot/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for PME potential library
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/psfgen/Makefile b/plugins/psfgen/Makefile
-index d9c7c85..0d9b80e 100644
---- a/plugins/psfgen/Makefile
-+++ b/plugins/psfgen/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for psfgen
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/psfgen/Makefile.pluginio b/plugins/psfgen/Makefile.pluginio
-index 29444f2..28a6213 100644
---- a/plugins/psfgen/Makefile.pluginio
-+++ b/plugins/psfgen/Makefile.pluginio
-@@ -5,7 +5,6 @@
- #     them itself, but at the moment this is a good short-term development
- #     path until we write something better.
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/qmtool/Makefile b/plugins/qmtool/Makefile
-index a8aafff..2a45307 100644
---- a/plugins/qmtool/Makefile
-+++ b/plugins/qmtool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = qmtool.tcl qmtool_analysis.tcl qmtool_atomedit.tcl \
-           qmtool_aux.tcl qmtool_charges.tcl qmtool_intcoor.tcl \
-diff --git a/plugins/ramaplot/Makefile b/plugins/ramaplot/Makefile
-index 29a1f23..be6e86a 100644
---- a/plugins/ramaplot/Makefile
-+++ b/plugins/ramaplot/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- FILES = ramaplot.tcl pkgIndex.tcl
- VERSION = 1.1
-diff --git a/plugins/readcharmmpar/Makefile b/plugins/readcharmmpar/Makefile
-index fffb98e..d257edd 100644
---- a/plugins/readcharmmpar/Makefile
-+++ b/plugins/readcharmmpar/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = readcharmmpar.tcl par_all27_prot_lipid_na.inp pkgIndex.tcl par_amber2charmm.inp
- VMVERSION = 1.1
-diff --git a/plugins/readcharmmtop/Makefile b/plugins/readcharmmtop/Makefile
-index 88c7ab5..c8cb771 100644
---- a/plugins/readcharmmtop/Makefile
-+++ b/plugins/readcharmmtop/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = readcharmmtop.tcl pkgIndex.tcl top_all27_prot_lipid_na.inp top_all27_hybrid.inp top_amber2charmm.inp
- VMVERSION = 1.0
-diff --git a/plugins/resptool/Makefile b/plugins/resptool/Makefile
-index 1f20b70..80e01eb 100644
---- a/plugins/resptool/Makefile
-+++ b/plugins/resptool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = resptool.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/rmsd/Makefile b/plugins/rmsd/Makefile
-index 23df59b..c328322 100644
---- a/plugins/rmsd/Makefile
-+++ b/plugins/rmsd/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = rmsd.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/rmsdtt/Makefile b/plugins/rmsdtt/Makefile
-index c914531..62b14fd 100644
---- a/plugins/rmsdtt/Makefile
-+++ b/plugins/rmsdtt/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = rmsdtt.tcl pkgIndex.tcl
- VMVERSION = 2.0
-diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile
-index f020ca0..9ab6914 100644
---- a/plugins/rnaview/Makefile
-+++ b/plugins/rnaview/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = rnaview.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/ruler/Makefile b/plugins/ruler/Makefile
-index 146cc4c..a7864d1 100644
---- a/plugins/ruler/Makefile
-+++ b/plugins/ruler/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = ruler.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/runante/Makefile b/plugins/runante/Makefile
-index 0410d50..a8fbe81 100644
---- a/plugins/runante/Makefile
-+++ b/plugins/runante/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = runante.tcl pkgIndex.tcl
- VMVERSION = 0.1
-diff --git a/plugins/saltbr/Makefile b/plugins/saltbr/Makefile
-index 7e4234a..f5358e2 100644
---- a/plugins/saltbr/Makefile
-+++ b/plugins/saltbr/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = saltbr.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/solvate/Makefile b/plugins/solvate/Makefile
-index b1c5d92..7dfcd9b 100644
---- a/plugins/solvate/Makefile
-+++ b/plugins/solvate/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- SOLVFILES = wat.top wat.pdb wat.psf solvate.tcl pkgIndex.tcl
- SOLVVERSION = 1.3
-diff --git a/plugins/ssrestraints/Makefile b/plugins/ssrestraints/Makefile
-index 81b79d8..dca38e7 100644
---- a/plugins/ssrestraints/Makefile
-+++ b/plugins/ssrestraints/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = ssrestraints.tcl ssrestraints_stride.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile
-index f0fb515..c077d53 100644
---- a/plugins/stamp/Makefile
-+++ b/plugins/stamp/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for stamp
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-@@ -101,7 +100,7 @@ OBJS = ${ARCHDIR}/a3to1.o \
- ${ARCHDIR}/stamp.exe: ${OBJS}
- 	LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe
- ${ARCHDIR}/stamp: ${OBJS}
--	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
-+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
-     
-     
- # Objects.
-diff --git a/plugins/stingtool/Makefile b/plugins/stingtool/Makefile
-index d7b84fe..477a97c 100644
---- a/plugins/stingtool/Makefile
-+++ b/plugins/stingtool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = stingtool.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/symmetrytool/Makefile b/plugins/symmetrytool/Makefile
-index 43adc25..6898a43 100644
---- a/plugins/symmetrytool/Makefile
-+++ b/plugins/symmetrytool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = symmetry.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/textview/Makefile b/plugins/textview/Makefile
-index 5e35a4a..ba98391 100644
---- a/plugins/textview/Makefile
-+++ b/plugins/textview/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = textview.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/timeline/Makefile b/plugins/timeline/Makefile
-index 3b9e7ac..a09c572 100644
---- a/plugins/timeline/Makefile
-+++ b/plugins/timeline/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = timeline.tcl pkgIndex.tcl
- VMVERSION = 2.0
-diff --git a/plugins/topotools/Makefile b/plugins/topotools/Makefile
-index a8af827..beb4b54 100644
---- a/plugins/topotools/Makefile
-+++ b/plugins/topotools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = pkgIndex.tcl README topotools.tcl topoatoms.tcl \
- 	topobonds.tcl topoangles.tcl topodihedrals.tcl topoimpropers.tcl \
-diff --git a/plugins/trunctraj/Makefile b/plugins/trunctraj/Makefile
-index 624b3e6..991b4e1 100644
---- a/plugins/trunctraj/Makefile
-+++ b/plugins/trunctraj/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = trunctraj.tcl pkgIndex.tcl
- VMVERSION = 1.5
-diff --git a/plugins/updater/Makefile b/plugins/updater/Makefile
-index 4e29538..3122421 100644
---- a/plugins/updater/Makefile
-+++ b/plugins/updater/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = updater.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/utilities/Makefile b/plugins/utilities/Makefile
-index df1ccf4..c18c048 100644
---- a/plugins/utilities/Makefile
-+++ b/plugins/utilities/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = utilities.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/vdna/Makefile b/plugins/vdna/Makefile
-index f994198..dd2d57b 100644
---- a/plugins/vdna/Makefile
-+++ b/plugins/vdna/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = vdna.tcl pkgIndex.tcl
- VMVERSION = 2.0
-diff --git a/plugins/viewmaster/Makefile b/plugins/viewmaster/Makefile
-index c5d1625..8d25c7e 100644
---- a/plugins/viewmaster/Makefile
-+++ b/plugins/viewmaster/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = viewmaster.tcl pkgIndex.tcl
- VMVERSION = 2.2
-diff --git a/plugins/vmdmovie/Makefile b/plugins/vmdmovie/Makefile
-index 10af8e2..cacc294 100644
---- a/plugins/vmdmovie/Makefile
-+++ b/plugins/vmdmovie/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = vmdmovie.tcl pkgIndex.tcl
- VMVERSION = 1.7
-diff --git a/plugins/vmdtkcon/Makefile b/plugins/vmdtkcon/Makefile
-index 5f6a05d..04de94f 100644
---- a/plugins/vmdtkcon/Makefile
-+++ b/plugins/vmdtkcon/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- TKCONFILES = vmdtkcon.tcl tkcon-modified.tcl pkgIndex.tcl tkcon-2.3 README
- DIR = $(PLUGINDIR)/noarch/tcl/vmdtkcon1.1
-diff --git a/plugins/volmapgui/Makefile b/plugins/volmapgui/Makefile
-index 9ece112..57ec111 100644
---- a/plugins/volmapgui/Makefile
-+++ b/plugins/volmapgui/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- COPYFILES = volmapgui.tcl pkgIndex.tcl
- DIR = $(PLUGINDIR)/noarch/tcl/volmapgui1.1
-diff --git a/plugins/zoomseq/Makefile b/plugins/zoomseq/Makefile
-index aa95b41..66ee516 100644
---- a/plugins/zoomseq/Makefile
-+++ b/plugins/zoomseq/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = zoomseq.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/vmd-1.8.7/configure b/vmd-1.8.7/configure
-index f01944a..b04bade 100755
---- a/vmd-1.8.7/configure
-+++ b/vmd-1.8.7/configure
-@@ -13,10 +13,10 @@
- $install_name = "vmd";
- 
- # Directory where VMD startup script is installed, should be in users' paths.
--$install_bin_dir="/usr/local/bin";
-+$install_bin_dir="gentoo-bindir";
- 
- # Directory where VMD files and executables are installed
--$install_library_dir="/usr/local/lib/$install_name";
-+$install_library_dir="gentoo-libdir/$install_name";
- 
- 
- # optionally override hard-coded defaults above with environment variables
-@@ -128,29 +128,6 @@ if ($ENV{VMDINSTALLLIBRARYDIR}) {
- # Configure script code begins here
- ############################################################################
- 
--## Test for existence of a properly compiled plugin tree
--if (!(-e "plugins")) {
--  print "\n";
--  print "VMD plugin directory not found.\n";
--  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--  print "into a 'plugins' directory linked or located in this directory.\n";
--  print "Be sure your PLUGINDIR environment variable is set before running\n";
--  print "'make distrib' in the plugin build area.\n";
--  print "\n";
--  die "Halting configuration until VMD plugins are built.\n";
--} else {
--  if (!(-e "plugins/include/vmdplugin.h")) {
--    print "\n";
--    print "VMD plugin include files or directory not found.\n";
--    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--    print "into a 'plugins' directory linked or located in this directory.\n";
--    print "Be sure your PLUGINDIR environment variable is set before running\n";
--    print "'make distrib' in the plugin build area.\n";
--    print "\n";
--    die "Halting configuration until VMD plugins are built.\n";
--  }
--} 
--
- #################### Parse command line options   ###########
- # list of allowed architectures
- @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
-@@ -435,7 +412,7 @@ chop($arch_no_math_float);
- 
- ################ Plugin options
- #
--$plugin_dir	= "../plugins";
-+$plugin_dir	= "gentoo-plugindir";
- $plugin_include = "-I$plugin_dir/include";
- $plugin_library = "";
- $plugin_libs    = "";
-@@ -448,7 +425,7 @@ $plugin_defines = "";
- @plugin_extra   = ();
- 
- if ($config_staticplugin) {
--  $molfile_dir = "$plugin_dir/$config_arch/molfile";
-+  $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
-   $plugin_include .= " -I$molfile_dir";
-   $plugin_library .= " -L$molfile_dir";
-   $plugin_libs    .= " -lmolfile_plugin";
-@@ -550,8 +527,8 @@ $fltkopengl_defines     = "-DVMDOPENGL -DVMDFLTKOPENGL -DVMDGRAPHICS";
- ################ FLTK GUI
- $fltk_defines     = "-DVMDGUI -DVMDFLTK";
- $fltk_dir         = "$vmd_library_dir/fltk";
--$fltk_include     = "-I$fltk_dir/include";
--$fltk_library     = "-L$fltk_dir/$config_arch";
-+$fltk_include     = "-Igentoo-fltk-include";
-+$fltk_library     = "-Lgentoo-fltk-libs";
- $fltk_libs        = "-lfltk -lX11";
- #@fltk_cc          = ('forms_ui.c');
- @fltk_cu          = ();
-@@ -612,8 +589,8 @@ $tcl_include      = "-I$stock_tcl_include_dir";
- if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
- $tcl_library      = "-L$stock_tcl_library_dir";
- if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
--$tcl_libs         = "-ltcl8.5";  
--if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
-+$tcl_libs         = "-ltcl";  
-+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
- 
- @tcl_cc           = ();
- @tcl_cu           = ();
-@@ -938,8 +915,8 @@ $cuda_libs        = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
- #######################
- $netcdf_defines     = "";
- $netcdf_dir         = "$vmd_library_dir/netcdf";
--$netcdf_include     = "-I$netcdf_dir/include";
--$netcdf_library     = "-L$netcdf_dir/lib_$config_arch";
-+$netcdf_include     = "-Igentoo-netcdf-include";
-+$netcdf_library     = "-Lgentoo-netcdf-libs";
- $netcdf_libs        = "-lnetcdf";
- @netcdf_cc          = ();
- @netcdf_cu          = ();
-@@ -1007,9 +984,9 @@ $pthreads_libs     = "-lpthread";
- $python_defines     = "-DVMDPYTHON";
- $python_dir         = "$vmd_library_dir/python";
- $numpy_dir          = "$vmd_library_dir/numpy";
--$python_include     = "-I$python_dir/lib_$config_arch/include/python2.5 -I$numpy_dir/lib_$config_arch/include -I$python_dir/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";
--$python_library     = "-L$python_dir/lib_$config_arch/lib/python2.5/config";
--$python_libs        = "-lpython2.5 -lpthread";
-+$python_include     = "-Igentoo-python-include -Igentoo-numpy-include";
-+$python_library     = "-Lgentoo-python-lib";
-+$python_libs        = "-lgentoo-python-link -lpthread";
- @python_h           = ('PythonTextInterp.h',
-                        'VMDTkinterMenu.h',
- 		       'py_commands.h',
-@@ -1621,8 +1598,8 @@ if ($config_arch eq "LINUX") {
- 
-     # XFree 4.0 Direct Rendering Interface and GLX 
-     $opengl_dir         = "/usr/X11R6";
--    $opengl_include     = "-I$opengl_dir/include";
--    $opengl_library     = "-L$opengl_dir/lib";
-+    $opengl_include     = "-Igentoo-opengl-include";
-+    $opengl_library     = "-Lgentoo-opengl-libs";
-     $opengl_libs        = "-lGL -lGLU"; 
-     # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
- 
-@@ -1650,15 +1627,15 @@ if ($config_arch eq "LINUX") {
-       $arch_lopts       .= "-i-static ";
-     } else {
-       # compling with GCC
--      $arch_cc          = "gcc";
--      $arch_ccpp        = "g++";
-+      $arch_cc          = "gentoo-gcc";
-+      $arch_ccpp        = "gentoo-g++";
-       $arch_depend_flag = "-MM";
--      $arch_shld        = "g++ -shared";
-+      $arch_shld        = "gentoo-g++ -shared";
-       $arch_shlibname   = "so";
-       $arch_shcppopts   = "-fPIC";
--      $arch_shldopts    = "";
--      $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3";
--      $arch_copts       = "-m32 -Wall -O3";
-+      $arch_shldopts    = "gentoo-ldflags";
-+      $arch_opt_flag    = "gentoo-cflags";
-+      $arch_copts       = "gentoo-cflags";
- 
-       if ($config_static) {
-         $arch_lopts       = "-static";
-@@ -1768,7 +1745,7 @@ if ($config_arch eq "LINUXAMD64") {
-       $arch_template_repository = "foobar";
-       $arch_shlibname   = "so";
-       $arch_shcppopts   = "-fPIC";
--      $arch_shldopts    = "";
-+      $arch_shldopts    = "gentoo-ldflags";
- 
-       if ($config_static) {
-         # link everything statically (this won't work due to libGL issues)
-@@ -2714,11 +2691,11 @@ LIBDIRS     = $LIBDIRS
- DEFINES     = $DEFINES
- 
- # compiler and compiler directives 
--CC          = $arch_cc
--CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CC          = gentoo-gcc
-+CFLAGS      = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
- 
--CCPP	    = $arch_ccpp
--CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CCPP	    = gentoo-g++
-+CPPFLAGS    = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
- 
- NVCC        = $arch_nvcc
- NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
-@@ -2766,7 +2743,7 @@ $config_progname: y.tab.h \$(VMD_OBJS)
- 	if [ ! -r ./$arch_template_repository ]; then \\
- 	  ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\
- 	fi; \\
--	\$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
-+	\$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
- 	\$(COMPILERC) \$(RCFLAGS)
- 
- install:
-@@ -2804,8 +2781,7 @@ install:
- 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
- 	\$(CD) $vmd_bin_dir ; \\
- 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
--	if [ ! -x "/bin/csh" ]; then \\
--		\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
-+	if [ -x "/bin/bash" ]; then \\
- 		\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
-diff --git a/vmd-1.8.7/src/Makefile b/vmd-1.8.7/src/Makefile
-index 971a8c1..fe4c635 100755
---- a/vmd-1.8.7/src/Makefile
-+++ b/vmd-1.8.7/src/Makefile
-@@ -432,7 +432,7 @@ vmd_WIN32: y.tab.h $(VMD_OBJS)
- 	if [ ! -r ./ ]; then \
- 	  ln -s ../src/ ./ ; \
- 	fi; \
--	$(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
-+	$(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
- 	$(COMPILERC) $(RCFLAGS)
- 
- install:
diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch b/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch
deleted file mode 100644
index cd1281e3b682..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
-index 18fb6dc..8659573 100644
---- a/plugins/molfile_plugin/Makefile
-+++ b/plugins/molfile_plugin/Makefile
-@@ -14,8 +14,8 @@ INCDIR = -I../include -I${SRCDIR}
- 
- VPATH = src ../include ${ARCHDIR}
- 
--SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
--SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
- 
- #
- # Rules
-diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
-index 1dfa768..9de3f6b 100644
---- a/plugins/molfile_plugin/src/cifplugin/Makefile
-+++ b/plugins/molfile_plugin/src/cifplugin/Makefile
-@@ -14,7 +14,7 @@ INCDIR = -I../include -I${SRCDIR}
- VPATH = src ../include ${ARCHDIR}
- 
- SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
--SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
- 
- #
- # Rules
diff --git a/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch b/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch
deleted file mode 100644
index 4fb7da420de9..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9-gentoo-base.patch
+++ /dev/null
@@ -1,295 +0,0 @@
- vmd-1.9/bin/vmd.sh   |    3 ++
- vmd-1.9/configure    |   88 +++++++++++++++++++-------------------------------
- vmd-1.9/src/Makefile |    6 +---
- 3 files changed, 37 insertions(+), 60 deletions(-)
-
-diff --git a/vmd-1.9/bin/vmd.sh b/vmd-1.9/bin/vmd.sh
-index 2da6656..6e5308f 100755
---- a/vmd-1.9/bin/vmd.sh
-+++ b/vmd-1.9/bin/vmd.sh
-@@ -400,6 +400,7 @@ esac
- 
- # set the path to a few external programs
- # Stride -- used to generate cartoon representations etc.
-+export STRIDE_BIN="gentoo-stride"
- if [ -z "$STRIDE_BIN" ]
- then
-   if [ -x "$MASTERVMDDIR/stride_$ARCH" ]
-@@ -410,6 +411,7 @@ then
- fi
- 
- # Surf -- used to generate molecular surfaces
-+export SURF_BIN="gentoo-surf"
- if [ -z "$SURF_BIN" ]
- then
-   if [ -x "$MASTERVMDDIR/surf_$ARCH" ]
-@@ -420,6 +422,7 @@ then
- fi
- 
- # Tachyon -- used to generate ray traced graphics
-+export TACHYON_BIN="gentoo-tachyon"
- if [ -z "$TACHYON_BIN" ]
- then
-   if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ]
-diff --git a/vmd-1.9/configure b/vmd-1.9/configure
-index 926bab0..d8c1459 100755
---- a/vmd-1.9/configure
-+++ b/vmd-1.9/configure
-@@ -13,10 +13,10 @@
- $install_name = "vmd";
- 
- # Directory where VMD startup script is installed, should be in users' paths.
--$install_bin_dir="/usr/local/bin";
-+$install_bin_dir="gentoo-bindir";
- 
- # Directory where VMD files and executables are installed
--$install_library_dir="/usr/local/lib/$install_name";
-+$install_library_dir="gentoo-libdir/$install_name";
- 
- 
- # optionally override hard-coded defaults above with environment variables
-@@ -132,28 +132,6 @@ if ($ENV{VMDINSTALLLIBRARYDIR}) {
- # Configure script code begins here
- ############################################################################
- 
--## Test for existence of a properly compiled plugin tree
--if (!(-e "plugins")) {
--  print "\n";
--  print "VMD plugin directory not found.\n";
--  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--  print "into a 'plugins' directory linked or located in this directory.\n";
--  print "Be sure your PLUGINDIR environment variable is set before running\n";
--  print "'make distrib' in the plugin build area.\n";
--  print "\n";
--  die "Halting configuration until VMD plugins are built.\n";
--} else {
--  if (!(-e "plugins/include/vmdplugin.h")) {
--    print "\n";
--    print "VMD plugin include files or directory not found.\n";
--    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--    print "into a 'plugins' directory linked or located in this directory.\n";
--    print "Be sure your PLUGINDIR environment variable is set before running\n";
--    print "'make distrib' in the plugin build area.\n";
--    print "\n";
--    die "Halting configuration until VMD plugins are built.\n";
--  }
--} 
- 
- #################### Parse command line options   ###########
- # list of allowed architectures
-@@ -413,7 +391,7 @@ $arch_rcflags     = "No resource compiler required on this platform.";
- 
- $arch_cc          = "cc";
- $arch_ccpp        = "CC";
--$arch_nvcc        = "/usr/local/encap/cuda-3.0/bin/nvcc";
-+$arch_nvcc        = "gentoo-nvcc";
- $arch_nvccflags   = "--ptxas-options=-v " . 
-                     "-gencode arch=compute_10,code=sm_10 " .
-                     "-gencode arch=compute_13,code=sm_13 " .
-@@ -451,7 +429,7 @@ chop($arch_no_math_float);
- 
- ################ Plugin options
- #
--$plugin_dir	= "../plugins";
-+$plugin_dir	= "gentoo-plugindir";
- $plugin_include = "-I$plugin_dir/include";
- $plugin_library = "";
- $plugin_libs    = "";
-@@ -464,7 +442,7 @@ $plugin_defines = "";
- @plugin_extra   = ();
- 
- if ($config_staticplugin) {
--  $molfile_dir = "$plugin_dir/$config_arch/molfile";
-+  $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
-   $plugin_include .= " -I$molfile_dir";
-   $plugin_library .= " -L$molfile_dir";
-   $plugin_libs    .= " -lmolfile_plugin";
-@@ -564,8 +542,8 @@ $fltkopengl_defines     = "-DVMDOPENGL -DVMDFLTKOPENGL";
- ################ FLTK GUI
- $fltk_defines     = "-DVMDGUI -DVMDFLTK";
- $fltk_dir         = "$vmd_library_dir/fltk";
--$fltk_include     = "-I$fltk_dir/include";
--$fltk_library     = "-L$fltk_dir/$config_arch";
-+$fltk_include     = "-Igentoo-fltk-include";
-+$fltk_library     = "-Lgentoo-fltk-libs";
- $fltk_libs        = "-lfltk -lX11";
- #@fltk_cc          = ('forms_ui.c');
- @fltk_cu          = ();
-@@ -626,8 +604,8 @@ $tcl_include      = "-I$stock_tcl_include_dir";
- if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
- $tcl_library      = "-L$stock_tcl_library_dir";
- if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
--$tcl_libs         = "-ltcl8.5";  
--if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
-+$tcl_libs         = "-ltcl";  
-+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
- 
- @tcl_cc           = ();
- @tcl_cu           = ();
-@@ -1004,8 +982,8 @@ $mpi_libs        = "-L/usr/mpi/gcc/mvapich-1.0.0/lib -lmpich -libverbs -libumad
- #######################
- $netcdf_defines     = "";
- $netcdf_dir         = "$vmd_library_dir/netcdf";
--$netcdf_include     = "-I$netcdf_dir/include";
--$netcdf_library     = "-L$netcdf_dir/lib_$config_arch";
-+$netcdf_include     = "-Igentoo-netcdf-include";
-+$netcdf_library     = "-Lgentoo-netcdf-libs";
- $netcdf_libs        = "-lnetcdf";
- @netcdf_cc          = ();
- @netcdf_cu          = ();
-@@ -1076,6 +1054,7 @@ $pthreads_libs     = "-lpthread";
- #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib";
- $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5";
- $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
-+$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
- 
- #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include";
- #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
-@@ -1085,7 +1064,7 @@ $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/l
- $python_defines     = "-DVMDPYTHON";
- $python_include     = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir";
- $python_library     = "-L$stock_python_library_dir";
--$python_libs        = "-lpython2.5 -lpthread";
-+$python_libs        = "$stock_python_library -lpthread";
- @python_h           = ('PythonTextInterp.h',
-                        'VMDTkinterMenu.h',
- 		       'py_commands.h',
-@@ -1807,8 +1786,8 @@ if ($config_arch eq "LINUX") {
- 
-     # XFree 4.0 Direct Rendering Interface and GLX 
-     $opengl_dir         = "/usr/X11R6";
--    $opengl_include     = "-I$opengl_dir/include";
--    $opengl_library     = "-L$opengl_dir/lib";
-+    $opengl_include     = "-Igentoo-opengl-include";
-+    $opengl_library     = "-Lgentoo-opengl-libs";
-     $opengl_libs        = "-lGL -lGLU"; 
-     # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
- 
-@@ -1836,15 +1815,15 @@ if ($config_arch eq "LINUX") {
-       $arch_lopts       .= "-i-static ";
-     } else {
-       # compling with GCC
--      $arch_cc          = "gcc";
--      $arch_ccpp        = "g++";
-+      $arch_cc          = "gentoo-gcc";
-+      $arch_ccpp        = "gentoo-g++";
-       $arch_depend_flag = "-MM";
--      $arch_shld        = "g++ -shared";
-+      $arch_shld        = "gentoo-g++ -shared";
-       $arch_shlibname   = "so";
-       $arch_shcppopts   = "-fPIC";
--      $arch_shldopts    = "";
--      $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3";
--      $arch_copts       = "-m32 -Wall -O3";
-+      $arch_shldopts    = "gentoo-ldflags";
-+      $arch_opt_flag    = "gentoo-cflags";
-+      $arch_copts       = "gentoo-cflags";
- 
-       if ($config_static) {
-         $arch_lopts       = "-static";
-@@ -1864,8 +1843,8 @@ if ($config_arch eq "LINUX") {
-     $arch_cppopts     = "";
- 
-     if ($config_cuda) {
--      $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include";
--      $cuda_library     = "-L/usr/local/encap/cuda-3.0/lib";
-+      $arch_nvccflags .= "gentoo-nvflags $cuda_include";
-+      $cuda_library     = "-Lgentoo-cuda-lib";
-     }
-     # a hack - to be removed, just keeps make happy
-     $arch_template_repository = "foobar";
-@@ -1955,7 +1934,7 @@ if ($config_arch eq "LINUXAMD64") {
-       $arch_template_repository = "foobar";
-       $arch_shlibname   = "so";
-       $arch_shcppopts   = "-fPIC";
--      $arch_shldopts    = "";
-+      $arch_shldopts    = "gentoo-ldflags";
- 
-       if ($config_static) {
-         # link everything statically (this won't work due to libGL issues)
-@@ -1986,7 +1965,7 @@ if ($config_arch eq "LINUXAMD64") {
- 
-     if ($config_cuda) {
-       $arch_nvccflags   .= " --machine 64 -O3 $cuda_include";
--      $cuda_library     = "-L/usr/local/encap/cuda-3.0/lib64";
-+      $cuda_library     = "-Lgentoo-cuda-lib";
-     }
- 
-     $arch_lex		= "flex"; # has problems with vendor lex
-@@ -2354,7 +2333,7 @@ if ($config_arch eq "MACOSXX86" || $config_arch eq "MACOSXX86_64") {
-       # $arch_nvccflags   .= " -O3 $cuda_include";
-       # make it continue to work with the older rev of CUDA for now
-       $arch_nvccflags   = " --ptxas-options=-v -O3 $cuda_include";
--      $cuda_library     = "-L/usr/local/cuda/lib";
-+      $cuda_library     = "-Lgentoo-cuda-lib";
-     }
-     if ($config_opencl) {
-       $opencl_libs        = "-framework OpenCL";
-@@ -2545,7 +2524,7 @@ if ($config_arch eq "SOLARISX86" || $config_arch eq "SOLARISX86_64") {
-           $arch_nvcc        = "/usr/local/cuda/bin/nvcc";
-           $arch_nvccflags   .= " -m64 -O3 -I/usr/local/cuda/include";
-           $cuda_libs        = "-lcudart";
--          $cuda_library     = "-L/usr/local/cuda/lib";
-+          $cuda_library     = "-Lgentoo-cuda-lib";
-         }
-       } else {
-         print "Configured for a 32-bit build.\n";
-@@ -2927,11 +2906,11 @@ LIBDIRS     = $LIBDIRS
- DEFINES     = $DEFINES
- 
- # compiler and compiler directives 
--CC          = $arch_cc
--CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CC          = gentoo-gcc
-+CFLAGS      = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
- 
--CCPP	    = $arch_ccpp
--CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CCPP	    = gentoo-g++
-+CPPFLAGS    = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
- 
- NVCC        = $arch_nvcc
- NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
-@@ -2979,7 +2958,7 @@ $config_progname: y.tab.h \$(VMD_OBJS)
- 	if [ ! -r ./$arch_template_repository ]; then \\
- 	  ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\
- 	fi; \\
--	\$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
-+	\$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
- 	\$(COMPILERC) \$(RCFLAGS)
- 
- install:
-@@ -3017,8 +2996,7 @@ install:
- 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
- 	\$(CD) $vmd_bin_dir ; \\
- 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
--	if [ ! -x "/bin/csh" ]; then \\
--		\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
-+	if [ -x "/bin/bash" ]; then \\
- 		\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
-diff --git a/vmd-1.9/src/Makefile b/vmd-1.9/src/Makefile
-index 18eff40..c301f91 100644
---- a/vmd-1.9/src/Makefile
-+++ b/vmd-1.9/src/Makefile
-@@ -446,7 +446,7 @@ vmd_WIN32: y.tab.h $(VMD_OBJS)
- 	if [ ! -r ./ ]; then \
- 	  ln -s ../src/ ./ ; \
- 	fi; \
--	$(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
-+	$(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
- 	$(COMPILERC) $(RCFLAGS)
- 
- install:
-@@ -459,10 +459,6 @@ install:
- 	if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
- 		$(MAKEDIR) "/usr/local/lib/vmd"/doc; \
- 	fi
--	-$(COPY) ../Announcement  "/usr/local/lib/vmd"
--	-$(COPY) ../README        "/usr/local/lib/vmd"
--	-$(COPY) ../LICENSE       "/usr/local/lib/vmd"
--	-$(COPY) ../doc/ug.pdf        "/usr/local/lib/vmd"/doc
- 	if [ -f /usr/local/lib/vmd/vmd_WIN32 ]; then \
-            $(MOVE) "/usr/local/lib/vmd/vmd_WIN32" "/usr/local/lib/vmd/OLD_vmd_WIN32" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_WIN32" ; fi
- 	-$(COPY) ../WIN32/vmd_WIN32 "/usr/local/lib/vmd"
diff --git a/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch b/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch
deleted file mode 100644
index d6b1afb0cafd..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9-gentoo-plugins.patch
+++ /dev/null
@@ -1,612 +0,0 @@
- plugins/Make-arch                             |    3 +-
- plugins/Makefile                              |   20 ++++---
- plugins/autopsf/Makefile                      |    4 +-
- plugins/catdcd/Makefile                       |    4 +-
- plugins/cionize/Makefile                      |    4 +-
- plugins/clustalw/Makefile                     |    2 +-
- plugins/cluster/Makefile                      |    2 +-
- plugins/hesstrans/Makefile                    |    2 +-
- plugins/libbiokit/Makefile                    |   14 +++---
- plugins/molfile_plugin/Makefile               |   62 ++++++++++++------------
- plugins/molfile_plugin/src/cifplugin/Makefile |   66 ++++++++++++------------
- plugins/phylotree/Makefile                    |    2 +-
- plugins/rnaview/Makefile                      |    2 +-
- plugins/stamp/Makefile                        |    2 +-
- 14 files changed, 96 insertions(+), 93 deletions(-)
-
-diff --git a/plugins/Make-arch b/plugins/Make-arch
-index 5d59ef3..ab57459 100755
---- a/plugins/Make-arch
-+++ b/plugins/Make-arch
-@@ -336,7 +336,8 @@ LINUX:
- 	"AR = ar" \
- 	"NM = nm -p" \
- 	"RANLIB = touch" \
--	"SHLD = gcc -shared"
-+	"SHLD = gcc -shared" \
-+	"SHXXLD = g++ -shared"
- 	
- LINUXALPHA:
- 	$(MAKE) dynlibs staticlibs bins \
-diff --git a/plugins/Makefile b/plugins/Makefile
-index 19f0e8b..57cbe32 100644
---- a/plugins/Makefile
-+++ b/plugins/Makefile
-@@ -132,25 +132,27 @@ distrib:
- 
- include Make-arch
- 
--molfilelibs:
--	cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1
--	cd molfile_plugin; $(MAKE) staticlibs && cd .. || exit 1
-+molfilelibs_static:
-+	$(MAKE) -C molfile_plugin staticlibs
-+
-+molfilelibs_dyn:
-+	$(MAKE) -C molfile_plugin dynlibs
- 
- win32molfilelibs:
- 	cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1
- 	cd molfile_plugin; $(MAKE) win32staticlibs && cd .. || exit 1
- 
--dynlibs: molfilelibs
--	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) dynlibs && cd .. || exit 1 ; done
-+dynlibs: molfilelibs_dyn
-+	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir dynlibs; done
- 
--staticlibs: molfilelibs
--	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) staticlibs && cd .. || exit 1 ; done
-+staticlibs: molfilelibs_static
-+	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir staticlibs; done
- 
- win32staticlibs: win32molfilelibs
- 	for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) win32staticlibs && cd .. || exit 1 ; done
- 
--bins:
--	for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) bins && cd .. || exit 1 ; done
-+bins: molfilelibs_dyn
-+	for dir in $(BUILDDIRS); do $(MAKE) -C $$dir bins; done
- 
- win32bins:
- 	for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) win32bins && cd .. || exit 1 ; done
-diff --git a/plugins/autopsf/Makefile b/plugins/autopsf/Makefile
-index e63d3c4..d217ed8 100644
---- a/plugins/autopsf/Makefile
-+++ b/plugins/autopsf/Makefile
-@@ -49,8 +49,8 @@ AUTOPSFOBJS=${ARCHDIR}/psfatom.o  \
- 
- ${ARCHDIR}/psfcheck.so : ${AUTOPSFOBJS}
- 	if [ -n "${TCLSHLD}" ]; \
--	then ${TCLSHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
--	else ${SHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
-+	then ${TCLSHLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \
-+	else ${SHXXLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \
- 	fi
- 
- ${ARCHDIR}/psfatom.o : psfatom.h psfatom.C
-diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile
-index 7a8f0f8..dc0d7a5 100644
---- a/plugins/catdcd/Makefile
-+++ b/plugins/catdcd/Makefile
-@@ -45,8 +45,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi
- 	LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
- 
- # all other platforms
--${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
--	${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
-+${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
- 
- ${ARCHDIR}/hash.o: hash.h hash.c
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
-diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile
-index c5fe136..5e9a379 100644
---- a/plugins/cionize/Makefile
-+++ b/plugins/cionize/Makefile
-@@ -52,8 +52,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI
- 	LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
- 
- # all other platforms
--${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
-+${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
- 
- ${ARCHDIR}/hash.o: hash.h hash.c
- 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
-diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile
-index b8fbba5..988ad06 100644
---- a/plugins/clustalw/Makefile
-+++ b/plugins/clustalw/Makefile
-@@ -66,7 +66,7 @@ OBJS = ${ARCHDIR}/alnscore.o \
- ${ARCHDIR}/clustalw.exe: ${OBJS}
- 	LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe
- ${ARCHDIR}/clustalw: ${OBJS}
--	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
-+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
-     
-     
- # Objects.
-diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile
-index 99d347e..c2d30ae 100644
---- a/plugins/cluster/Makefile
-+++ b/plugins/cluster/Makefile
-@@ -48,7 +48,7 @@ ${ARCHDIR}/cluster.exe : ${OBJS}
- 
- # all other platforms
- ${ARCHDIR}/cluster : ${OBJS}
--	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
- 
- ${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o
-diff --git a/plugins/hesstrans/Makefile b/plugins/hesstrans/Makefile
-index 903e88b..50fa625 100644
---- a/plugins/hesstrans/Makefile
-+++ b/plugins/hesstrans/Makefile
-@@ -67,7 +67,7 @@ HESSTRANSOBJS=${ARCHDIR}/newmat1.o \
- ${ARCHDIR}/hesstrans.so : ${HESSTRANSOBJS}
- 	if [ -n "${TCLSHLD}" ]; \
- 	then ${TCLSHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
--	else ${SHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
-+	else ${SHXXLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
- 	fi
- 
- #
-diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile
-index 7a66d08..da764dd 100644
---- a/plugins/libbiokit/Makefile
-+++ b/plugins/libbiokit/Makefile
-@@ -98,7 +98,7 @@ OBJS = ${DYNLIBOBJS} \
- ${ARCHDIR}/tcl_libbiokit.so : ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS}
- 	if [ -n "${TCLSHLD}" ]; \
- 	then ${TCLSHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
--	else ${SHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
-+	else ${SHXXLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \
- 	fi
- ${ARCHDIR}/tcl_libbiokit_wrap.o : ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp
- 	${CXX} ${CXXFLAGS} ${TCLINC} ${INCDIR} -c ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp $(COPTO)${ARCHDIR}/tcl_libbiokit_wrap.o
-@@ -111,7 +111,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i
- ${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}
- 	LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe
- ${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
- ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o
- 
-@@ -119,7 +119,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
- ${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}
- 	LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe
- ${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
- ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o
- 
-@@ -127,7 +127,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
- ${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}
- 	LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe
- ${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
- ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o
- 
-@@ -135,7 +135,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
- ${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}
- 	LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe
- ${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
- ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o
- 
-@@ -143,7 +143,7 @@ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
- ${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}
- 	LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe
- ${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
- ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o
- 
-@@ -151,7 +151,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
- ${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}
- 	LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe
- ${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}
--	${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
- ${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o
-     
-diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
-index 172a217..345f64c 100644
---- a/plugins/molfile_plugin/Makefile
-+++ b/plugins/molfile_plugin/Makefile
-@@ -15,7 +15,7 @@ INCDIR = -I../include -I${SRCDIR}
- VPATH = src ../include ${ARCHDIR}
- 
- SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
--SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
- 
- #
- # Rules
-@@ -142,7 +142,7 @@ abinitplugin.so: ${ARCHDIR}/abinitplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-@@ -163,13 +163,13 @@ babelplugin.so: ${ARCHDIR}/babelplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- hoomdplugin.so: ${ARCHDIR}/hoomdplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS)
- 
- parmplugin.so: ${ARCHDIR}/parmplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
-@@ -187,40 +187,40 @@ webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
- 
- graspplugin.so: ${ARCHDIR}/graspplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- msmsplugin.so: ${ARCHDIR}/msmsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- stlplugin.so: ${ARCHDIR}/stlplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- cubeplugin.so: ${ARCHDIR}/cubeplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- edmplugin.so: ${ARCHDIR}/edmplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- brixplugin.so: ${ARCHDIR}/brixplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pltplugin.so: ${ARCHDIR}/pltplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- rst7plugin.so: ${ARCHDIR}/rst7plugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- parm7plugin.so: ${ARCHDIR}/parm7plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vtfplugin.so: ${ARCHDIR}/vtfplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-@@ -235,7 +235,7 @@ tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-@@ -265,52 +265,52 @@ moldenplugin.so: ${ARCHDIR}/moldenplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- phiplugin.so: ${ARCHDIR}/phiplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- grdplugin.so: ${ARCHDIR}/grdplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- dxplugin.so: ${ARCHDIR}/dxplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- situsplugin.so: ${ARCHDIR}/situsplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- spiderplugin.so: ${ARCHDIR}/spiderplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mapplugin.so: ${ARCHDIR}/mapplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- avsplugin.so: ${ARCHDIR}/avsplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- fs4plugin.so: ${ARCHDIR}/fs4plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pqrplugin.so: ${ARCHDIR}/pqrplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mol2plugin.so: ${ARCHDIR}/mol2plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- bgfplugin.so: ${ARCHDIR}/bgfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gridplugin.so: ${ARCHDIR}/gridplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- carplugin.so: ${ARCHDIR}/carplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mdfplugin.so: ${ARCHDIR}/mdfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- cpmdlogplugin.so: ${ARCHDIR}/cpmdlogplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-@@ -325,7 +325,7 @@ basissetplugin.so: ${ARCHDIR}/basissetplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- xsfplugin.so: ${ARCHDIR}/xsfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- jsplugin.so: ${ARCHDIR}/jsplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
-index 1dfa768..bd6eceb 100644
---- a/plugins/molfile_plugin/src/cifplugin/Makefile
-+++ b/plugins/molfile_plugin/src/cifplugin/Makefile
-@@ -13,8 +13,8 @@ INCDIR = -I../include -I${SRCDIR}
- 
- VPATH = src ../include ${ARCHDIR}
- 
--SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
--SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN"
-+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
- 
- #
- # Rules
-@@ -84,10 +84,10 @@ mesg:
- #
- 
- biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- cifplugin.so: ${ARCHDIR}/cifplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-@@ -105,10 +105,10 @@ babelplugin.so: ${ARCHDIR}/babelplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- parmplugin.so: ${ARCHDIR}/parmplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS)
-@@ -126,40 +126,40 @@ webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS)
- 
- graspplugin.so: ${ARCHDIR}/graspplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- msmsplugin.so: ${ARCHDIR}/msmsplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- stlplugin.so: ${ARCHDIR}/stlplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- cubeplugin.so: ${ARCHDIR}/cubeplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- edmplugin.so: ${ARCHDIR}/edmplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- brixplugin.so: ${ARCHDIR}/brixplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pltplugin.so: ${ARCHDIR}/pltplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- rst7plugin.so: ${ARCHDIR}/rst7plugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- parm7plugin.so: ${ARCHDIR}/parm7plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vtfplugin.so: ${ARCHDIR}/vtfplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-@@ -174,7 +174,7 @@ tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-@@ -201,58 +201,58 @@ moldenplugin.so: ${ARCHDIR}/moldenplugin.o
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- phiplugin.so: ${ARCHDIR}/phiplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- grdplugin.so: ${ARCHDIR}/grdplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- dxplugin.so: ${ARCHDIR}/dxplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- situsplugin.so: ${ARCHDIR}/situsplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- spiderplugin.so: ${ARCHDIR}/spiderplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mapplugin.so: ${ARCHDIR}/mapplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- avsplugin.so: ${ARCHDIR}/avsplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- fs4plugin.so: ${ARCHDIR}/fs4plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- pqrplugin.so: ${ARCHDIR}/pqrplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mol2plugin.so: ${ARCHDIR}/mol2plugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- bgfplugin.so: ${ARCHDIR}/bgfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gridplugin.so: ${ARCHDIR}/gridplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- carplugin.so: ${ARCHDIR}/carplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- mdfplugin.so: ${ARCHDIR}/mdfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- gamessplugin.so: ${ARCHDIR}/gamessplugin.o 
- 	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- xsfplugin.so: ${ARCHDIR}/xsfplugin.o 
--	$(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
-+	$(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS)
- 
- #
- # object files
-diff --git a/plugins/phylotree/Makefile b/plugins/phylotree/Makefile
-index 6442747..0aceb4d 100644
---- a/plugins/phylotree/Makefile
-+++ b/plugins/phylotree/Makefile
-@@ -54,7 +54,7 @@ ${ARCHDIR}/upgmaclu.exe : ${OBJS}
- 
- # all other platforms
- ${ARCHDIR}/upgmaclu : ${OBJS}
--	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm
-+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm
- 
- ${ARCHDIR}/upgmaclu.o: ${SRCDIR}/upgmaclu.c
- 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/upgmaclu.c $(COPTO)${ARCHDIR}/upgmaclu.o
-diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile
-index 503695e..e7019a6 100644
---- a/plugins/rnaview/Makefile
-+++ b/plugins/rnaview/Makefile
-@@ -67,7 +67,7 @@ OBJS = ${ARCHDIR}/analyze.o \
- ${ARCHDIR}/rnaview.exe: ${OBJS}
- 	LINK ${OBJS} /OUT:${ARCHDIR}/rnaview.exe
- ${ARCHDIR}/rnaview: ${OBJS}
--	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm
-+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm
- 
- ${ARCHDIR}/analyze.o: ${SRCDIR}/analyze.c
- 	${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/analyze.c $(COPTO)${ARCHDIR}/analyze.o
-diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile
-index f0fb515..aa8f6b6 100644
---- a/plugins/stamp/Makefile
-+++ b/plugins/stamp/Makefile
-@@ -101,7 +101,7 @@ OBJS = ${ARCHDIR}/a3to1.o \
- ${ARCHDIR}/stamp.exe: ${OBJS}
- 	LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe
- ${ARCHDIR}/stamp: ${OBJS}
--	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
-+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
-     
-     
- # Objects.
diff --git a/sci-chemistry/vmd/files/vmd.desktop b/sci-chemistry/vmd/files/vmd.desktop
deleted file mode 100644
index fe09518a8eef..000000000000
--- a/sci-chemistry/vmd/files/vmd.desktop
+++ /dev/null
@@ -1,14 +0,0 @@
-[Desktop Entry]
-Comment=Visual Molecular Dynamics
-Exec=/usr/bin/vmd
-GenericName=Visual Molecular Dynamics
-Icon=/usr/share/pixmaps/vmd.png
-Name=VMD
-NoDisplay=false
-Path=$HOME
-StartupNotify=true
-Terminal=1
-TerminalOptions=
-Type=Application
-Categories=Science;Application;
-X-KDE-SubstituteUID=false
diff --git a/sci-chemistry/vmd/files/vmd.png b/sci-chemistry/vmd/files/vmd.png
deleted file mode 100644
index 33126483ca80..000000000000
--- a/sci-chemistry/vmd/files/vmd.png
+++ /dev/null
diff --git a/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild b/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild
index 96a0c3c74252..ffbab7cecf10 100644
--- a/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild,v 1.7 2011/03/22 13:53:26 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild,v 1.8 2011/06/13 12:25:25 jlec Exp $
 
 EAPI="3"
 
@@ -50,8 +50,11 @@ QA_DT_HASH_x86="usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
 pkg_nofetch() {
 	elog "Please download ${A} from"
 	elog "${VMD_DOWNLOAD}"
+	elog "and"
+	elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
 	elog "after agreeing to the license and then move it to "
 	elog "${DISTDIR}"
+
 }
 
 src_prepare() {
diff --git a/sci-chemistry/vmd/vmd-1.9.ebuild b/sci-chemistry/vmd/vmd-1.9.ebuild
index 137dc78023d6..41b5b15758fe 100644
--- a/sci-chemistry/vmd/vmd-1.9.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.ebuild,v 1.3 2011/03/27 11:02:31 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.ebuild,v 1.4 2011/06/13 12:25:25 jlec Exp $
 
 EAPI="3"
 
@@ -55,6 +55,8 @@ QA_DT_HASH_x86="usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
 pkg_nofetch() {
 	elog "Please download ${A} from"
 	elog "${VMD_DOWNLOAD}"
+	elog "and"
+	elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
 	elog "after agreeing to the license and then move it to "
 	elog "${DISTDIR}"
 }
author	Justin Lecher <jlec@gentoo.org>	2011-06-13 12:25:26 +0000
committer	Justin Lecher <jlec@gentoo.org>	2011-06-13 12:25:26 +0000
commit	64070377e5a19bb7e35463bd17bbe2b6a2538367 (patch)
tree	d36f8e106d17a384278ae0fc440a565a2bd976a9 /sci-chemistry/vmd
parent	Removed FEATURES=loadpolicy for profiles/selinux (diff)
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